Atropos output error

[RB-008]

Dear Experts,,
I need urgent help. I use ANTs for mouse MRI brain analysis in Ubuntu 22 LTS. I am new to ANTs and following the manuals. For segmentation, I used the N4_corrected image as the input image. Following the script pasted below, only brain mask and segment (single image) output was produced, not any other output.

dim=3
img=/mnt/data_analysis/mouse_brain/data_ants/ants/N4_corrected.nii.gz
op=/mnt/data_analysis/mouse_brain/data_ants/ants/
ImageMath $dim ${op}mask.nii.gz Normalize $img
ThresholdImage $dim ${op}mask.nii.gz ${op}mask.nii.gz 0.05 1
Atropos -d $dim -x ${op}mask.nii.gz -c [5,0.001] -m [0.2,1x1x1] -i kmeans[3]
-o ${op}_seg.nii.gz -a $img

This script produces mask and lap images with no other output.
dim=3
n=3
img=/mnt/data_analysis/mouse_brain/data_ants/ants_output_spmtpm/N4_corrected.nii.gz
op=/mnt/data_analysis/mouse_brain/data_ants/ants/
ImageMath $dim ${op}mask.nii.gz Normalize $img
ThresholdImage $dim ${op}mask.nii.gz ${op}mask.nii.gz 0.1 1
outvar=[${op}_segk.nii.gz,${op}_prob%0d.nii.gz]
Atropos -d $dim -x ${op}mask.nii.gz c [5,0.001] -m [0.2,1x1x1] -i kmeans[$n] -o $outvar -a $img
lap=${op}lap.nii.gz
ImageMath $dim $lap Laplacian $img
inputfeatures=" -a $lap -a $img "
outvar=[${op}_seg.nii.gz,${op}_prob%0d.nii.gz]
Atropos -d $dim -x ${op}mask.nii.gz c [5,0.001] -m [0.2,1x1x1]
-i priorprobabilityimages[$n,${op}_prob%0d.nii.gz,0.25]
-k HistogramParzenWindows -o $outvar $inputfeatures

Error:
file /mnt/data_analysis/mouse_brain/data_ants/ants/_prob1.nii.gz does not exist.
Input prior probability image could not be read: /mnt/data_analysis/mouse_brain/data_ants/ants/_prob1.nii.gz

Could you please help me analyze the mouse brain to get TPM and show me how to modify the script accordingly?

Regards
Ramesh

[cookpa]

Please put your code in markdown formatted blocks by enclosing them in triple backquotes

```
code
```

It seems the issue is that the first segmentation command is not producing prior probability images. Add the --verbose option to Atropos, and let us know what it says.

[gdevenyi]

(You can edit user's comments as a maintainer of the repo)

[RB-008]

script&output.zip
Please find the attached file. For the script with verbose command and output files. Since the --verbose output is lengthier, I attached it as text files.

Thanks
Ramesh

[cookpa]

From ants_seg2.txt:

dim=3
n=3
img=/mnt/data_analysis/mouse_brain/data_ants/ants_output_spmtpm/N4_corrected.nii.gz
op=/mnt/data_analysis/mouse_brain/data_ants/ants/
ImageMath $dim ${op}mask.nii.gz Normalize $img
ThresholdImage $dim ${op}mask.nii.gz ${op}mask.nii.gz 0.1 1
outvar=[${op}_segk.nii.gz,${op}_prob%0d.nii.gz]
Atropos -d $dim -x ${op}mask.nii.gz c [5,0.001] -m [0.2,1x1x1] -i kmeans[$n] -o $outvar -a $img
lap=${op}lap.nii.gz
ImageMath $dim $lap Laplacian $img
inputfeatures=" -a $lap -a $img "
outvar=[${op}_seg.nii.gz,${op}_prob%0d.nii.gz]
Atropos -d $dim -x ${op}mask.nii.gz c [5,0.001] -m [0.2,1x1x1] \
 -i priorprobabilityimages[$n,${op}_prob%0d.nii.gz,0.25] \
 -k HistogramParzenWindows -o $outvar $inputfeatures \
 --verbose
 
 Input mask image could not be read.

Running Atropos for 3-dimensional images.
 file /mnt/data_analysis/mouse_brain/data_ants/ants/_prob1.nii.gz does not exist . 
Input prior probability image could not be read: /mnt/data_analysis/mouse_brain/data_ants/ants/_prob1.nii.gz

Atropos -d $dim -x ${op}mask.nii.gz c [5,0.001] -m [0.2,1x1x1] -i kmeans[$n] -o $outvar -a $img

This should be -c, not c. This command needs to run first, or you won't have any priors to input to the second Atropos call.

If you do

set -x

before running your commands, you can see what is happening including the expansion of the variables.

[RB-008]

Thank you very much. I got required output.