bids-apps / mindboggle Goto Github PK

The README lists this:
docker run -ti -v $PWD/ds114_test1:/home/jovyan/work/data bids/mindboggle /home/jovyan/work/data /home/jovyan/work/data/derivatives/ participant

Yet what I think you mean is:
docker run -ti -v $PWD/ds114_test1:/home/jovyan/work/data bids/mindboggle /home/jovyan/work/data /home/jovyan/work/data participant

The run.py file appends "derivatives" onto the output directory. So, as-written, it would go into work/data/derivatives/derivatives/mindboggle

The docker image should be re-built. Many bug exist.

It can translate to --fs_openmp and --mb_num_threads of the mindboggle123 script.

As-is, the run.py will look for T1 images with "ses-" in the filename, but the directory structure is still:
BIDS/sub-#/anat/sub-#_ses-# rather than
BIDS/sub-#/ses-#/sub-#_ses-#

What software should be used to open files with the extension .white? I opened the notepad with garbled characters

Please at least add simple smoke tests

https://googledrive.com/host/0B2JWN60ZLkgkMEw4bW5VUUpSdFU/ds114_test1_with_freesurfer.tar.gz @akeshavan

Hey there,

I was wondering if there are any plans to make the complete mindboggle pipeline available as a BIDS app? More precisely, running mindboggle123 on a BIDS input to create an output like:

bids_dir/
   derivatives/
      mindboggle/
        freesurfer/
          sub-*/
             mri/ 
             label/
             surf/
        ants/
          sub-*/
              antsBrainSegmentation.nii.gz
              antsCorticalThickness.nii.gz
        mindboggled/
          sub-*/
               exploded/
               features/
               labels/

Would that be an useful feature people might be interested in?

Best, Peer