StephDcTUM

Ok, I will have at --output-spaces T1w: That registers to my individual T1w but actually I want my anat T1w and func of all my subjects registered to the template...

do you mean I should give the docker more space? I think standard is 10GB. So increase it to 20GB?

I think the problem is that this file: /home/code/ciftify/ciftify/data/91282_Greyordinates/Atlas_ROIs.2.nii.gz does not exist for copying. ciftify is a path specified in the docker container I created. How does the ciftify code...

Yes, because this is used to build the docker container: # setting up an install of ciftify (manual version) inside the container ADD https://api.github.com/repos/edickie/ciftify/git/refs/heads/master version.json RUN mkdir /home/code && git...

but still it works until here: Running: wb_command -add-to-spec-file /ciftify/sub-68/MNINonLinear/fsaverage_LR32k/sub-68.32k_fs_LR.wb.spec INVALID /ciftify/sub-68/MNINonLinear/T1w.nii.gz Running: wb_command -add-to-spec-file /ciftify/sub-68/T1w/fsaverage_LR32k/sub-68.32k_fs_LR.wb.spec INVALID /ciftify/sub-68/T1w/T1w.nii.gz Running: mkdir -p /ciftify/zz_templates Running: cp /home/code/ciftify/ciftify/data/91282_Greyordinates/Atlas_ROIs.2.nii.gz /ciftify/zz_templates/Atlas_ROIs.2.nii.gz so it copies the...

Thanks a lot! The output of fmriprep is RAS orientation, but I would need to change that into LAS orientation and give ciftify as input the LAS oriented images. Do...

Thank a lot for the reply. So I can just download msm_mac_v3 (in my case) and set the PATH to this file? Best

@renxili which Computer, Python Version and OS are you using?

I tried with(without compiling anything): export PATH=$PATH:/../MSM/msm (older version linked on the ciftiy homepage) and PATH=$PATH:/../MSM/msm_mac_v3 but it didnt work. I had a look into the code: ciftify_recon_all is calling...

yes, I am using also Catalina. what happens when you type in your terminal "which msm"? (when already set the PATH to your msm)