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MICA-MNI / micapipe

micapipe from the Multimodal imaging and connectome analysis lab (http://mica-mni.github.io) at the Montreal Neurological Institute. Read The Docs documentation below
http://micapipe.readthedocs.io
GNU General Public License v3.0
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'Subject 01 doesn't have T1_nativepro warp to MNI152.' #37

Closed roryjpiper closed 1 year ago

roryjpiper commented 2 years ago

Hi - I am trying to run mica-pipe via Docker. It has completed 'proc_structural', but will not let me run 'proc_dwi' due to the following error:

rorypiper@MS00048528 mica-pipe-test % docker run -ti --rm \ -v /Users/rorypiper/Desktop/mica-pipe-test/bids:/bids_dataset:ro \ -v /Users/rorypiper/Desktop/mica-pipe-test/out:/output_directory \ -v /Users/rorypiper/Desktop/mica-pipe-test/tmp:/tmp \ -v /Applications/freesurfer/license.txt:/opt/freesurfer-6.0.0/freesurfer_license_file.txt \ micalab/micapipe:latest \ -out /output_directory \ -sub 01 \ -bids /bids_dataset \ -proc_dwi -ses 01 \ -nocleanup \

Some packages in this Docker container are non-free If you are considering commercial use of this container, please consult the relevant license: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Licence INFO: /root/matlab/startup.m does not exist ... creating -------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /opt/freesurfer-6.0.0 FSFAST_HOME /opt/freesurfer-6.0.0/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /opt/freesurfer-6.0.0/subjects MNI_DIR /opt/freesurfer-6.0.0/mni FSL_DIR /opt/fsl-6.0.0

MICA pipeline - (Version v0.1.1 'Roadrunner') 
    Subject: 01 Session: ses-01

[ WARNING ]..... fix was not found, ICA-FIX will be skipped

[ INFO ]..... micapipe will use 6 threads for multicore processing

[ INFO ]..... Subject 01 directory exist

[ INFO ]..... Inputs of proc_dwi: tmpDir : /tmp dwi_main : DEFAULT dwi_rpe : DEFAULT rpe_all : FALSE Affine only: FALSE Processing : LOCAL

**-------------------------------------------------------------

[ ERROR ]..... Subject 01 doesn't have T1_nativepro warp to MNI152. Run -proc_structural

-------------------------------------------------------------**

roryjpiper commented 2 years ago

@royj23 - have you encountered this before?

rcruces commented 2 years ago

Hi, I recomend you to pull the version v.0.1.2 from the docker hub. 

export DOCKER_CONTENT_TRUST=0
docker pull micalab/micapipe:v0.1.2

Then try to run again -proc_struct and -proc_dwi only. I don't see any issues with you freesurfer license.