# GPA module not executing 

**URL:** <https://discourse.slicer.org/t/gpa-module-not-executing/34583>\
**Category:** Support\
**Tags:** slicermorph\
**Created:** [February 28, 2024, 4:35am UTC](https://discourse.slicer.org/t/gpa-module-not-executing/34583 "2024-02-28T04:35:24Z")\
**Posts on this page:** 11\
**Page:** 1

<div class="post-metadata">

**Author:** ![megvdb](https://avatars.discourse-cdn.com/v4/letter/m/b2d939/32.png) [@megvdb](https://discourse.slicer.org/u/megvdb)\
**Post date:** [February 28, 2024, 4:35am UTC](https://discourse.slicer.org/t/gpa-module-not-executing/34583/1 "2024-02-28T04:35:24Z")

</div>

Operating system: Mac OS  
Slicer version: 5.6.0  
Expected behavior: Trying to execute GPA+PCA  
Actual behavior: wont run!

Hi! I have used ALPACA to get landmarks for 9 species and I selected these files in the GPA module as mark.json files. I selected my output folder. However when I hit execute nothing is happening, any thoughts?

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<div class="post-metadata">

**Author:** ![muratmaga](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/muratmaga/32/3622_2.png) [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Post date:** [February 28, 2024, 4:47am UTC](https://discourse.slicer.org/t/gpa-module-not-executing/34583/2 "2024-02-28T04:47:19Z")

</div>

Please open the log file (CTRL/CMD + 0), and copy and paste the full log file.

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<div class="post-metadata">

**Author:** ![muratmaga](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/muratmaga/32/3622_2.png) [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Post date:** [February 28, 2024, 10:59pm UTC](https://discourse.slicer.org/t/gpa-module-not-executing/34583/3 "2024-02-28T22:59:56Z")

</div>

Also you are using an older version of the SLicer. Please install the current stable (5.6.1) and retry.

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<div class="post-metadata">

**Author:** ![coco](https://avatars.discourse-cdn.com/v4/letter/c/8797f3/32.png) [@coco](https://discourse.slicer.org/u/coco)\
**Post date:** [June 12, 2024, 1:18pm UTC](https://discourse.slicer.org/t/gpa-module-not-executing/34583/4 "2024-06-12T13:18:33Z")

</div>

Hello,  
I encountered similar issues whilst using .mrk.json files but resolved the issues after changing format (saving new files as fcsv)  
Isn’t supposed to work with both file formats though ?  
Thanks and having a great time with slicermorph thus far !

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<div class="post-metadata">

**Author:** ![maryam\_shakeri](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/maryam_shakeri/32/78189_2.png) [@maryam\_shakeri](https://discourse.slicer.org/u/maryam_shakeri)\
**Post date:** [October 9, 2024, 10:10pm UTC](https://discourse.slicer.org/t/gpa-module-not-executing/34583/5 "2024-10-09T22:10:39Z")

</div>

I am having this issue as well. I’m using a newer version of Slicer and have about 38 landmarks saved as .json files. When I click execute, nothing happens.  
I’m wondering - do I need to have two sets of landmarks (from the shapes I am comparing) from the get-go? Or can I set one as the ‘standard’ somehow and compare the rest of my samples to this one?

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<div class="post-metadata">

**Author:** ![muratmaga](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/muratmaga/32/3622_2.png) [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Post date:** [October 9, 2024, 10:31pm UTC](https://discourse.slicer.org/t/gpa-module-not-executing/34583/6 "2024-10-09T22:31:56Z")

</div>

Can you provide the log file? You can get to it by hitting ctrl+0

> [@maryam\_shakeri](#):
>
> do I need to have two sets of landmarks (from the shapes I am comparing) from the get-go?

No, you don’t need to set of landmark. You just need all the samples to have exactly the same number of landmarks as others. Please provide the log file, without that we can’t know why this is not working.

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<div class="post-metadata">

**Author:** ![maryam\_shakeri](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/maryam_shakeri/32/78189_2.png) [@maryam\_shakeri](https://discourse.slicer.org/u/maryam_shakeri)\
**Post date:** [October 10, 2024, 12:42am UTC](https://discourse.slicer.org/t/gpa-module-not-executing/34583/7 "2024-10-10T00:42:53Z")

</div>

Hi,  
Thanks for your reply! The log file is :

Slicer version …: 5.6.2 (revision 32448 / f10cd8c) win-amd64 - installed release  
Operating system …: Windows / Professional / (Build 22621, Code Page 65001) - 64-bit  
Memory …: 32491 MB physical, 37355 MB virtual  
CPU …: GenuineIntel , 20 cores, 20 logical processors  
VTK configuration …: OpenGL2 rendering, TBB threading  
Qt configuration …: version 5.15.2, with SSL, requested OpenGL 3.2 (compatibility profile)  
Internationalization …: disabled, language=  
Developer mode …: disabled  
Application path …: C:/Users/GrafLab/AppData/Local/slicer.org/Slicer 5.6.2/bin  
libpng warning: iCCP: profile ‘ICC Profile’: ‘CMYK’: invalid ICC profile color space  
libpng warning: iCCP: known incorrect sRGB profile

ModuleType: CommandLineModule

Resample Scalar/Vector/DWI Volume command line:

C:/Users/GrafLab/AppData/Local/slicer.org/Slicer 5.6.2/bin/…/lib/Slicer-5.6/cli-modules/ResampleScalarVectorDWIVolume.exe --hfieldtype h-Field --interpolation linear --transform\_order output-to-input --image\_center input --spacing 0.025000000372529,0.025000000372529,0.025000000372529 --size 140,194,339 --origin 5.90012,-1.55799,19.2427 --direction\_matrix -0.99802077918573,0.0348755839426684,-0.0523279829524778,-0.0348755837543809,-0.999391244391407,-0.00091338841198455,-0.0523279845904687,0.000913388445507022,0.998629534873536 --number\_of\_thread 0 --default\_pixel\_value 0 --window\_function c --spline\_order 3 --transform\_matrix 1,0,0,0,1,0,0,0,1,0,0,0 --transform a C:/Users/GrafLab/AppData/Local/Temp/Slicer/BAGAE\_vtkMRMLScalarVolumeNodeC.nrrd C:/Users/GrafLab/AppData/Local/Temp/Slicer/BAGAE\_vtkMRMLScalarVolumeNodeE.nrrd

Resample Scalar/Vector/DWI Volume completed without errors

Switch to module: “VolumeRendering”  
Switch to module: “Segmentations”  
Switch to module: “SegmentEditor”  
QLayout::addChildLayout: layout “” already has a parent  
ctkSliderWidget::setSingleStep() 0 is out of bounds. 0 10 1  
Switch to module: “CropVolume”  
Found CommandLine Module, target is C:/Users/GrafLab/AppData/Local/slicer.org/Slicer 5.6.2/bin/…/lib/Slicer-5.6/cli-modules/ResampleScalarVectorDWIVolume.exe

ModuleType: CommandLineModule

Resample Scalar/Vector/DWI Volume command line:

