MSMsulc files not found within singularity image

[ljhearne]

I have built a singularity image using docker which is functioning correctly. However it doesn't find the appropriate MSM files.

Here is the error: Cannot find 'msm' binary. Please download and install MSM from https://github.com/ecr05/MSM_HOCR_macOSX, or run with the "--surf_reg FS" option

Critically, when using the --surf_reg FS flag it works fine.

Do I need to install the MSM binaries and mount them to the singularity image?

Here is my code:

module purge
module load singularity
subject='10189'

#bids_input='/scratch/qm89/data/prepro/'
export freesufer_license='/projects/qm89/license.txt'
export FS_LICENSE='/projects/qm89/license.txt'
export ciftify_container='/scratch/qm89/Containers/tigrlab_fmriprep_ciftify.simg'

## build the mounts
singdir='/mnt/'
bidsdir=${singdir}data/rawdata
outdir=${singdir}data/prepro
workdir=${singdir}scratch/

singularity run --cleanenv --bind /scratch/qm89:/mnt \
  ${ciftify_container} \
      ${bidsdir} ${outdir} participant \
      --participant_label=${subject} \
      --fmriprep-workdir ${workdir} \
      --n_cpus 8 \
      --fs-license /mnt/license.txt \
    --task_label='rest' \
    --v

[edickie]

No, your right. The msm binary should be in the docker image. I'll troubleshoot tomorrow and see if I can replicate the problem on my end.

Thanks for letting me know, Erin

On Thu, Nov 1, 2018 at 5:32 PM ljhearne notifications@github.com wrote:

I have built a singularity image using docker which is functioning correctly. However it doesn't find the appropriate MSM files.

Here is the error: Cannot find 'msm' binary. Please download and install MSM from https://github.com/ecr05/MSM_HOCR_macOSX, or run with the "--surf_reg FS" option

Critically, when using the --surf_reg FS flag it works fine.

Do I need to install the MSM binaries and mount them to the singularity image?

Here is my code:

module purge module load singularity subject='10189'

bids_input='/scratch/qm89/data/prepro/'

export freesufer_license='/projects/qm89/license.txt' export FS_LICENSE='/projects/qm89/license.txt' export ciftify_container='/scratch/qm89/Containers/tigrlab_fmriprep_ciftify.simg'

build the mounts

singdir='/mnt/' bidsdir=${singdir}data/rawdata outdir=${singdir}data/prepro workdir=${singdir}scratch/

singularity run --cleanenv --bind /scratch/qm89:/mnt \ ${ciftify_container} \ ${bidsdir} ${outdir} participant \ --participant_label=${subject} \ --fmriprep-workdir ${workdir} \ --n_cpus 8 \ --fs-license /mnt/license.txt \ --task_label='rest' \ --v

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[edickie]

Update. The msm binaries are in the container but they are not user execuable. Will fix and re-upload a newer version to dockerhub tomorrow.

[ljhearne]

Great! I can test on my end later this week.

[edickie]

new image just pushed to dockerhub! version 1.1.8-2.1.1

(note: this one also has an updated fmriprep version (1.1.8) and python dependencies) let me know if that is an issue.