# Sliding semilandmarks
**URL:** https://discourse.slicer.org/t/sliding-semilandmarks/39828
**Category:** SlicerMorph
**Created:** [October 23, 2024, 10:50pm UTC](https://discourse.slicer.org/t/sliding-semilandmarks/39828 "2024-10-23T22:50:54Z")
**Posts on this page:** 10
**Page:** 1
### Author:  [@Logan\_Moore](https://discourse.slicer.org/u/Logan_Moore)
#### Post date: [October 23, 2024, 10:50pm UTC](https://discourse.slicer.org/t/sliding-semilandmarks/39828/1 "2024-10-23T22:50:54Z")
Hi guys,
I hope you are well, I just want to make sure I am understanding the workflow of Slicermorph and SlicermorphR correctly. Apologies if this seems simple but I must have have an error somewhere and it is driving me
When looking at the SlicermorphR page my code is essentially the same
```auto
##set your working directory!
files=dir(patt='json')
fixed.LMs <- 1:2
semi.LMs <- 3:82
#Array is LAND, DIM, IND
#where LAND is the number of landmarks
#where DIM is the number of dimensions
#where INd is the number of individuals
samples=gsub(".json","",fixed=T, files)
LMs <- array(dim=c(82,3,10))
for (i in 1:10) LMs[,,i] = read.markups.json(files[i])
dimnames(LMs) <- list(paste0("LM_",1:82), c("x", "y", "z"), samples)
#read in the curves file
curves<-as.matrix(read.csv("curves.csv", header=FALSE))
#completes a GPA without sliding
defaultGPA<- gpagen(A=LMs, surfaces = semi.LMs, ProcD = TRUE)
```
This runs and completes without issue, and everything is great, it is sliding that seems to be an issue.
If I understand correctly, I will run a PCA based on the newly acquired GPA.
Something like this:
```auto
DefaultPCA = gm.prcomp(defaultGPA$coords)
```
If I am sliding by Procrustes distance, it would look like this:
```auto
PDGPA<- gpagen(A=LMs, curves=curves, surfaces = semi.LMs, ProcD = TRUE)
```
then
```auto
PDPCA = gm.prcomp(PDGPA$coords)
```
Then, to get it out, it would be the following?
```auto
geomorph2slicermorph2(gpa=defaultGPA, pca=DefaultPCA, paste0(output.path, "sliding'))
geomorph2slicermorph2(gpa=PDGPA, pca=PDPCA, paste0(output.path, "PDsliding')).
```
This then would give me files that I could then put back into Slicermorph to do visual analysis, correct?
Apologies again, I’ve been really wracking my brain on what is going wrong today.
---
### Author:  [@Logan\_Moore](https://discourse.slicer.org/u/Logan_Moore)
#### Post date: [October 23, 2024, 11:53pm UTC](https://discourse.slicer.org/t/sliding-semilandmarks/39828/2 "2024-10-23T23:53:20Z")
> [@Logan\_Moore](#):
>
> `geomorph2slicermorph2(gpa=defaultGPA, pca=DefaultPCA, paste0(output.path, "sliding'))`
The good news is that its an output path issue, that bad news is that no matter how many times I format the output path, nothing shows up in the folder.
I currently altered it from the example as follows:
output.path=“C:/Users/Logan/Desktop/geomorph”
---
### Author:  [@Logan\_Moore](https://discourse.slicer.org/u/Logan_Moore)
#### Post date: [October 24, 2024, 12:21am UTC](https://discourse.slicer.org/t/sliding-semilandmarks/39828/3 "2024-10-24T00:21:09Z")
Alrighty guys, never mind me. I found my error, I was missing a singular “/” and it was dumping the materials to my desktop. Everything is working as intended.