C:/Users/GrafLab/AppData/Local/slicer.org/Slicer 5.6.2/bin/…/lib/Slicer-5.6/cli-modules/ResampleScalarVectorDWIVolume.exe --hfieldtype h-Field --interpolation linear --transform\_order output-to-input --image\_center input --spacing 0.025000000372529,0.025000000372529,0.025000000372529 --size 149,245,366 --origin 6.15869,-1.55289,18.5764 --direction\_matrix -0.99802077918573,0.0348755839426684,-0.0523279829524778,-0.0348755837543809,-0.999391244391407,-0.00091338841198455,-0.0523279845904687,0.000913388445507022,0.998629534873536 --number\_of\_thread 0 --default\_pixel\_value 0 --window\_function c --spline\_order 3 --transform\_matrix 1,0,0,0,1,0,0,0,1,0,0,0 --transform a C:/Users/GrafLab/AppData/Local/Temp/Slicer/BAGAE\_vtkMRMLScalarVolumeNodeE.nrrd C:/Users/GrafLab/AppData/Local/Temp/Slicer/BAGAE\_vtkMRMLScalarVolumeNodeE.nrrd

Input port 0 of algorithm vtkImageMapToWindowLevelColors (0000017A5CC24E90) has 0 connections but is not optional.

Input port 0 of algorithm vtkImageThreshold (0000017A5C703740) has 0 connections but is not optional.

Input port 0 of algorithm vtkImageMapToWindowLevelColors (0000017A5CC24E90) has 0 connections but is not optional.

Input port 0 of algorithm vtkImageReslice (0000017A56A43210) has 0 connections but is not optional.

Input port 0 of algorithm vtkImageMapToWindowLevelColors (0000017A5CC24E90) has 0 connections but is not optional.

Input port 0 of algorithm vtkImageThreshold (0000017A5C703740) has 0 connections but is not optional.

Input port 0 of algorithm vtkImageMapToWindowLevelColors (0000017A5CC24E90) has 0 connections but is not optional.

Input port 0 of algorithm vtkImageReslice (0000017A56A43210) has 0 connections but is not optional.

Input port 0 of algorithm vtkImageMapToWindowLevelColors (0000017A5CC24E90) has 0 connections but is not optional.

Input port 0 of algorithm vtkImageThreshold (0000017A5C703740) has 0 connections but is not optional.

Input port 0 of algorithm vtkImageMapToWindowLevelColors (0000017A5CC24E90) has 0 connections but is not optional.

Input port 0 of algorithm vtkImageReslice (0000017A58A04880) has 0 connections but is not optional.  
Switch to module: “SegmentEditor”  
ctkSliderWidget::setSingleStep() 0 is out of bounds. 0 10 1  
ctkSliderWidget::setSingleStep() 0 is out of bounds. 0 10 1  
Switch to module: “CropVolume”  
Switch to module: “Markups”  
Switch to module: “CropVolume”  
Switch to module: “Data”  
ctkRangeWidget::setSingleStep( 100 ) is outside valid bounds  
Switch to module: “VolumeRendering”  
Switch to module: “CropVolume”  
Found CommandLine Module, target is C:/Users/GrafLab/AppData/Local/slicer.org/Slicer 5.6.2/bin/…/lib/Slicer-5.6/cli-modules/ResampleScalarVectorDWIVolume.exe

Resample Scalar/Vector/DWI Volume command line:

C:/Users/GrafLab/AppData/Local/slicer.org/Slicer 5.6.2/bin/…/lib/Slicer-5.6/cli-modules/ResampleScalarVectorDWIVolume.exe --hfieldtype h-Field --interpolation linear --transform\_order output-to-input --image\_center input --spacing 0.025000000372529,0.025000000372529,0.025000000372529 --size 150,263,388 --origin 6.20134,-1.07981,18.0242 --direction\_matrix -0.99802077918573,0.0348755839426684,-0.0523279829524778,-0.0348755837543809,-0.999391244391407,-0.00091338841198455,-0.0523279845904687,0.000913388445507022,0.998629534873536 --number\_of\_thread 0 --default\_pixel\_value 0 --window\_function c --spline\_order 3 --transform\_matrix 1,0,0,0,1,0,0,0,1,0,0,0 --transform a C:/Users/GrafLab/AppData/Local/Temp/Slicer/BAGAE\_vtkMRMLScalarVolumeNodeC.nrrd C:/Users/GrafLab/AppData/Local/Temp/Slicer/BAGAE\_vtkMRMLScalarVolumeNodeF.nrrd

Resample Scalar/Vector/DWI Volume completed without errors

Switch to module: “VolumeRendering”  
Switch to module: “SegmentEditor”  
ctkSliderWidget::setSingleStep() 0 is out of bounds. 0 10 1  
void \_\_cdecl qSlicerSaveDataDialogPrivate::updateStatusIconFromMessageCollection(int,class vtkMRMLMessageCollection \*,bool) Data save information: “”  
void \_\_cdecl qSlicerSaveDataDialogPrivate::updateStatusIconFromMessageCollection(int,class vtkMRMLMessageCollection \*,bool) Data save information: “”  
void \_\_cdecl qSlicerSaveDataDialogPrivate::updateStatusIconFromMessageCollection(int,class vtkMRMLMessageCollection \*,bool) Data save information: “”  
void \_\_cdecl qSlicerSaveDataDialogPrivate::updateStatusIconFromMessageCollection(int,class vtkMRMLMessageCollection \*,bool) Data save information: “”  
Switch to module: “Data”  
Switch to module: “SegmentEditor”  
Switch to module: “Segmentations”  
“Model” Reader has successfully read the file  
Switch to module: “Markups”  
Switch to module: “Data”  
Switch to module: “Markups”  
Switch to module: “GPA”  
Collecting pandas  
Downloading pandas-2.2.3-cp39-cp39-win\_amd64.whl.metadata (19 kB)  
Requirement already satisfied: numpy\>=1.22.4 in c:\users\graflab\appdata\local\slicer.org\slicer 5.6.2\lib\python\lib\site-packages (from pandas) (1.26.1)  
Requirement already satisfied: python-dateutil\>=2.8.2 in c:\users\graflab\appdata\local\slicer.org\slicer 5.6.2\lib\python\lib\site-packages (from pandas) (2.8.2)  
Collecting pytz\>=2020.1 (from pandas)  
Downloading pytz-2024.2-py2.py3-none-any.whl.metadata (22 kB)  
Collecting tzdata\>=2022.7 (from pandas)  
Downloading tzdata-2024.2-py2.py3-none-any.whl.metadata (1.4 kB)  
Requirement already satisfied: six\>=1.5 in c:\users\graflab\appdata\local\slicer.org\slicer 5.6.2\lib\python\lib\site-packages (from python-dateutil\>=2.8.2-\>pandas) (1.16.0)  
Downloading pandas-2.2.3-cp39-cp39-win\_amd64.whl (11.6 MB)  
---------------------------------------- 11.6/11.6 MB 81.8 MB/s eta 0:00:00  
Downloading pytz-2024.2-py2.py3-none-any.whl (508 kB)  
---------------------------------------- 508.0/508.0 kB ? eta 0:00:00  
Downloading tzdata-2024.2-py2.py3-none-any.whl (346 kB)  
--------------------------------------- 346.6/346.6 kB 22.4 MB/s eta 0:00:00  
Installing collected packages: pytz, tzdata, pandas  
Successfully installed pandas-2.2.3 pytz-2024.2 tzdata-2024.2  
Traceback (most recent call last):  
File “C:/Users/GrafLab/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/GPA.py”, line 1022, in onSelectLandmarkFiles  
self.LM\_dir\_name = os.path.dirname(self.inputFilePaths[0])  
IndexError: tuple index out of range  
Switch to module: “Markups”  
void \_\_cdecl qSlicerSaveDataDialogPrivate::updateStatusIconFromMessageCollection(int,class vtkMRMLMessageCollection \*,bool) Data save information: “”  
void \_\_cdecl qSlicerSaveDataDialogPrivate::updateStatusIconFromMessageCollection(int,class vtkMRMLMessageCollection \*,bool) Data save information: “”  
void \_\_cdecl qSlicerSaveDataDialogPrivate::updateStatusIconFromMessageCollection(int,class vtkMRMLMessageCollection \*,bool) Data save information: “”  
void \_\_cdecl qSlicerSaveDataDialogPrivate::updateStatusIconFromMessageCollection(int,class vtkMRMLMessageCollection \*,bool) Data save information: “”  
void \_\_cdecl qSlicerSaveDataDialogPrivate::updateStatusIconFromMessageCollection(int,class vtkMRMLMessageCollection \*,bool) Data save information: “”  
void \_\_cdecl qSlicerSaveDataDialogPrivate::updateStatusIconFromMessageCollection(int,class vtkMRMLMessageCollection \*,bool) Data save information: “”  
void \_\_cdecl qSlicerSaveDataDialogPrivate::updateStatusIconFromMessageCollection(int,class vtkMRMLMessageCollection \*,bool) Data save information: “”  
void \_\_cdecl qSlicerSaveDataDialogPrivate::updateStatusIconFromMessageCollection(int,class vtkMRMLMessageCollection \*,bool) Data save information: “”  
void \_\_cdecl qSlicerSaveDataDialogPrivate::updateStatusIconFromMessageCollection(int,class vtkMRMLMessageCollection \*,bool) Data save information: “”  
void \_\_cdecl qSlicerSaveDataDialogPrivate::updateStatusIconFromMessageCollection(int,class vtkMRMLMessageCollection \*,bool) Data save information: “”  
void \_\_cdecl qSlicerSaveDataDialogPrivate::updateStatusIconFromMessageCollection(int,class vtkMRMLMessageCollection \*,bool) Data save information: “”  
void \_\_cdecl qSlicerSaveDataDialogPrivate::updateStatusIconFromMessageCollection(int,class vtkMRMLMessageCollection \*,bool) Data save information: “”  
void \_\_cdecl qSlicerSaveDataDialogPrivate::updateStatusIconFromMessageCollection(int,class vtkMRMLMessageCollection \*,bool) Data save information: “”  
void \_\_cdecl qSlicerSaveDataDialogPrivate::updateStatusIconFromMessageCollection(int,class vtkMRMLMessageCollection \*,bool) Data save information: “”  
void \_\_cdecl qSlicerSaveDataDialogPrivate::updateStatusIconFromMessageCollection(int,class vtkMRMLMessageCollection \*,bool) Data save information: “”  
void \_\_cdecl qSlicerSaveDataDialogPrivate::updateStatusIconFromMessageCollection(int,class vtkMRMLMessageCollection \*,bool) Data save information: “”  
void \_\_cdecl qSlicerSaveDataDialogPrivate::updateStatusIconFromMessageCollection(int,class vtkMRMLMessageCollection \*,bool) Data save information: “”  
void \_\_cdecl qSlicerSaveDataDialogPrivate::updateStatusIconFromMessageCollection(int,class vtkMRMLMessageCollection \*,bool) Data save information: “”  
void \_\_cdecl qSlicerSaveDataDialogPrivate::updateStatusIconFromMessageCollection(int,class vtkMRMLMessageCollection \*,bool) Data save information: “”  
void \_\_cdecl qSlicerSaveDataDialogPrivate::updateStatusIconFromMessageCollection(int,class vtkMRMLMessageCollection \*,bool) Data save information: “”  
void \_\_cdecl qSlicerSaveDataDialogPrivate::updateStatusIconFromMessageCollection(int,class vtkMRMLMessageCollection \*,bool) Data save information: “”  
void \_\_cdecl qSlicerSaveDataDialogPrivate::updateStatusIconFromMessageCollection(int,class vtkMRMLMessageCollection \*,bool) Data save information: “”  
void \_\_cdecl qSlicerSaveDataDialogPrivate::updateStatusIconFromMessageCollection(int,class vtkMRMLMessageCollection \*,bool) Data save information: “”  
void \_\_cdecl qSlicerSaveDataDialogPrivate::updateStatusIconFromMessageCollection(int,class vtkMRMLMessageCollection \*,bool) Data save information: “”  
void \_\_cdecl qSlicerSaveDataDialogPrivate::updateStatusIconFromMessageCollection(int,class vtkMRMLMessageCollection \*,bool) Data save information: “”  
void \_\_cdecl qSlicerSaveDataDialogPrivate::updateStatusIconFromMessageCollection(int,class vtkMRMLMessageCollection \*,bool) Data save information: “”  
void \_\_cdecl qSlicerSaveDataDialogPrivate::updateStatusIconFromMessageCollection(int,class vtkMRMLMessageCollection \*,bool) Data save information: “”  
void \_\_cdecl qSlicerSaveDataDialogPrivate::updateStatusIconFromMessageCollection(int,class vtkMRMLMessageCollection \*,bool) Data save information: “”  
void \_\_cdecl qSlicerSaveDataDialogPrivate::updateStatusIconFromMessageCollection(int,class vtkMRMLMessageCollection \*,bool) Data save information: “”  
void \_\_cdecl qSlicerSaveDataDialogPrivate::updateStatusIconFromMessageCollection(int,class vtkMRMLMessageCollection \*,bool) Data save information: “”  
void \_\_cdecl qSlicerSaveDataDialogPrivate::updateStatusIconFromMessageCollection(int,class vtkMRMLMessageCollection \*,bool) Data save information: “”  
void \_\_cdecl qSlicerSaveDataDialogPrivate::updateStatusIconFromMessageCollection(int,class vtkMRMLMessageCollection \*,bool) Data save information: “”  
void \_\_cdecl qSlicerSaveDataDialogPrivate::updateStatusIconFromMessageCollection(int,class vtkMRMLMessageCollection \*,bool) Data save information: “”  
void \_\_cdecl qSlicerSaveDataDialogPrivate::updateStatusIconFromMessageCollection(int,class vtkMRMLMessageCollection \*,bool) Data save information: “”  
void \_\_cdecl qSlicerSaveDataDialogPrivate::updateStatusIconFromMessageCollection(int,class vtkMRMLMessageCollection \*,bool) Data save information: “”  
void \_\_cdecl qSlicerSaveDataDialogPrivate::updateStatusIconFromMessageCollection(int,class vtkMRMLMessageCollection \*,bool) Data save information: “”  
void \_\_cdecl qSlicerSaveDataDialogPrivate::updateStatusIconFromMessageCollection(int,class vtkMRMLMessageCollection \*,bool) Data save information: “”  
void \_\_cdecl qSlicerSaveDataDialogPrivate::updateStatusIconFromMessageCollection(int,class vtkMRMLMessageCollection \*,bool) Data save information: “”  
