[antsBrainExtraction.sh] Output directory ignored when using "-q" argument.

[mathdugre]

Describe the problem

Running antsBrainExtraction.sh with the -q flag ignores the -o flag.

To Reproduce

Execution without the -q create the output folder as expected.

$ TMPLT="/opt/templates/OASIS"
$ DATASET="LMU_2"
$ SUBJECT_ID="0025362"
$ antsBrainExtraction.sh \
>  -d 3 \
>  -a /data/input/sub-${SUBJECT_ID}/ses-1/anat/sub-${SUBJECT_ID}_ses-1_run-1_T1w.nii.gz \
>  -e ${TMPLT}/T_template0.nii.gz \
>  -m ${TMPLT}/T_template0_BrainCerebellumProbabilityMask.nii.gz \
>  -o /data/output/${DATASET}/sub-${SUBJECT_ID}/

Will run Atropos segmentation with K=3. Classes labeled in order of mean intensity. Assuming CSF=1, GM=2, WM=3

The output directory "/data/output/LMU_2/sub-0025362" does not exist. Making it.

With the -q flag, it create a temporary folder in the current directory. Then it fails to run.

$ TMPLT="/opt/templates/OASIS"
$ DATASET="LMU_2"
$ SUBJECT_ID="0025362"
$ antsBrainExtraction.sh \
>  -q \
>  -d 3 \
>  -a /data/input/sub-${SUBJECT_ID}/ses-1/anat/sub-${SUBJECT_ID}_ses-1_run-1_T1w.nii.gz \
>  -e ${TMPLT}/T_template0.nii.gz \
>  -m ${TMPLT}/T_template0_BrainCerebellumProbabilityMask.nii.gz \
>  -o /data/output/${DATASET}/sub-${SUBJECT_ID}/

Will run Atropos segmentation with K=3. Classes labeled in order of mean intensity. Assuming CSF=1, GM=2, WM=3

The output directory "/path/to/working/directory//tmp20758/" does not exist. Making it.
---------------------  Running antsBrainExtraction.sh on hostname  ---------------------

--------------------------------------------------------------------------------------
 Bias correction of anatomical images (pre brain extraction)
   1) pre-process by truncating the image intensities
   2) run N4
--------------------------------------------------------------------------------------

Expected output was not produced.  The N4 corrected image doesn't exist:

System information (please complete the following information)

• OS: ubuntu
• OS version: focal-20221019
• Type of system: Docker container

ANTs version information

• ANTs code version:

$ antsRegistration --version
ANTs Version: v2.4.2.post12-gf022d4f
Compiled: Nov 28 2022 21:17:54

• ANTs installation type: Compiled from source in a Docker container using f022d4f

[cookpa]

Try -q 1

[mathdugre]

That did the trick. Thank you!