Does leftfrontallobe.nii.gz overlay properly in tkmedit? eg, tkmedit subject orig.mgz -surfs -overlay leftfrontallobe.nii.gz -fminmax .5 1 doug
On 03/26/2013 07:20 AM, Daniel Lumsden wrote: > Bruce > > Many thanks - that's given me a lot more guidance. Following the help, > i've put together the command below: > > mri_surf2vol --hemi lh --template <path to>/orig.mgz --outvol <path to > where I want the file>/leftfrontallobe.nii.gz --surfval <path > to>/left_frontal_lobe.gii --fillribbon --volregidentity mov07 > > Where mov07 is my subjid and left_frontal_lobe.gii is the surface I've > generated from the label files to run in probtrakx. This command runs, > but produces and empty nifti file. I've changed the output to .mgz > with similar effect. I've substituted the rawavg.mgz file for the > orig.mgz file, and tried both .nii.gz and .mgz versions of both files > and still get an empty output file. The subject is in my $SUBJECTS_DIR. > > Is there a way to check the .gii files? I generated them using > label2surf, having used mris_convert to convert the lh.white and > rh.white files from the surf folder for my subject to lh.white.asc and > rh.white.asc. > > Thank you again for your help. > > Dan > > > > Date: Mon, 25 Mar 2013 14:59:28 -0400 > > From: fis...@nmr.mgh.harvard.edu > > To: doclums...@hotmail.com > > CC: freesurfer@nmr.mgh.harvard.edu > > Subject: Re: [Freesurfer] surf2vol > > > > Hi Dan > > > > try using mri_surf2vol instead (it has a much bigger help, thanks to > > Doug0 > > Bruce > > On Mon, 25 Mar 2013, Daniel Lumsden wrote: > > > > > Dear All > > > > > > Apologies for what I'm sure is a very basic question. I'm new to > using freesurfer, and would like to generate cortical > > > parcellations for running in probtrakx. I have followed the > instructions from various sources and have managed to generate the > > > parcellations from recon-all, extract the label files from the > parcellation, then use mri_mergelabels and label2surf to generate > > > the the .gii files needed for probtrakx. I'd like to be able to > display the surface files for illustrative purposes, but I'm > > > struggling to apply the surf2vol command. > > > > > > From the terminal window I can see that the commands required are: > > > > > > surf2vol <surf> <refvol> <outvol> <convention> > > > > > > I presume that <surf> is the .gii file I'm trying to visualise, > and <outvol> is to specify the name of the output volume the > > > command will generate, but what should I be using as the <refvol>? > I would be very grateful for any guidance. Please accept my > > > apologies if I've missed a very obvious online explanation for > this and thank you in advance. > > > > > > Dan Lumsden > > > Clinical Research Fellow > > > > > > > > > > > > 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. > > > _______________________________________________ > 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: 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
