Thank you!
Julie
On 19/04/2017 11:49 pm, "Harms, Michael" mharms@wustl.edu wrote:
I’ve previously created an .annot version of the Gordon parcellation. It is attached.
-- Michael Harms, Ph.D.
Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave.Tel: 314-747-6173 St. Louis, MO 63110Email: mharms@wustl.edu
On 4/18/17, 11:43 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Julie Hall" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of julie.hall@sydney.edu.au> wrote:
Hi Bruce,
The Gordon Parcellation is in MNI space and the authors used Freesurfer. Should I then run this new parcellation per subject? I don¹t have a color table for this parcellation atlas, and I am not sure how to create this?
I have a gifti file too, would it be easier to convert that into a mgz file? When I try mris_convert I get the following error message:
** num_dim violation: num_dim = 2, yet dim[1] = 1 ** num_dim violation: num_dim = 2, yet dim[1] = 1 mrisReadGIFTIfile: GIFTI file Parcels_L.func.gii is invalid! mris_convert: could not read surface file Parcels_L.func.gii
Thank you! Julie
On 14/04/2017 12:00 am, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Julie
what space is the Gordon Parcellation in? Did they use FreeSurfer? If so, then you just need to map it to each of your subjects.
And how is a surface-based parcellation stored in a nifti file?
cheers Bruce
On Wed, 12 Apr 2017, Julie Hall wrote:
Hi experts,
I would like to use a different atlas other than the 'default' Freesurfer atlases, namely the Gordon Parcellation (surface based parcellation of 333 ROIs of the cortex) to segment my T1 datasets. So I can go on to use these segmentations for DTI connectome analysis using MRTrix (or MatLab). I have two questions:
- I have this atlas as a nifti file. Do I need to transform this atlas into a different file for it to run in freesurfer?
- Can I run this step in autorecon3 (step 28)? Or should I rerun
recon-all all together? If so, could you help me with what commands I need to run (mris_ca_train?)²
Thank you, Julie
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