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 <gr...@nmr.mgh.harvard.edu > <mailto:gr...@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: <5252ccc3.5070...@nmr.mgh.harvard.edu > <mailto: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 > <mailto:freesurfer-requ...@nmr.mgh.harvard.edu>" > > <freesurfer-requ...@nmr.mgh.harvard.edu > <mailto:freesurfer-requ...@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 <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > > <mailto: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> > <mailto: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> > > <mailto: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 > > > > _______________________________________________ > 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 gr...@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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
