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 <gr...@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FSL masks applied to Freesurfer surfaces? 116(14) To: freesurfer@nmr.mgh.harvard.edu Message-ID: <5252ccc3.5070...@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-requ...@nmr.mgh.harvard.edu" > <freesurfer-requ...@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 <gr...@nmr.mgh.harvard.edu > <mailto:gr...@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.8050...@nmr.mgh.harvard.edu > <mailto:524eeb0c.8050...@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 Adjunct Professor, SDSU
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