Hi, Douglas
Just to check if I correctly understood you, when you said "mri_label2vol can go in both directions" did you mean it can also create a label from a volume or a binary mask? If so, could you please explain how? I read documentation on wiki and help from the command itself and could not see how to accomplish that. I could only find how to create a volume from a label. What I need to do is to get a mask like the binLeftHippoHead.mgz (attached) and create a label. Assuming it is possible, I could also make labels for Hippocampal body and head, merge the 3 labels into an annot file. This way i can use Freeview to load the whole hippocampal surface and discriminate the 3 segments by colors with the annot file. I guess I will get a result like the picture I get after loading lh.pial and lh.aparc.annot.
Thank you.
Cheers,
Marcos.
Em Ter, 2013-10-08 às 11:22 -0400, Douglas N Greve escreveu: 
Hi Ruth, use this version of mni152reg
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mni152reg

mri_label2vol can go in both directions (and can take any file types, 
ie, mgz, nii, nii.gz, etc)

doug

On 10/08/2013 01:34 AM, Ruth Carper wrote:
> 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 
> <mailto:greve@nmr.mgh.harvard.edu>>
> Subject: Re: [Freesurfer] FSL masks applied to Freesurfer surfaces?
> 116(14)
> To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>
> Message-ID: <5252CCC3.5070601@nmr.mgh.harvard.edu 
> <mailto: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 
> <mailto:freesurfer-request@nmr.mgh.harvard.edu>"
> > <freesurfer-request@nmr.mgh.harvard.edu 
> <mailto:freesurfer-request@nmr.mgh.harvard.edu>>
> > *To:* freesurfer@nmr.mgh.harvard.edu 
> <mailto: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>
> > <mailto: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> 
> <mailto: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>
> > <mailto: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
> Adjunct Professor, SDSU
>
>
>
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