Errors with Using Mindboggle w/ Preprocessed Freesurfer Data

Summary of what happened:

Hello, I am getting started using Mindboggle and running preprocessed data from freesurfer. I had no problem running the example data provided, but am running into some issues using my own data.

Command used (and if a helper script was used, a link to the helper script or the command generated):


Environment (Docker, Singularity, custom installation):

Data formatted according to a validatable standard? Please provide the output of the validator:

Relevant log outputs (up to 20 lines):

ValueError: cannot reshape array of size 147252 into shape (15663107,4)

This one occurs multiple times giving different value errors

OSError: Output key: surface_files Template: /home/jovyan/work/DCA001__1233107/surf/lh.pial returned no files

Screenshots / relevant information:

After further inspection, none of folders for any of our cases have this “lh.pial”, file, which the example data does have. Instead, we have “lh.area.pial” and “lh.curv.pial” for both lh and rh. This is presumably interfering with the mindboggle code.

(3) Screen shot (attached); last error before program terminates.

Please let me know if you have solutions in mind to any or all these errors. I greatly appreciate your help.

Hi @Aryan_Govil and welcome to Neurostars!

I have retagged your post as “Software Support” and have reorganized your post to conform to the Software Support template. As you can see, there is some information you are missing that would help someone debug your problems. Feel free to edit your post to add the requested information.