Not sure, we have not been using that flag in a while. When you look at the volume in freeview, you can see what the code is by clicking on a voxel. You can change the offset by including --base-offset XXX to mri_aparc2aseg,

On 1/24/2020 2:40 PM, Grodin, Erica wrote:

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Hi Doug,

Thanks for your reply. I ran the mris_ca_label command manually using the lh.atlas2005_simple.gcs and rh atlas. I then ran the mri_aparc2aseg with the --a2005s flag, which gives me an aparc.a2005s image. However, when I try to extract the VOIs that I need from that image I end up with an empty file and when I look at the aparc.a2005s image, the intensities only seem to go up to the 2000's instead of the 9000's which is what I need for the VOIs.

I'm wondering if I am using the wrong .gcs file, but the simple 2005 one is the only one that seems appropriate.

Thanks for your help! Erica

---------------------- Erica Grodin, Ph.D. Postdoctoral Fellow University of California, Dept. of Psychology and Psychiatry ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu Sent: Thursday, January 16, 2020 3:40 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Flag for recon-all to output aparc2005 labels (freesurfer 6.0)

I don't think so, but you can run mris_ca_label by hand. Look in the recon-all.log file for the command, then use the 2005 tif instead of the 2009 tif. I think it should work.

On 1/16/2020 3:31 PM, Grodin, Erica wrote:

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Hello,

I am running recon-all on my data using freesurfer 6.0 which is working correctly. However, I need to create some VOIs which labels are only outputted from the aparc2005 set and do not appear in the aparc2009 set; specifically:

9001, 9501 ctx-lh-primary-motor, ctx-rh-primary-motor

9005, 9505 ctx-lh-prim-sec-somatosensory, ctx-rh- prim-sec-somatosensory

9002, 9502 ctx-lh-premotor, ctx-rh-premotor

9004, 9504 ctx-lh-posterior-parietal, ctx-rh-posterior-parietal

Is there a flag or some other option to output the 2005 set in addition to the 2009?

Thank you for your help,

Erica Grodin

---------------------- Erica Grodin, Ph.D. Postdoctoral Fellow University of California, Dept. of Psychology and Psychiatry

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