[Neuroimaging] [PySurfer] How to use different surface meshes in PySurfer?

Rolando Masis-Obando rolandomasisobando at gmail.com
Mon May 25 14:11:51 EDT 2020

Hi Alexandre and Eric,

Thank you so much to you both!

For future researchers interested in using different inflations, these are
the steps I took:

*0. My OS:*
Catalina 10.15.4

*1. install freesurfer:*
download freesurfer (I used the pkg installer for freesurfer 7.1.0):
follow installation instructions:

*2. in terminal:*
export FREESURFER_HOME=/Applications/freesurfer/7.1.0
source $FREESURFER_HOME/SetUpFreeSurfer.sh

*3. fix permissions in terminal (*otherwise mris_inflate won't be able to
read or write from other freesurfer directories*):*
sudo chmod -R a+w $FREESURFER_HOME/subjects/

*4. navigate to surface folder in terminal:*
cd /Applications/freesurfer/7.1.0/subjects/fsaverage6/surf

*5. Run mris_inflate function on both hemispheres *(in my case, I'm going
to be using iterations n=5)
mris_inflate -n 5  lh.smoothwm lh.5_inflated
mris_inflate -n 5  rh.smoothwm rh.5_inflated

*6. call new inflated brain with pysurfer using python (for me, inside a
jupyter notebook)*
subject_id = 'fsaverage6'
hemi =  'split'
surf = '5_inflated'
brain = Brain(subject_id, hemi, surf, cortex='low_contrast',views=['lat',

*7. Celebrate!*

Thanks again for your help.


On Mon, May 25, 2020 at 2:56 AM Alexandre Gramfort <
alexandre.gramfort at inria.fr> wrote:

> see https://surfer.nmr.mgh.harvard.edu/fswiki/mris_inflate
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