---
### Author:  [@muratmaga](https://discourse.slicer.org/u/muratmaga)
#### Post date: [October 24, 2024, 12:50am UTC](https://discourse.slicer.org/t/sliding-semilandmarks/39828/4 "2024-10-24T00:50:23Z")
Glad to hear that things are working. BTW the way, first GPA is redundant:
```auto
defaultGPA<- gpagen(A=LMs, surfaces = semi.LMs, ProcD = TRUE)
```
Just do
```auto
PDGPA<- gpagen(A=LMs, curves=curves, surfaces = semi.LMs, ProcD = TRUE)
PDPCA = gm.prcomp(PDGPA$coords)
geomorph2slicermorph2(gpa=PDGPA, pca=PDPCA, paste0(output.path, "PDsliding')).
```
---
### Author:  [@Logan\_Moore](https://discourse.slicer.org/u/Logan_Moore)
#### Post date: [October 29, 2024, 2:02am UTC](https://discourse.slicer.org/t/sliding-semilandmarks/39828/5 "2024-10-29T02:02:24Z")
Hi Murat,
I did adjust my code, as you suggested, my collaborates were really big on just wanting to see the output matched, so I did the regular GPA for that reason.
One quick follow-up: do you know why the slide landmarks and analysis won’t load into Slicermorph? I am on Slicer 5.6.2 with Slicermoprh version 5151748 and when I try to load an external analysis from R it just sits there blankly. I have included some data here for you to see ([https://drive.google.com/drive/folders/1QYhMn4o3DRkgmaNVSiaU0QsQBlKkcl6q?usp=drive\_link](https://drive.google.com/drive/folders/1QYhMn4o3DRkgmaNVSiaU0QsQBlKkcl6q?usp=drive_link)).
The original processed data still works, just not the items from Gemoorph2Slicermorph.
---
### Author:  [@muratmaga](https://discourse.slicer.org/u/muratmaga)
#### Post date: [October 29, 2024, 2:04am UTC](https://discourse.slicer.org/t/sliding-semilandmarks/39828/6 "2024-10-29T02:04:00Z")
I don’t have permission to download the date.
---
### Author:  [@Logan\_Moore](https://discourse.slicer.org/u/Logan_Moore)
#### Post date: [October 29, 2024, 2:05am UTC](https://discourse.slicer.org/t/sliding-semilandmarks/39828/7 "2024-10-29T02:05:44Z")
Lets see if this one works: [5PDsliding - Google Drive](https://drive.google.com/drive/folders/1QYhMn4o3DRkgmaNVSiaU0QsQBlKkcl6q?usp=sharing)
---
### Author:  [@muratmaga](https://discourse.slicer.org/u/muratmaga)
#### Post date: [October 29, 2024, 3:31am UTC](https://discourse.slicer.org/t/sliding-semilandmarks/39828/8 "2024-10-29T03:31:06Z")
I successfully loaded this dataset into GPA module, no errors or anything?
I don’t know whether the results make sense, but at least you should be able to get without an issue.
I used a slightly newer version from October 11th. Try with a newer version, particularly if you are using the JSON formatted log files like the one your provided. The GPA in stable version is a bit stale. We are waiting for the new stable to come out in the next few weeks.
---
### Author:  [@Logan\_Moore](https://discourse.slicer.org/u/Logan_Moore)
#### Post date: [October 29, 2024, 3:47am UTC](https://discourse.slicer.org/t/sliding-semilandmarks/39828/9 "2024-10-29T03:47:04Z")
Ah, yes, thank you! It does seem to be an issue on 5.6.2. The preview build worked immediately. Thanks for the tip!
---
### Author:  [@muratmaga](https://discourse.slicer.org/u/muratmaga)
#### Post date: [October 29, 2024, 4:55am UTC](https://discourse.slicer.org/t/sliding-semilandmarks/39828/10 "2024-10-29T04:55:25Z")
Yes, we need some of the features in the later preview version of Slicer, so SlicerMorph in 5.6.2 doesn’t have all the capability of later versions. A new stable will be out soon!