void \_\_cdecl qSlicerSaveDataDialogPrivate::updateStatusIconFromMessageCollection(int,class vtkMRMLMessageCollection \*,bool) Data save information: “”  
Switch to module: “GPA”  
Loaded 39 subjects with 1 landmark points.  
C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py:94: RuntimeWarning: invalid value encountered in divide  
shape=shape/np.linalg.norm(shape)  
Traceback (most recent call last):  
File “C:/Users/GrafLab/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/GPA.py”, line 1209, in onLoad  
self.LM.doGpa(self.BoasOption)  
File “C:/Users/GrafLab/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/GPA.py”, line 229, in doGpa  
self.lm, self.mShape=gpa\_lib.runGPA(self.lmOrig)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 125, in runGPA  
allLandmarkSets = procrustesAlign(allLandmarkSets[:,:,0],allLandmarkSets)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 142, in procrustesAlign  
allLandmarkSets[:,:,index] = alignShape(mean, allLandmarkSets[:,:,index])  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 102, in alignShape  
u,s,v=sp.svd(np.dot(np.transpose(refShape),shape), full\_matrices=True)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\scipy\linalg\_decomp\_svd.py”, line 108, in svd  
a1 = \_asarray\_validated(a, check\_finite=check\_finite)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\scipy\_lib\_util.py”, line 240, in \_asarray\_validated  
a = toarray(a)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\numpy\lib\function\_base.py”, line 630, in asarray\_chkfinite  
raise ValueError(  
ValueError: array must not contain infs or NaNs  
Loaded 39 subjects with 1 landmark points.  
C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py:94: RuntimeWarning: invalid value encountered in divide  
shape=shape/np.linalg.norm(shape)  
Traceback (most recent call last):  
File “C:/Users/GrafLab/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/GPA.py”, line 1209, in onLoad  
self.LM.doGpa(self.BoasOption)  
File “C:/Users/GrafLab/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/GPA.py”, line 229, in doGpa  
self.lm, self.mShape=gpa\_lib.runGPA(self.lmOrig)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 125, in runGPA  
allLandmarkSets = procrustesAlign(allLandmarkSets[:,:,0],allLandmarkSets)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 142, in procrustesAlign  
allLandmarkSets[:,:,index] = alignShape(mean, allLandmarkSets[:,:,index])  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 102, in alignShape  
u,s,v=sp.svd(np.dot(np.transpose(refShape),shape), full\_matrices=True)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\scipy\linalg\_decomp\_svd.py”, line 108, in svd  
a1 = \_asarray\_validated(a, check\_finite=check\_finite)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\scipy\_lib\_util.py”, line 240, in \_asarray\_validated  
a = toarray(a)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\numpy\lib\function\_base.py”, line 630, in asarray\_chkfinite  
raise ValueError(  
ValueError: array must not contain infs or NaNs  
Loaded 39 subjects with 1 landmark points.  
C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py:94: RuntimeWarning: invalid value encountered in divide  
shape=shape/np.linalg.norm(shape)  
Traceback (most recent call last):  
File “C:/Users/GrafLab/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/GPA.py”, line 1209, in onLoad  
self.LM.doGpa(self.BoasOption)  
File “C:/Users/GrafLab/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/GPA.py”, line 229, in doGpa  
self.lm, self.mShape=gpa\_lib.runGPA(self.lmOrig)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 125, in runGPA  
allLandmarkSets = procrustesAlign(allLandmarkSets[:,:,0],allLandmarkSets)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 142, in procrustesAlign  
allLandmarkSets[:,:,index] = alignShape(mean, allLandmarkSets[:,:,index])  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 102, in alignShape  
u,s,v=sp.svd(np.dot(np.transpose(refShape),shape), full\_matrices=True)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\scipy\linalg\_decomp\_svd.py”, line 108, in svd  
a1 = \_asarray\_validated(a, check\_finite=check\_finite)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\scipy\_lib\_util.py”, line 240, in \_asarray\_validated  
a = toarray(a)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\numpy\lib\function\_base.py”, line 630, in asarray\_chkfinite  
raise ValueError(  
ValueError: array must not contain infs or NaNs  
Loaded 39 subjects with 1 landmark points.  
C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py:94: RuntimeWarning: invalid value encountered in divide  
shape=shape/np.linalg.norm(shape)  
Traceback (most recent call last):  
File “C:/Users/GrafLab/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/GPA.py”, line 1209, in onLoad  
self.LM.doGpa(self.BoasOption)  
File “C:/Users/GrafLab/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/GPA.py”, line 229, in doGpa  
self.lm, self.mShape=gpa\_lib.runGPA(self.lmOrig)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 125, in runGPA  
allLandmarkSets = procrustesAlign(allLandmarkSets[:,:,0],allLandmarkSets)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 142, in procrustesAlign  
allLandmarkSets[:,:,index] = alignShape(mean, allLandmarkSets[:,:,index])  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 102, in alignShape  
u,s,v=sp.svd(np.dot(np.transpose(refShape),shape), full\_matrices=True)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\scipy\linalg\_decomp\_svd.py”, line 108, in svd  
a1 = \_asarray\_validated(a, check\_finite=check\_finite)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\scipy\_lib\_util.py”, line 240, in \_asarray\_validated  
a = toarray(a)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\numpy\lib\function\_base.py”, line 630, in asarray\_chkfinite  
raise ValueError(  
ValueError: array must not contain infs or NaNs  
Loaded 39 subjects with 1 landmark points.  
C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py:94: RuntimeWarning: invalid value encountered in divide  
shape=shape/np.linalg.norm(shape)  
Traceback (most recent call last):  
File “C:/Users/GrafLab/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/GPA.py”, line 1209, in onLoad  
self.LM.doGpa(self.BoasOption)  
File “C:/Users/GrafLab/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/GPA.py”, line 229, in doGpa  
self.lm, self.mShape=gpa\_lib.runGPA(self.lmOrig)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 125, in runGPA  
allLandmarkSets = procrustesAlign(allLandmarkSets[:,:,0],allLandmarkSets)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 142, in procrustesAlign  
allLandmarkSets[:,:,index] = alignShape(mean, allLandmarkSets[:,:,index])  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 102, in alignShape  
u,s,v=sp.svd(np.dot(np.transpose(refShape),shape), full\_matrices=True)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\scipy\linalg\_decomp\_svd.py”, line 108, in svd  
a1 = \_asarray\_validated(a, check\_finite=check\_finite)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\scipy\_lib\_util.py”, line 240, in \_asarray\_validated  
a = toarray(a)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\numpy\lib\function\_base.py”, line 630, in asarray\_chkfinite  
raise ValueError(  
ValueError: array must not contain infs or NaNs  
Loaded 39 subjects with 1 landmark points.  
C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py:94: RuntimeWarning: invalid value encountered in divide  
shape=shape/np.linalg.norm(shape)  
Traceback (most recent call last):  
File “C:/Users/GrafLab/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/GPA.py”, line 1209, in onLoad  
self.LM.doGpa(self.BoasOption)  
File “C:/Users/GrafLab/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/GPA.py”, line 229, in doGpa  
self.lm, self.mShape=gpa\_lib.runGPA(self.lmOrig)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 125, in runGPA  
allLandmarkSets = procrustesAlign(allLandmarkSets[:,:,0],allLandmarkSets)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 142, in procrustesAlign  
allLandmarkSets[:,:,index] = alignShape(mean, allLandmarkSets[:,:,index])  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 102, in alignShape  
u,s,v=sp.svd(np.dot(np.transpose(refShape),shape), full\_matrices=True)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\scipy\linalg\_decomp\_svd.py”, line 108, in svd  
a1 = \_asarray\_validated(a, check\_finite=check\_finite)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\scipy\_lib\_util.py”, line 240, in \_asarray\_validated  
