Yes, you can just run
/path/to/your/local/copy/mri_glmfit-sim
On 09/09/2014 05:49 PM, Eryilmaz, Huseyin Hamdi wrote:
Hi Doug,
I don't seem to have the permission to change the contents of that folder. So I can't really copy it over. Is it possible to run this locally? I'm working on a linux workstation at Martinos and when I ask the source, it gives me that folder:
which mri_glmfit-sim
/usr/local/freesurfer/stable5_0_0/bin/mri_glmfit-sim
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Tuesday, September 09, 2014 5:24 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh
You can just copy it over the old one (but make a backup of it first)
On 09/09/2014 04:21 PM, Eryilmaz, Huseyin Hamdi wrote:
Hi Doug,
Thanks for your reply. I can certainly test it. Could you tell me how I can run this new 'mri_glmfit-sim' you sent me? The original 'mri_glmfit-sim' that I use is under '/usr/local/freesurfer/stable5_0_0/bin/'
Best, Hamdi
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Monday, September 08, 2014 11:48 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Monte Carlo Sim output / sig.masked.mgh
That was an oversight. I've attached a version that should work. Can you test it for me? Once I know it works I'll check it in to tree. doug
On 09/03/2014 12:30 PM, Eryilmaz, Huseyin Hamdi wrote:
Dear FS experts,
I have a question about a MC output file. When I run the MC sim (using mri_glmfit-sim) on the surface, it generates a bunch of files including a 'sig.masked.mgh', which is nice for displaying the significance map limited to the clusters that survive the MC correction. However, when I run it on the volume, it doesn't generate this specific file. Does anyone know the reason for that? Is there an alternative way to display the significance map that show only the clusters that survive the MC correction?
Many thanks! Hamdi
--
Hamdi Eryilmaz, PhD
Massachusetts General Hospital A.A. Martinos Center for Biomedical Imaging Psychiatric Neuroimaging Division 149 13th St, Charlestown, MA 02129 Phone: +1 617 643 7462 Email:heryilmaz@partners.org mailto:heryilmaz@partners.org
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer