Thanks for the reply.
Couple of follow up questions.
(1) Which "ID" should be used when creating the mask? The "mc-z.abs.th23.sig.cluster.mgh" file contains clusters labeled based on z values (i.e., non-integers such as -3.698970, +2.130768, etc). Is it possible to divide the *.mgh file by itself to produce a file with 1's where clusters exist? That approach would work in FSL, but I am not quite sure what tools exist in FS or how to use them.
(2) How would one visualize the resulting label file in tksurfer? Using "File-->Label-->Load Label" results in yellow specks showing up on the brain surface, but the spatial locations aren't correct (they don't correspond to where clusters exist on the original volume).
Any help would be appreciated.
Message: 13 Date: Wed, 06 Jun 2012 18:04:56 -0400 From: Douglas Greve greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Creating a label from an .mgh file To: freesurfer@nmr.mgh.harvard.edu Message-ID: 4FCFD408.6050402@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed
you can use mri_cor2label, eg, for cluster #2, something like
mri_cor2label --id 2 --i cluster.mgh --o cluster2.label
doug
On 6/6/12 4:22 PM, Ilia wrote:
Hello,
How would one create a label (to be used as an input for "mris_anatomical_stats") based on a a statistical map generated by qdec (for example, the result of a Monte Carlo simulation such as "mc-z.abs.th23.sig.cluster.mgh").
The goal is to obtain average cortical thickness for regions where qdec detected significance.
Thank you!! _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Sorry, use the "ocn" file, not the cluster file. This should have integer values, one for each cluster. doug
On 06/08/2012 01:04 PM, Ilia wrote:
Thanks for the reply.
Couple of follow up questions.
(1) Which "ID" should be used when creating the mask? The "mc-z.abs.th23.sig.cluster.mgh" file contains clusters labeled based on z values (i.e., non-integers such as -3.698970, +2.130768, etc). Is it possible to divide the *.mgh file by itself to produce a file with 1's where clusters exist? That approach would work in FSL, but I am not quite sure what tools exist in FS or how to use them.
(2) How would one visualize the resulting label file in tksurfer? Using "File-->Label-->Load Label" results in yellow specks showing up on the brain surface, but the spatial locations aren't correct (they don't correspond to where clusters exist on the original volume).
Any help would be appreciated.
Message: 13 Date: Wed, 06 Jun 2012 18:04:56 -0400 From: Douglas Grevegreve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Creating a label from an .mgh file To: freesurfer@nmr.mgh.harvard.edu Message-ID:4FCFD408.6050402@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed
you can use mri_cor2label, eg, for cluster #2, something like
mri_cor2label --id 2 --i cluster.mgh --o cluster2.label
doug
On 6/6/12 4:22 PM, Ilia wrote:
Hello,
How would one create a label (to be used as an input for "mris_anatomical_stats") based on a a statistical map generated by qdec (for example, the result of a Monte Carlo simulation such as "mc-z.abs.th23.sig.cluster.mgh").
The goal is to obtain average cortical thickness for regions where qdec detected significance.
Thank you!! _______________________________________________ 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
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Ilia