# Error in ALPACA/MALPACA with photogrammetry meshes

**URL:** <https://discourse.slicer.org/t/error-in-alpaca-malpaca-with-photogrammetry-meshes/37709>\
**Category:** Support\
**Created:** [August 5, 2024, 5:44pm UTC](https://discourse.slicer.org/t/error-in-alpaca-malpaca-with-photogrammetry-meshes/37709 "2024-08-05T17:44:12Z")\
**Posts on this page:** 10\
**Page:** 1

<div class="post-metadata">

**Author:** ![ATroyelli](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/atroyelli/32/66917_2.png) [@ATroyelli](https://discourse.slicer.org/u/ATroyelli)\
**Post date:** [August 5, 2024, 5:44pm UTC](https://discourse.slicer.org/t/error-in-alpaca-malpaca-with-photogrammetry-meshes/37709/1 "2024-08-05T17:44:12Z")

</div>

Operating system: Windows 10 pro (X64)  
Slicer version: 5.6.2  
Expected behavior: I hope to be able to automatically place landmarks in 3D meshes generated by photogrammetry, employing templates made with microtomography.  
Actual behavior: I attach the screenshots of the errors and warnings.

![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/c/0/c0517ed9f6660a2baf5e82b02dcba4f9fe77b11d.png)

![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/1/d/1d5da0939afe6cd43d6e0dd677b0bb9d8e595157.jpeg)

![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/6/d/6dbfbc32b60e6022516950d10e1e60ee6128cd3b.png)

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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:** [August 5, 2024, 11:30pm UTC](https://discourse.slicer.org/t/error-in-alpaca-malpaca-with-photogrammetry-meshes/37709/2 "2024-08-05T23:30:28Z")

</div>

Please copy and paste the errors. Screenshots are too blurry to read.

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<div class="post-metadata">

**Author:** ![ATroyelli](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/atroyelli/32/66917_2.png) [@ATroyelli](https://discourse.slicer.org/u/ATroyelli)\
**Post date:** [August 6, 2024, 4:54pm UTC](https://discourse.slicer.org/t/error-in-alpaca-malpaca-with-photogrammetry-meshes/37709/3 "2024-08-06T16:54:34Z")

</div>

Hello, thanks for reply. I´m sorry about screenshots quality, it´s were a lot notifications.

Switch to module: “ALPACA”

ReadDataInternal ((unknown)): File D:/Users/Adrian/Documents/Sync/Adrian/Tesis Doctoral/Bases de Datos/Especimenes/3D/FotogrametrÍa/Ingroup/Craneos/Chve\Chve\_MACN-Ma\_14821\_Cr.ply does not contain coordinate system information. Assuming LPS.

“Model” Reader has successfully read the file “D:/Users/Adrian/Documents/Sync/Adrian/Tesis Doctoral/Bases de Datos/Especimenes/3D/FotogrametrÍa/Ingroup/Craneos/Chve\Chve\_MACN-Ma\_14821\_Cr.ply” “[0.12s]”

ReadDataInternal ((unknown)): File D:/Users/Adrian/Documents/Sync/Adrian/Tesis Doctoral/Análisis/Lmkando/ALPACA/Mesh Templates/Chve\_MACN-Ma\_35.337\_Cr.ply does not contain coordinate system information. Assuming LPS.

“Model” Reader has successfully read the file “D:/Users/Adrian/Documents/Sync/Adrian/Tesis Doctoral/Análisis/Lmkando/ALPACA/Mesh Templates/Chve\_MACN-Ma\_35.337\_Cr.ply” “[0.93s]”

parameters are {‘projectionFactor’: 1.0, ‘pointDensity’: 1.0, ‘normalSearchRadius’: 2.0, ‘FPFHNeighbors’: 100, ‘FPFHSearchRadius’: 5.0, ‘distanceThreshold’: 3.0, ‘maxRANSAC’: 1000000, ‘ICPDistanceThreshold’: 1.5, ‘alpha’: 2.0, ‘beta’: 2.0, ‘CPDIterations’: 100, ‘CPDTolerance’: 0.001, ‘Acceleration’: False, ‘BCPDFolder’: ‘’}

:: Loading point clouds and downsampling

Scale length are 83.40928102753698 90.81990677220223

Voxel Size is 1.5165323823188541

Scaling factor is 1

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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:** [August 6, 2024, 5:35pm UTC](https://discourse.slicer.org/t/error-in-alpaca-malpaca-with-photogrammetry-meshes/37709/4 "2024-08-06T17:35:05Z")

</div>

There are no errors in the log you shared. ALPACA seems to be working (or at least no generating any errors up to that point). Why do you think there is an error?  
Can you share your data?

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<div class="post-metadata">

**Author:** ![ATroyelli](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/atroyelli/32/66917_2.png) [@ATroyelli](https://discourse.slicer.org/u/ATroyelli)\
**Post date:** [August 6, 2024, 6:52pm UTC](https://discourse.slicer.org/t/error-in-alpaca-malpaca-with-photogrammetry-meshes/37709/5 "2024-08-06T18:52:00Z")

</div>

So far I have not obtained the output with the coordinates of landmarks in the target specimens

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<div class="post-metadata">

**Author:** ![ATroyelli](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/atroyelli/32/66917_2.png) [@ATroyelli](https://discourse.slicer.org/u/ATroyelli)\
**Post date:** [August 6, 2024, 6:59pm UTC](https://discourse.slicer.org/t/error-in-alpaca-malpaca-with-photogrammetry-meshes/37709/6 "2024-08-06T18:59:40Z")

</div>

These are errors at other set of specimens:

GetArrayItemsStringProperty: markups property is not an array

Traceback (most recent call last):

File “C:/ProgramData/[slicer.org/Slicer](http://slicer.org/Slicer) 5.6.2/[slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/ALPACA.py](http://slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/ALPACA.py)”, line 951, in onApplyLandmarkMulti

logic.runLandmarkMultiprocess(

File “C:/ProgramData/[slicer.org/Slicer](http://slicer.org/Slicer) 5.6.2/[slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/ALPACA.py](http://slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/ALPACA.py)”, line 1561, in runLandmarkMultiprocess

array = self.pairwiseAlignment(

File “C:/ProgramData/[slicer.org/Slicer](http://slicer.org/Slicer) 5.6.2/[slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/ALPACA.py](http://slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/ALPACA.py)”, line 1618, in pairwiseAlignment

sourceLandmarks, sourceLMNode = self.loadAndScaleFiducials(

File “C:/ProgramData/[slicer.org/Slicer](http://slicer.org/Slicer) 5.6.2/[slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/ALPACA.py](http://slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/ALPACA.py)”, line 2866, in loadAndScaleFiducials

sourceLandmarkNode = slicer.util.loadMarkups(fiducial)

File “C:\ProgramData[slicer.org]([http://slicer.org](http://slicer.org))\Slicer 5.6.2\bin\Python\slicer\util.py”, line 863, in loadMarkups

return loadNodeFromFile(filename, “MarkupsFile”)

File “C:\ProgramData[slicer.org]([http://slicer.org](http://slicer.org))\Slicer 5.6.2\bin\Python\slicer\util.py”, line 734, in loadNodeFromFile

raise RuntimeError(errorMessage)

RuntimeError: Failed to load node from file: D:/Users/Adrian/Documents/Sync/Adrian/Tesis Doctoral/Análisis/Lmkando/ALPACA/.mrkps.json Templates/Dasypus\_septemcinctus\_MACN-Ma\_13220\_Cr.mrk.json

Error: Loading D:/Users/Adrian/Documents/Sync/Adrian/Tesis Doctoral/Análisis/Lmkando/ALPACA/.mrkps.json Templates/Dasypus\_septemcinctus\_MACN-Ma\_13220\_Cr.mrk.json - load failed.

I have exported landmarks coordinates in .pts file into .mrks.json format to use in ALPACA. I share these files with you so you can see if there is any inconsistency between them

(Attachment Chaetophractus\_vellerosus\_MACN-Ma\_35.337\_Cr.mrk.json is missing)

(Attachment Chaetophractus\_vellerosus\_MACN-Ma\_35.337\_Cr.pts is missing)

---

<div class="post-metadata">

**Author:** ![ATroyelli](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/atroyelli/32/66917_2.png) [@ATroyelli](https://discourse.slicer.org/u/ATroyelli)\
**Post date:** [August 6, 2024, 7:04pm UTC](https://discourse.slicer.org/t/error-in-alpaca-malpaca-with-photogrammetry-meshes/37709/7 "2024-08-06T19:04:17Z")

</div>

These are errors at other set of specimens:

GetArrayItemsStringProperty: markups property is not an array

Traceback (most recent call last):

