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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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FC missing ROIs for all parcellations #106

Open kbatista-gr opened 7 months ago

kbatista-gr commented 7 months ago

My FC matrices have one or two missing ROIs for all parcellations. For example, for Schaefer-100, there should 150 rows in the FC file, but my matrices contain only 149. I'm using v.0.2.2, docker.

rcruces commented 5 months ago

Can you please share the command you used. And the resolution of your inputs.

kbatista-gr commented 5 months ago

Hi, Congratulations on releasing a new version! But, in the case of fMRI processing, I'm still have a missing ROI for Schaefer parcellations. However, one more ROI in the case of Destrieux atlas. DTI OK. My fMRI data were acquired with 2x2x2mm resolution and 104x104 matrix and 72 slices. Command: docker run -ti --rm \ -v ${bidsdir}:/bids \ -v ${out}:/out \ -v ${tmp}:/tmp \ -v ${FSLdir}:/opt/license.txt \ micalab/micapipe:v0.2.3 \ -bids /bids -out /out -tmpDir /tmp -fs_licence /opt/license.txt -threads 10 \ -sub sub-${sub} \ -ses rest \ -proc_structural -proc_surf -post_structural -MPC -mpc_acq T1map -regSynth -GD -proc_flair \ -proc_dwi \ -SC -tracts 20M \ -proc_func \ -noFIX -NSR \ -mainScanStr task-rest_bold \ -func_pe /bids/sub-${sub}/ses-rest/fmap/sub-${sub}_ses-rest_dir-AP_epi.nii.gz \ -func_rpe /bids/sub-${sub}/ses-rest/fmap/sub-${sub}_ses-rest_dir-PA_epi.nii.gz