micapipe from the Multimodal imaging and connectome analysis lab (http://mica-mni.github.io) at the Montreal Neurological Institute. Read The Docs documentation below
If you've tried running this with BrainSpace code already, how did you do so and what went wrong?
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Other information
I am trying to run -proc_dwi. The DTI data I obtained from the Philips 3T MRI scanner. I have a *.bval file consisting of b=0, b=1000. no phase image.
When I run the docker command (v0.2.0)
bids=/home/sue/micapipe/BIDS
out=/home/sue/micapipe/output
fs_lic=/home/sue/micapipe/FreeSurferLicense/license.txt
tmp=/home/sue/micapipe/tmp
sub=001
docker run -d --name micapipe --rm \
-v ${bids}:/bids \
-v ${out}:/out \
-v ${fs_lic}:/opt/licence.txt \
micalab/micapipe:v0.2.3 \
-bids /bids -out /out -fs_licence /opt/licence.txt -threads 10 \
-sub $sub \
-proc_structural \
-proc_surf \
-freesurfer \
-post_structural \
-proc_dwi \
-SC \
-proc_func \
-mainScanStr task-rest_bold \
-NSR \
-noFIX \
-GD \
-QC_subj
I get the message [ERROR].... DWI string or path does not match the default:try to set it with -dwi_main .
I modified the code according to this suggestion as follows:
bids=/home/sue/micapipe/BIDS
out=/home/sue/micapipe/output
fs_lic=/home/sue/micapipe/FreeSurferLicense/license.txt
tmp=/home/sue/micapipe/tmp
sub=001
dwiDir=/home/sue/micapipe/BIDS/sub-001/dwi
docker run -d --name micapipe --rm \
-v ${bids}:/bids \
-v ${out}:/out \
-v ${fs_lic}:/opt/licence.txt \
micalab/micapipe:v0.2.3 \
-bids /bids -out /out -fs_licence /opt/licence.txt -threads 10 \
-sub $sub \
-proc_structural \
-proc_surf \
-freesurfer \
-post_structural \
-proc_dwi -dwi_main ${dwiDir}/sub-001_dwi.nii.gz \
-SC \
-proc_func \
-mainScanStr task-rest_bold \
-NSR \
-noFIX \
-GD \
-QC_subj
I get the message [ERROR].... B0 threshold is not a valid inegrer: DEFAULT
If I don't run proc_dwi and SC, it runs smoothly.
I'm not sure how to get around this, and am stuck.
I am trying to run -proc_dwi. The DTI data I obtained from the Philips 3T MRI scanner. I have a *.bval file consisting of b=0, b=1000. no phase image. When I run the docker command (v0.2.0) bids=/home/sue/micapipe/BIDS out=/home/sue/micapipe/output fs_lic=/home/sue/micapipe/FreeSurferLicense/license.txt tmp=/home/sue/micapipe/tmp sub=001 docker run -d --name micapipe --rm \ -v ${bids}:/bids \ -v ${out}:/out \ -v ${fs_lic}:/opt/licence.txt \ micalab/micapipe:v0.2.3 \ -bids /bids -out /out -fs_licence /opt/licence.txt -threads 10 \ -sub $sub \ -proc_structural \ -proc_surf \ -freesurfer \ -post_structural \ -proc_dwi \ -SC \ -proc_func \ -mainScanStr task-rest_bold \ -NSR \ -noFIX \ -GD \ -QC_subj
I get the message [ERROR].... DWI string or path does not match the default:try to set it with -dwi_main.
I modified the code according to this suggestion as follows: bids=/home/sue/micapipe/BIDS out=/home/sue/micapipe/output fs_lic=/home/sue/micapipe/FreeSurferLicense/license.txt tmp=/home/sue/micapipe/tmp sub=001 dwiDir=/home/sue/micapipe/BIDS/sub-001/dwi docker run -d --name micapipe --rm \ -v ${bids}:/bids \ -v ${out}:/out \ -v ${fs_lic}:/opt/licence.txt \ micalab/micapipe:v0.2.3 \ -bids /bids -out /out -fs_licence /opt/licence.txt -threads 10 \ -sub $sub \ -proc_structural \ -proc_surf \ -freesurfer \ -post_structural \ -proc_dwi -dwi_main ${dwiDir}/sub-001_dwi.nii.gz \ -SC \ -proc_func \ -mainScanStr task-rest_bold \ -NSR \ -noFIX \ -GD \ -QC_subj I get the message [ERROR].... B0 threshold is not a valid inegrer: DEFAULT If I don't run proc_dwi and SC, it runs smoothly.
I'm not sure how to get around this, and am stuck.
I am running on a server with Ubuntu 20.04