Hi Doug,
mri_label2vol says it creates an mgz from a label, I need to do the reverse. I'm starting with a mask_MNI.mgz (brought from FSL's MNI space via mri_convert) and I need to be able to use that mask to extract thickness from the individual subject.
Also, mni152reg fails because it expects to write a tmp file into an FSL directory rather than a Freesurfer directory. The FSL standards directory is write protected for obvious reasons. Can I redirect the temporary file? Error message:
“mkdir:
/usr/local/fsl/data/standard/tmp.fslregister.9446: Permission denied”
Message: 17
Date: Mon, 07 Oct 2013 11:01:23 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] FSL masks applied to Freesurfer surfaces?
116(14)
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <5252CCC3.5070601@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Hi Ruth, run mni152reg for each subject to create a registration from
the subject to the 152. Then use mri_label2vol to map the mask into each
subject's space.
doug
On 10/05/2013 04:08 PM, Ruth Carper wrote:
> Doug,
> I'd like to get them into the individual's space, but I assume
I have
> to get there by way of fsaverage? Final goal is to have a regional
> thickness measure for each individual subject.
> Ruth Carper
>
>
> ------------------------------------------------------------------------
> *From:* "freesurfer-request@nmr.mgh.harvard.edu"
> <freesurfer-request@nmr.mgh.harvard.edu>
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Sent:* Saturday, October 5, 2013 9:00 AM
> *Subject:* Freesurfer Digest, Vol 116, Issue 14
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 04 Oct 2013 12:21:32 -0400
> From: Douglas N Greve <greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>
> Subject: Re: [Freesurfer] FSL masks applied to Freesurfer surfaces?
> To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>
> Message-ID: <524EEB0C.8050400@nmr.mgh.harvard.edu
> <mailto:524EEB0C.8050400@nmr.mgh.harvard.edu>>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Do you want to transfer them to fsaverage space or to the individual
> anatomical space?
> doug
>
>
> On 10/04/2013 01:42 AM, Ruth Carper wrote:
> > Hi,
> > I'd like to take some masks that I have in MNI standard space in FSL
> > and map them to Freesurfer surface space. The goal is to extract
> > measures of average cortical thickness (or area or etc) for those
> > regions for each subject. Is there a standard way to do this?
>
>
> >
> >
Ruth Carper, PhD
Assoc. Project Scientist, UCSD