a = toarray(a)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\numpy\lib\function\_base.py”, line 630, in asarray\_chkfinite  
raise ValueError(  
ValueError: array must not contain infs or NaNs  
Loaded 39 subjects with 1 landmark points.  
C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py:94: RuntimeWarning: invalid value encountered in divide  
shape=shape/np.linalg.norm(shape)  
Traceback (most recent call last):  
File “C:/Users/GrafLab/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/GPA.py”, line 1209, in onLoad  
self.LM.doGpa(self.BoasOption)  
File “C:/Users/GrafLab/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/GPA.py”, line 229, in doGpa  
self.lm, self.mShape=gpa\_lib.runGPA(self.lmOrig)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 125, in runGPA  
allLandmarkSets = procrustesAlign(allLandmarkSets[:,:,0],allLandmarkSets)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 142, in procrustesAlign  
allLandmarkSets[:,:,index] = alignShape(mean, allLandmarkSets[:,:,index])  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 102, in alignShape  
u,s,v=sp.svd(np.dot(np.transpose(refShape),shape), full\_matrices=True)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\scipy\linalg\_decomp\_svd.py”, line 108, in svd  
a1 = \_asarray\_validated(a, check\_finite=check\_finite)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\scipy\_lib\_util.py”, line 240, in \_asarray\_validated  
a = toarray(a)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\numpy\lib\function\_base.py”, line 630, in asarray\_chkfinite  
raise ValueError(  
ValueError: array must not contain infs or NaNs  
Loaded 39 subjects with 1 landmark points.  
C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py:94: RuntimeWarning: invalid value encountered in divide  
shape=shape/np.linalg.norm(shape)  
Traceback (most recent call last):  
File “C:/Users/GrafLab/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/GPA.py”, line 1209, in onLoad  
self.LM.doGpa(self.BoasOption)  
File “C:/Users/GrafLab/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/GPA.py”, line 229, in doGpa  
self.lm, self.mShape=gpa\_lib.runGPA(self.lmOrig)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 125, in runGPA  
allLandmarkSets = procrustesAlign(allLandmarkSets[:,:,0],allLandmarkSets)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 142, in procrustesAlign  
allLandmarkSets[:,:,index] = alignShape(mean, allLandmarkSets[:,:,index])  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 102, in alignShape  
u,s,v=sp.svd(np.dot(np.transpose(refShape),shape), full\_matrices=True)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\scipy\linalg\_decomp\_svd.py”, line 108, in svd  
a1 = \_asarray\_validated(a, check\_finite=check\_finite)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\scipy\_lib\_util.py”, line 240, in \_asarray\_validated  
a = toarray(a)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\numpy\lib\function\_base.py”, line 630, in asarray\_chkfinite  
raise ValueError(  
ValueError: array must not contain infs or NaNs  
Loaded 39 subjects with 1 landmark points.  
C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py:94: RuntimeWarning: invalid value encountered in divide  
shape=shape/np.linalg.norm(shape)  
Traceback (most recent call last):  
File “C:/Users/GrafLab/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/GPA.py”, line 1209, in onLoad  
self.LM.doGpa(self.BoasOption)  
File “C:/Users/GrafLab/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/GPA.py”, line 229, in doGpa  
self.lm, self.mShape=gpa\_lib.runGPA(self.lmOrig)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 125, in runGPA  
allLandmarkSets = procrustesAlign(allLandmarkSets[:,:,0],allLandmarkSets)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 142, in procrustesAlign  
allLandmarkSets[:,:,index] = alignShape(mean, allLandmarkSets[:,:,index])  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 102, in alignShape  
u,s,v=sp.svd(np.dot(np.transpose(refShape),shape), full\_matrices=True)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\scipy\linalg\_decomp\_svd.py”, line 108, in svd  
a1 = \_asarray\_validated(a, check\_finite=check\_finite)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\scipy\_lib\_util.py”, line 240, in \_asarray\_validated  
a = toarray(a)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\numpy\lib\function\_base.py”, line 630, in asarray\_chkfinite  
raise ValueError(  
ValueError: array must not contain infs or NaNs  
Loaded 39 subjects with 1 landmark points.  
C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py:94: RuntimeWarning: invalid value encountered in divide  
shape=shape/np.linalg.norm(shape)  
Traceback (most recent call last):  
File “C:/Users/GrafLab/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/GPA.py”, line 1209, in onLoad  
self.LM.doGpa(self.BoasOption)  
File “C:/Users/GrafLab/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/GPA.py”, line 229, in doGpa  
self.lm, self.mShape=gpa\_lib.runGPA(self.lmOrig)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 125, in runGPA  
allLandmarkSets = procrustesAlign(allLandmarkSets[:,:,0],allLandmarkSets)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 142, in procrustesAlign  
allLandmarkSets[:,:,index] = alignShape(mean, allLandmarkSets[:,:,index])  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 102, in alignShape  
u,s,v=sp.svd(np.dot(np.transpose(refShape),shape), full\_matrices=True)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\scipy\linalg\_decomp\_svd.py”, line 108, in svd  
a1 = \_asarray\_validated(a, check\_finite=check\_finite)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\scipy\_lib\_util.py”, line 240, in \_asarray\_validated  
a = toarray(a)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\numpy\lib\function\_base.py”, line 630, in asarray\_chkfinite  
raise ValueError(  
ValueError: array must not contain infs or NaNs  
Loaded 39 subjects with 1 landmark points.  
C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py:94: RuntimeWarning: invalid value encountered in divide  
shape=shape/np.linalg.norm(shape)  
Traceback (most recent call last):  
File “C:/Users/GrafLab/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/GPA.py”, line 1209, in onLoad  
self.LM.doGpa(self.BoasOption)  
File “C:/Users/GrafLab/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/GPA.py”, line 229, in doGpa  
self.lm, self.mShape=gpa\_lib.runGPA(self.lmOrig)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 125, in runGPA  
allLandmarkSets = procrustesAlign(allLandmarkSets[:,:,0],allLandmarkSets)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 142, in procrustesAlign  
allLandmarkSets[:,:,index] = alignShape(mean, allLandmarkSets[:,:,index])  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 102, in alignShape  
u,s,v=sp.svd(np.dot(np.transpose(refShape),shape), full\_matrices=True)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\scipy\linalg\_decomp\_svd.py”, line 108, in svd  
a1 = \_asarray\_validated(a, check\_finite=check\_finite)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\scipy\_lib\_util.py”, line 240, in \_asarray\_validated  
a = toarray(a)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\numpy\lib\function\_base.py”, line 630, in asarray\_chkfinite  
raise ValueError(  
ValueError: array must not contain infs or NaNs  
Loaded 39 subjects with 1 landmark points.  
C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py:94: RuntimeWarning: invalid value encountered in divide  
shape=shape/np.linalg.norm(shape)  
Traceback (most recent call last):  
File “C:/Users/GrafLab/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/GPA.py”, line 1209, in onLoad  
self.LM.doGpa(self.BoasOption)  
File “C:/Users/GrafLab/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/GPA.py”, line 229, in doGpa  
self.lm, self.mShape=gpa\_lib.runGPA(self.lmOrig)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 125, in runGPA  
allLandmarkSets = procrustesAlign(allLandmarkSets[:,:,0],allLandmarkSets)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 142, in procrustesAlign  
allLandmarkSets[:,:,index] = alignShape(mean, allLandmarkSets[:,:,index])  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 102, in alignShape  
u,s,v=sp.svd(np.dot(np.transpose(refShape),shape), full\_matrices=True)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\scipy\linalg\_decomp\_svd.py”, line 108, in svd  
a1 = \_asarray\_validated(a, check\_finite=check\_finite)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\scipy\_lib\_util.py”, line 240, in \_asarray\_validated  
