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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The attached package contains the Gordon parcellation as .annot files (on the surface), as well as a script that contains the exact details of how that was accomplished.

Cheers, -MH

-- 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 4/13/17, 9:01 AM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of 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?)”

Thank you, Julie

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.