File “C:/ProgramData/[slicer.org/Slicer](http://slicer.org/Slicer) 5.6.2/[slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/ALPACA.py](http://slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/ALPACA.py)”, line 951, in onApplyLandmarkMulti

logic.runLandmarkMultiprocess(

File “C:/ProgramData/[slicer.org/Slicer](http://slicer.org/Slicer) 5.6.2/[slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/ALPACA.py](http://slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/ALPACA.py)”, line 1561, in runLandmarkMultiprocess

array = self.pairwiseAlignment(

File “C:/ProgramData/[slicer.org/Slicer](http://slicer.org/Slicer) 5.6.2/[slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/ALPACA.py](http://slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/ALPACA.py)”, line 1618, in pairwiseAlignment

sourceLandmarks, sourceLMNode = self.loadAndScaleFiducials(

File “C:/ProgramData/[slicer.org/Slicer](http://slicer.org/Slicer) 5.6.2/[slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/ALPACA.py](http://slicer.org/Extensions-32448/SlicerMorph/lib/Slicer-5.6/qt-scripted-modules/ALPACA.py)”, line 2866, in loadAndScaleFiducials

sourceLandmarkNode = slicer.util.loadMarkups(fiducial)

File “C:\ProgramData[slicer.org]([http://slicer.org/](http://slicer.org/))\Slicer 5.6.2\bin\Python\slicer\util.py”, line 863, in loadMarkups

return loadNodeFromFile(filename, “MarkupsFile”)

File “C:\ProgramData[slicer.org]([http://slicer.org/](http://slicer.org/))\Slicer 5.6.2\bin\Python\slicer\util.py”, line 734, in loadNodeFromFile

raise RuntimeError(errorMessage)

RuntimeError: Failed to load node from file: D:/Users/Adrian/Documents/Sync/Adrian/Tesis Doctoral/Análisis/Lmkando/ALPACA/.mrkps.json Templates/Dasypus\_septemcinctus\_MACN-Ma\_13220\_Cr.mrk.json

Error: Loading D:/Users/Adrian/Documents/Sync/Adrian/Tesis Doctoral/Análisis/Lmkando/ALPACA/.mrkps.json Templates/Dasypus\_septemcinctus\_MACN-Ma\_13220\_Cr.mrk.json - load failed.

I have exported landmarks coordinates in .pts file into .mrks.json format to use in ALPACA as templates. I share these files with you so you can see if there is any inconsistency between them. These coordinates correspond to the same specimen. The targets are made from photogrammetry

{  
“@schema”: “[https://raw.githubusercontent.com/Slicer/Slicer/main/Modules/Loadable/Markups/Resources/Schema/markups-schema-v1.0.0.json#](https://raw.githubusercontent.com/Slicer/Slicer/main/Modules/Loadable/Markups/Resources/Schema/markups-schema-v1.0.0.json#)”,  
“markups”: {  
“type”: “Fiducial”,  
“coordinateSystem”: “LPS”,  
“controlPoints”: [  
{  
“label”: “S001”,  
“position”: [28.2039, -11.7751, -23.4144]  
},  
{  
“label”: “S002”,  
“position”: [30.7783, -2.5996, -23.5616]  
},  
{  
“label”: “S003”,  
“position”: [34.5365, -5.6058, -24.4696]  
},  
{  
“label”: “S004”,  
“position”: [34.3649, -8.8592, -25.0441]  
},  
{  
“label”: “S005”,  
“position”: [32.5503, -15.4687, -21.2761]  
},  
{  
“label”: “S006”,  
“position”: [32.6481, -16.1612, -21.0283]  
},  
{  
“label”: “S007”,  
“position”: [33.0748, -23.1936, -19.5325]  
},  
{  
“label”: “S008”,  
“position”: [34.8293, -35.2878, -16.7713]  
},  
{  
“label”: “S009”,  
“position”: [37.6284, -45.621, -15.4776]  
},  
{  
“label”: “S010”,  
“position”: [37.7541, -52.0187, -18.2158]  
},  
{  
“label”: “S011”,  
“position”: [30.2662, -47.3469, -21.1346]  
},  
{  
“label”: “S012”,  
“position”: [31.9175, -49.9682, -20.7883]  
},  
{  
“label”: “S013”,  
“position”: [31.797, -53.7763, -17.8025]  
},  
{  
“label”: “S014”,  
“position”: [34.0789, -54.5117, -18.8703]  
},  
{  
“label”: “S015”,  
“position”: [32.7307, -66.5737, -15.9977]  
},  
{  
“label”: “S016”,  
“position”: [34.4706, -67.4384, -14.0772]  
},  
{  
“label”: “S017”,  
“position”: [30.9929, -69.1461, -12.278]  
},  
{  
“label”: “S018”,  
“position”: [30.9918, -71.5094, -14.5013]  
},  
{  
“label”: “S019”,  
“position”: [34.3105, -70.4575, -14.0783]  
},  
{  
“label”: “S020”,  
“position”: [22.0601, -59.8185, -4.3684]  
},  
{  
“label”: “S021”,  
“position”: [21.2183, -51.53, -6.167]  
},  
{  
“label”: “S022”,  
“position”: [23.7331, -52.9365, -5.6439]  
},  
{  
“label”: “S023”,  
“position”: [26.3594, -52.3965, -4.987]  
},  
{  
“label”: “S024”,  
“position”: [27.2593, -48.7112, -4.3994]  
},  
{  
“label”: “S025”,  
“position”: [27.2033, -45.1583, -3.6922]  
},  
{  
“label”: “S026”,  
“position”: [27.5837, -42.8516, -3.6907]  
},  
{  
“label”: “S027”,  
“position”: [28.6185, -40.8036, -4.1694]  
},  
{  
“label”: “S028”,  
“position”: [30.354, -39.374, -6.3381]  
},  
{  
“label”: “S029”,  
“position”: [30.134, -37.8104, -8.5109]  
},  
{  
“label”: “S030”,  
“position”: [29.3568, -36.7186, -11.0536]  
},  
{  
“label”: “S031”,  
“position”: [30.2651, -36.7179, -13.2742]  
},  
{  
“label”: “S032”,  
“position”: [31.4022, -38.953, -15.2223]  
},  
{  
“label”: “S033”,  
“position”: [29.7892, -36.8959, -14.4028]  
},  
{  
“label”: “S034”,  
“position”: [28.7399, -32.9148, -14.8616]  
},  
{  
“label”: “S035”,  
“position”: [22.4619, -23.9445, -26.5049]  
},  
{  
“label”: “S036”,  
“position”: [20.4977, -25.435, -24.278]  
},  
{  
“label”: “S037”,  
“position”: [18.7416, -30.3332, -17.9179]  
},  
{  
“label”: “S038”,  
“position”: [17.446, -38.1628, -17.5902]  
},  
{  
“label”: “S039”,  
“position”: [19.4214, -33.9421, -14.2639]  
},  
{  
“label”: “S040”,  
“position”: [21.8329, -33.0524, -11.2296]  
},  
{  
“label”: “S041”,  
“position”: [23.1472, -33.3997, -9.3929]  
},  
{  
“label”: “S042”,  
“position”: [24.5036, -33.9116, -7.8147]  
},  
{  
“label”: “S043”,  
“position”: [25.2918, -36.8534, -6.0291]  
},  
{  
“label”: “S044”,  
“position”: [23.9786, -40.2156, -4.7997]  
},  
{  
“label”: “S045”,  
“position”: [21.1875, -42.5474, -5.8932]  
},  
{  
“label”: “S046”,  
“position”: [19.5283, -44.1903, -6.7014]  
},  
{  
“label”: “S047”,  
“position”: [19.8511, -46.0734, -18.7032]  
},  
{  
“label”: “S048”,  
“position”: [25.2619, -48.0425, -17.9808]  
},  
{  
“label”: “S049”,  
“position”: [21.7544, -51.9731, -12.4034]  
},  
{  
“label”: “S050”,  
“position”: [20.8697, -51.3901, -9.0766]  
},  
{  
“label”: “S051”,  
“position”: [18.9073, -57.9055, -11.5839]  
},  
{  
“label”: “S052”,  
“position”: [18.7048, -54.2922, -7.3396]  
},  
{  
“label”: “S053”,  
“position”: [19.5858, -51.7116, -6.311]  
},  
{  
“label”: “S054”,  
“position”: [21.1874, -47.516, -5.2966]  
},  
{  
“label”: “S055”,  
“position”: [21.471, -44.8523, -4.753]  
},  
{  
“label”: “S056”,  
“position”: [18.7903, -46.6607, -7.1211]  
},  
{  
“label”: “S057”,  
“position”: [17.7536, -50.5154, -7.6184]  
},  
{  
“label”: “S058”,  
“position”: [16.8194, -53.8868, -8.4897]  
},  
{  
“label”: “S059”,  
“position”: [16.1963, -57.7051, -9.886]  
},  
{  
“label”: “S060”,  
“position”: [16.4379, -62.4612, -11.0545]  
},  
{  
“label”: “S061”,  
“position”: [16.393, -68.0004, -13.2447]  
},  
{  
“label”: “S062”,  
“position”: [14.816, -69.5355, -18.758]  
},  
{  
“label”: “S063”,  
“position”: [14.453, -68.8529, -23.9153]  
},  
{  
“label”: “S064”,  
“position”: [14.8945, -67.1808, -27.8276]  
},  
{  
“label”: “S065”,  
“position”: [15.9928, -66.0758, -30.5778]  
},  
{  
“label”: “S066”,  
“position”: [16.3754, -49.6166, -31.4364]  
},  
{  
“label”: “S067”,  
“position”: [24.3607, -22.4297, -28.8041]  
},  
{  
“label”: “S068”,  
“position”: [31.8064, -0.147, -27.6045]  
},  
{  
“label”: “S069”,  
“position”: [35.3245, -5.5974, -25.6323]  
},  
{  
“label”: “S070”,  
“position”: [34.6841, -14.2653, -25.2997]  
},  
{  
“label”: “S071”,  
“position”: [37.0433, -36.4687, -23.1609]  
},  
{  
“label”: “S072”,  
“position”: [37.6952, -45.9551, -21.9758]  
},  
{  
“label”: “S073”,  
“position”: [34.7364, -49.763, -23.5898]  
},  
{  
“label”: “S074”,  
“position”: [36.836, -58.6946, -22.5678]  
},  
{  
“label”: “S075”,  
“position”: [37.3222, -65.9218, -21.5574]  
},  
{  
“label”: “S076”,  
“position”: [33.2897, -71.4615, -16.0583]  
},  
{  
“label”: “S077”,  
“position”: [30.3094, -72.4527, -23.9958]  
},  
{  
“label”: “S078”,  
“position”: [23.0219, -63.885, -6.1466]  
},  
{  
“label”: “S079”,  
“position”: [16.0445, -67.8117, -30.3247]  
},  
{  
“label”: “S080”,  
“position”: [21.5849, -72.0162, -27.4299]  
},  
{  
“label”: “S081”,  
“position”: [31.5413, -12.0461, -31.3811]  
},  
{  
“label”: “S082”,  
“position”: [34.0389, -2.4053, -30.5007]  
},  
{  
“label”: “S083”,  
“position”: [35.9265, -5.375, -28.2896]  
},  
{  
“label”: “S084”,  
“position”: [34.9265, -8.9477, -26.2527]  
},  
{  
“label”: “S085”,  
“position”: [35.9972, -15.5302, -28.7637]  
},  
{  
“label”: “S086”,  
“position”: [36.2983, -16.4345, -28.7023]  
},  
{  
“label”: “S087”,  
“position”: [37.1298, -23.4627, -28.73]  
},  
{  
“label”: “S088”,  
“position”: [40.0277, -35.9994, -28.2364]  
},  
{  
“label”: “S089”,  
“position”: [42.396, -46.2419, -26.4495]  
},  
{  
“label”: “S090”,  
“position”: [40.4619, -52.5142, -23.7891]  
},  
{  
“label”: “S091”,  
“position”: [33.2611, -47.4521, -28.2027]  
},  
{  
“label”: “S092”,  
“position”: [34.7311, -50.2332, -27.1256]  
},  
{  
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Version 1.0  
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S145 3.6914497e+001 -6.7478607e+001 -4.2356552e+001

---

<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:** [August 6, 2024, 7:34pm UTC](https://discourse.slicer.org/t/error-in-alpaca-malpaca-with-photogrammetry-meshes/37709/8 "2024-08-06T19:34:37Z")

</div>

I will need two models and the markup file to see where these are coming from.

---

<div class="post-metadata">

**Author:** ![ATroyelli](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/atroyelli/32/66917_2.png) [@ATroyelli](https://discourse.slicer.org/u/ATroyelli)\
**Post date:** [August 6, 2024, 7:43pm UTC](https://discourse.slicer.org/t/error-in-alpaca-malpaca-with-photogrammetry-meshes/37709/9 "2024-08-06T19:43:12Z")

</div>

Ok, I can´t send by this mail. I´ll sending by your mail.

---

<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:** [August 6, 2024, 8:26pm UTC](https://discourse.slicer.org/t/error-in-alpaca-malpaca-with-photogrammetry-meshes/37709/10 "2024-08-06T20:26:07Z")

</div>

You need to upload somewhere you can share the link to file (dropbox, onedrive, google drive etc…)