a = toarray(a)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\numpy\lib\function\_base.py”, line 630, in asarray\_chkfinite  
raise ValueError(  
ValueError: array must not contain infs or NaNs  
Loaded 39 subjects with 1 landmark points.  
C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py:94: RuntimeWarning: invalid value encountered in divide  
shape=shape/np.linalg.norm(shape)  
Traceback (most recent call last):  
File “C:/Users/GrafLab/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/GPA.py”, line 1209, in onLoad  
self.LM.doGpa(self.BoasOption)  
File “C:/Users/GrafLab/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/GPA.py”, line 229, in doGpa  
self.lm, self.mShape=gpa\_lib.runGPA(self.lmOrig)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 125, in runGPA  
allLandmarkSets = procrustesAlign(allLandmarkSets[:,:,0],allLandmarkSets)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 142, in procrustesAlign  
allLandmarkSets[:,:,index] = alignShape(mean, allLandmarkSets[:,:,index])  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 102, in alignShape  
u,s,v=sp.svd(np.dot(np.transpose(refShape),shape), full\_matrices=True)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\scipy\linalg\_decomp\_svd.py”, line 108, in svd  
a1 = \_asarray\_validated(a, check\_finite=check\_finite)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\scipy\_lib\_util.py”, line 240, in \_asarray\_validated  
a = toarray(a)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\numpy\lib\function\_base.py”, line 630, in asarray\_chkfinite  
raise ValueError(  
ValueError: array must not contain infs or NaNs  
Loaded 39 subjects with 1 landmark points.  
C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py:94: RuntimeWarning: invalid value encountered in divide  
shape=shape/np.linalg.norm(shape)  
Traceback (most recent call last):  
File “C:/Users/GrafLab/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/GPA.py”, line 1209, in onLoad  
self.LM.doGpa(self.BoasOption)  
File “C:/Users/GrafLab/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/GPA.py”, line 229, in doGpa  
self.lm, self.mShape=gpa\_lib.runGPA(self.lmOrig)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 125, in runGPA  
allLandmarkSets = procrustesAlign(allLandmarkSets[:,:,0],allLandmarkSets)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 142, in procrustesAlign  
allLandmarkSets[:,:,index] = alignShape(mean, allLandmarkSets[:,:,index])  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 102, in alignShape  
u,s,v=sp.svd(np.dot(np.transpose(refShape),shape), full\_matrices=True)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\scipy\linalg\_decomp\_svd.py”, line 108, in svd  
a1 = \_asarray\_validated(a, check\_finite=check\_finite)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\scipy\_lib\_util.py”, line 240, in \_asarray\_validated  
a = toarray(a)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\numpy\lib\function\_base.py”, line 630, in asarray\_chkfinite  
raise ValueError(  
ValueError: array must not contain infs or NaNs  
Loaded 39 subjects with 1 landmark points.  
C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py:94: RuntimeWarning: invalid value encountered in divide  
shape=shape/np.linalg.norm(shape)  
Traceback (most recent call last):  
File “C:/Users/GrafLab/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/GPA.py”, line 1209, in onLoad  
self.LM.doGpa(self.BoasOption)  
File “C:/Users/GrafLab/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/GPA.py”, line 229, in doGpa  
self.lm, self.mShape=gpa\_lib.runGPA(self.lmOrig)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 125, in runGPA  
allLandmarkSets = procrustesAlign(allLandmarkSets[:,:,0],allLandmarkSets)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 142, in procrustesAlign  
allLandmarkSets[:,:,index] = alignShape(mean, allLandmarkSets[:,:,index])  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 102, in alignShape  
u,s,v=sp.svd(np.dot(np.transpose(refShape),shape), full\_matrices=True)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\scipy\linalg\_decomp\_svd.py”, line 108, in svd  
a1 = \_asarray\_validated(a, check\_finite=check\_finite)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\scipy\_lib\_util.py”, line 240, in \_asarray\_validated  
a = toarray(a)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\numpy\lib\function\_base.py”, line 630, in asarray\_chkfinite  
raise ValueError(  
ValueError: array must not contain infs or NaNs  
Loaded 39 subjects with 1 landmark points.  
C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py:94: RuntimeWarning: invalid value encountered in divide  
shape=shape/np.linalg.norm(shape)  
Traceback (most recent call last):  
File “C:/Users/GrafLab/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/GPA.py”, line 1209, in onLoad  
self.LM.doGpa(self.BoasOption)  
File “C:/Users/GrafLab/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/GPA.py”, line 229, in doGpa  
self.lm, self.mShape=gpa\_lib.runGPA(self.lmOrig)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 125, in runGPA  
allLandmarkSets = procrustesAlign(allLandmarkSets[:,:,0],allLandmarkSets)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 142, in procrustesAlign  
allLandmarkSets[:,:,index] = alignShape(mean, allLandmarkSets[:,:,index])  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 102, in alignShape  
u,s,v=sp.svd(np.dot(np.transpose(refShape),shape), full\_matrices=True)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\scipy\linalg\_decomp\_svd.py”, line 108, in svd  
a1 = \_asarray\_validated(a, check\_finite=check\_finite)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\scipy\_lib\_util.py”, line 240, in \_asarray\_validated  
a = toarray(a)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\numpy\lib\function\_base.py”, line 630, in asarray\_chkfinite  
raise ValueError(  
ValueError: array must not contain infs or NaNs  
Loaded 39 subjects with 1 landmark points.  
C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py:94: RuntimeWarning: invalid value encountered in divide  
shape=shape/np.linalg.norm(shape)  
Traceback (most recent call last):  
File “C:/Users/GrafLab/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/GPA.py”, line 1209, in onLoad  
self.LM.doGpa(self.BoasOption)  
File “C:/Users/GrafLab/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/GPA.py”, line 229, in doGpa  
self.lm, self.mShape=gpa\_lib.runGPA(self.lmOrig)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 125, in runGPA  
allLandmarkSets = procrustesAlign(allLandmarkSets[:,:,0],allLandmarkSets)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 142, in procrustesAlign  
allLandmarkSets[:,:,index] = alignShape(mean, allLandmarkSets[:,:,index])  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 102, in alignShape  
u,s,v=sp.svd(np.dot(np.transpose(refShape),shape), full\_matrices=True)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\scipy\linalg\_decomp\_svd.py”, line 108, in svd  
a1 = \_asarray\_validated(a, check\_finite=check\_finite)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\scipy\_lib\_util.py”, line 240, in \_asarray\_validated  
a = toarray(a)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\numpy\lib\function\_base.py”, line 630, in asarray\_chkfinite  
raise ValueError(  
ValueError: array must not contain infs or NaNs  
Result import failed: Missing file  
Loaded 39 subjects with 1 landmark points.  
C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py:94: RuntimeWarning: invalid value encountered in divide  
shape=shape/np.linalg.norm(shape)  
Traceback (most recent call last):  
File “C:/Users/GrafLab/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/GPA.py”, line 1209, in onLoad  
self.LM.doGpa(self.BoasOption)  
File “C:/Users/GrafLab/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/GPA.py”, line 229, in doGpa  
self.lm, self.mShape=gpa\_lib.runGPA(self.lmOrig)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 125, in runGPA  
allLandmarkSets = procrustesAlign(allLandmarkSets[:,:,0],allLandmarkSets)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 142, in procrustesAlign  
allLandmarkSets[:,:,index] = alignShape(mean, allLandmarkSets[:,:,index])  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 102, in alignShape  
u,s,v=sp.svd(np.dot(np.transpose(refShape),shape), full\_matrices=True)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\scipy\linalg\_decomp\_svd.py”, line 108, in svd  
