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:
External Email - Use Caution
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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of Greve, Douglas N.,Ph.D.
<dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu>
Sent: Thursday, January 16, 2020 3:40 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu><mailto: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:
External Email - Use Caution
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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