a1 = \_asarray\_validated(a, check\_finite=check\_finite)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\scipy\_lib\_util.py”, line 240, in \_asarray\_validated  
a = toarray(a)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\numpy\lib\function\_base.py”, line 630, in asarray\_chkfinite  
raise ValueError(  
ValueError: array must not contain infs or NaNs  
Result import failed: Missing file  
Loaded 39 subjects with 1 landmark points.  
C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py:94: RuntimeWarning: invalid value encountered in divide  
shape=shape/np.linalg.norm(shape)  
Traceback (most recent call last):  
File “C:/Users/GrafLab/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/GPA.py”, line 1209, in onLoad  
self.LM.doGpa(self.BoasOption)  
File “C:/Users/GrafLab/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/GPA.py”, line 229, in doGpa  
self.lm, self.mShape=gpa\_lib.runGPA(self.lmOrig)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 125, in runGPA  
allLandmarkSets = procrustesAlign(allLandmarkSets[:,:,0],allLandmarkSets)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 142, in procrustesAlign  
allLandmarkSets[:,:,index] = alignShape(mean, allLandmarkSets[:,:,index])  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 102, in alignShape  
u,s,v=sp.svd(np.dot(np.transpose(refShape),shape), full\_matrices=True)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\scipy\linalg\_decomp\_svd.py”, line 108, in svd  
a1 = \_asarray\_validated(a, check\_finite=check\_finite)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\scipy\_lib\_util.py”, line 240, in \_asarray\_validated  
a = toarray(a)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\numpy\lib\function\_base.py”, line 630, in asarray\_chkfinite  
raise ValueError(  
ValueError: array must not contain infs or NaNs  
Excluded landmarks: [‘f.mark’]  
Traceback (most recent call last):  
File “C:/Users/GrafLab/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/GPA.py”, line 1195, in onLoad  
self.LMExclusionList=[int(x) for x in self.LMExclusionList]  
File “C:/Users/GrafLab/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/GPA.py”, line 1195, in   
self.LMExclusionList=[int(x) for x in self.LMExclusionList]  
ValueError: invalid literal for int() with base 10: ‘f.mark’  
Excluded landmarks: [‘f.mark’]  
Traceback (most recent call last):  
File “C:/Users/GrafLab/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/GPA.py”, line 1195, in onLoad  
self.LMExclusionList=[int(x) for x in self.LMExclusionList]  
File “C:/Users/GrafLab/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/GPA.py”, line 1195, in   
self.LMExclusionList=[int(x) for x in self.LMExclusionList]  
ValueError: invalid literal for int() with base 10: ‘f.mark’  
Loaded 39 subjects with 1 landmark points.  
C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py:94: RuntimeWarning: invalid value encountered in divide  
shape=shape/np.linalg.norm(shape)  
Traceback (most recent call last):  
File “C:/Users/GrafLab/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/GPA.py”, line 1209, in onLoad  
self.LM.doGpa(self.BoasOption)  
File “C:/Users/GrafLab/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/GPA.py”, line 229, in doGpa  
self.lm, self.mShape=gpa\_lib.runGPA(self.lmOrig)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 125, in runGPA  
allLandmarkSets = procrustesAlign(allLandmarkSets[:,:,0],allLandmarkSets)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 142, in procrustesAlign  
allLandmarkSets[:,:,index] = alignShape(mean, allLandmarkSets[:,:,index])  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 102, in alignShape  
u,s,v=sp.svd(np.dot(np.transpose(refShape),shape), full\_matrices=True)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\scipy\linalg\_decomp\_svd.py”, line 108, in svd  
a1 = \_asarray\_validated(a, check\_finite=check\_finite)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\scipy\_lib\_util.py”, line 240, in \_asarray\_validated  
a = toarray(a)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\numpy\lib\function\_base.py”, line 630, in asarray\_chkfinite  
raise ValueError(  
ValueError: array must not contain infs or NaNs  
Loaded 39 subjects with 1 landmark points.  
C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py:94: RuntimeWarning: invalid value encountered in divide  
shape=shape/np.linalg.norm(shape)  
Traceback (most recent call last):  
File “C:/Users/GrafLab/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/GPA.py”, line 1209, in onLoad  
self.LM.doGpa(self.BoasOption)  
File “C:/Users/GrafLab/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/GPA.py”, line 229, in doGpa  
self.lm, self.mShape=gpa\_lib.runGPA(self.lmOrig)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 125, in runGPA  
allLandmarkSets = procrustesAlign(allLandmarkSets[:,:,0],allLandmarkSets)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 142, in procrustesAlign  
allLandmarkSets[:,:,index] = alignShape(mean, allLandmarkSets[:,:,index])  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 102, in alignShape  
u,s,v=sp.svd(np.dot(np.transpose(refShape),shape), full\_matrices=True)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\scipy\linalg\_decomp\_svd.py”, line 108, in svd  
a1 = \_asarray\_validated(a, check\_finite=check\_finite)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\scipy\_lib\_util.py”, line 240, in \_asarray\_validated  
a = toarray(a)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\numpy\lib\function\_base.py”, line 630, in asarray\_chkfinite  
raise ValueError(  
ValueError: array must not contain infs or NaNs  
Loaded 39 subjects with 1 landmark points.  
C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py:94: RuntimeWarning: invalid value encountered in divide  
shape=shape/np.linalg.norm(shape)  
Traceback (most recent call last):  
File “C:/Users/GrafLab/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/GPA.py”, line 1209, in onLoad  
self.LM.doGpa(self.BoasOption)  
File “C:/Users/GrafLab/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/GPA.py”, line 229, in doGpa  
self.lm, self.mShape=gpa\_lib.runGPA(self.lmOrig)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 125, in runGPA  
allLandmarkSets = procrustesAlign(allLandmarkSets[:,:,0],allLandmarkSets)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 142, in procrustesAlign  
allLandmarkSets[:,:,index] = alignShape(mean, allLandmarkSets[:,:,index])  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 102, in alignShape  
u,s,v=sp.svd(np.dot(np.transpose(refShape),shape), full\_matrices=True)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\scipy\linalg\_decomp\_svd.py”, line 108, in svd  
a1 = \_asarray\_validated(a, check\_finite=check\_finite)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\scipy\_lib\_util.py”, line 240, in \_asarray\_validated  
a = toarray(a)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\numpy\lib\function\_base.py”, line 630, in asarray\_chkfinite  
raise ValueError(  
ValueError: array must not contain infs or NaNs  
Loaded 39 subjects with 1 landmark points.  
C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py:94: RuntimeWarning: invalid value encountered in divide  
shape=shape/np.linalg.norm(shape)  
Traceback (most recent call last):  
File “C:/Users/GrafLab/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/GPA.py”, line 1209, in onLoad  
self.LM.doGpa(self.BoasOption)  
File “C:/Users/GrafLab/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/GPA.py”, line 229, in doGpa  
self.lm, self.mShape=gpa\_lib.runGPA(self.lmOrig)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 125, in runGPA  
allLandmarkSets = procrustesAlign(allLandmarkSets[:,:,0],allLandmarkSets)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 142, in procrustesAlign  
allLandmarkSets[:,:,index] = alignShape(mean, allLandmarkSets[:,:,index])  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 102, in alignShape  
u,s,v=sp.svd(np.dot(np.transpose(refShape),shape), full\_matrices=True)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\scipy\linalg\_decomp\_svd.py”, line 108, in svd  
a1 = \_asarray\_validated(a, check\_finite=check\_finite)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\scipy\_lib\_util.py”, line 240, in \_asarray\_validated  
a = toarray(a)  
File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\numpy\lib\function\_base.py”, line 630, in asarray\_chkfinite  
raise ValueError(  
ValueError: array must not contain infs or NaNs

---

<div class="post-metadata">

**Author:** ![maryam\_shakeri](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/maryam_shakeri/32/78189_2.png) [@maryam\_shakeri](https://discourse.slicer.org/u/maryam_shakeri)\
**Post date:** [October 10, 2024, 12:45am UTC](https://discourse.slicer.org/t/gpa-module-not-executing/34583/8 "2024-10-10T00:45:12Z")

</div>

I see - so I must enter both landmark file sets at once? That may be the issue as I currently have been trying only one sample’s landmarks. Apologies for the naive question; I’m very new to slicer!

---

<div class="post-metadata">

**Author:** ![muratmaga](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/muratmaga/32/3622_2.png) [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Post date:** [October 10, 2024, 1:20am UTC](https://discourse.slicer.org/t/gpa-module-not-executing/34583/9 "2024-10-10T01:20:03Z")

</div>

> [@maryam\_shakeri](#):
>
> Loaded 39 subjects with 1 landmark points.  
> C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py:94: RuntimeWarning: invalid value encountered in divide  
> shape=shape/np.linalg.norm(shape)  
> Traceback (most recent call last):  
> File “C:/Users/GrafLab/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/GPA.py”, line 1209, in onLoad  
> self.LM.doGpa(self.BoasOption)  
> File “C:/Users/GrafLab/AppData/Local/slicer.org/Slicer 5.6.2/slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/GPA.py”, line 229, in doGpa  
> self.lm, self.mShape=gpa\_lib.runGPA(self.lmOrig)  
> File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 125, in runGPA  
> allLandmarkSets = procrustesAlign(allLandmarkSets[:,:,0],allLandmarkSets)  
> File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 142, in procrustesAlign  
> allLandmarkSets[:,:,index] = alignShape(mean, allLandmarkSets[:,:,index])  
> File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\slicer.org\Extensions-32448\SlicerMorph\lib\Slicer-5.6\qt-scripted-modules\Support\gpa\_lib.py”, line 102, in alignShape  
> u,s,v=sp.svd(np.dot(np.transpose(refShape),shape), full\_matrices=True)  
> File “C:\Users\GrafLab\AppData\Local\slicer.org\Slicer 5.6.2\lib\Python\Lib\site-packages\scipy\linalg\_decomp\_svd.py”, line 108, in svd  
> a1 = \_asarray\_validated(a, check\_finite=check\_finite)

This is the issue. There is only 1 landmark point in 39 files. The covariance matrix is singular and everything breaks apart. You can’t do a shape analysis with a single landmark.

If this is not what you are trying to do (i.e., work with a single landmark), then please share your dataset. Otherwise perhaps review our GPA module tutorials to understand how it works: [GitHub - SlicerMorph/Tutorials: SlicerMorph module tutorials](https://github.com/SlicerMorph/Tutorials).

---

<div class="post-metadata">

**Author:** ![maryam\_shakeri](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/maryam_shakeri/32/78189_2.png) [@maryam\_shakeri](https://discourse.slicer.org/u/maryam_shakeri)\
**Post date:** [October 10, 2024, 5:05pm UTC](https://discourse.slicer.org/t/gpa-module-not-executing/34583/10 "2024-10-10T17:05:44Z")

</div>

I was under the impression that each point placed (ie each .json file) was a landmark. How can I place landmarks if not in the markups module?

Thanks!

---

<div class="post-metadata">

**Author:** ![muratmaga](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/muratmaga/32/3622_2.png) [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Post date:** [October 10, 2024, 7:07pm UTC](https://discourse.slicer.org/t/gpa-module-not-executing/34583/11 "2024-10-10T19:07:00Z")

</div>

A pointList markup type can store many control points (aka landmarks). Please read our tutorials. Including the ones for Markups from the link I shared above.