it sounds like the problem is in label2surf. Where did that come from? On 03/27/2013 12:09 PM, Daniel Lumsden wrote: > Doug > > When I try to overlay the .gii files on the orig volume I get the > following message: > > "Either this surface does not contain valid volume geometry > information, or freeview failed to read the information. This surface > may not align with volumes and other surfaces" > > > I presume this means there is a problem with how I've generated the > .gi files? I'm happy the lh.anatomicalregion.label files are working > fine because I can generate volumetric masks from them. > > > To get the .gii files I've taken the rh.white and lh.white from the > surf folder and copied them into the folder I'm running the terminal > in. I'm then using the command: > > > mris_convert rh.white rh.white.asc > > > Then: > > > echo lh.frontallobe.label > left_frontal_lobe.txt > > > (which checking gives me a text file of that name with one line, > lh.frontallobe.label) > > > Then: > > > label2surf -s lh.white.asc -l left_frontal_lobe.txt -o > left_frontal_lobe.gii > > > All of the named files are in the same folder. > > > > Thank you again. Confusingly, it does seem like probtrackx is doing > something with the .gii files! > > > Dan > > > Sorry, I meant does the left_frontal_lobe.gii overlay properly on the orig > volume? > doug > On 03/27/2013 04:41 AM, Daniel Lumsden wrote: > > Doug > > > > The .nii.gz file is completely empty and doesn't come up on any viewer > > (fslview, tkmedit, freeview, mricron etc). The .gi files I've > > generated appear to be tracking in probtrackx (though slowly on my > > laptop - probably not expected given the sizes of the surfaces). I can > > also generate binary volumetric masks from the labels using > > mri_binarize (though they are a little bit "speckled" - with scattered > > blank voxels). > > > > On my installation I'm having some intermittent difficulties with > > tkmedit and tksurfer (not consistently opening, sometimes coming up > > with "bus error"). Freeview is opening consistently though. I'm not > > sure if this could be having an affect but I was planning on > > reinstalling freesurfer today to see if that fixed it. > > > > Thank you again for your help > > > > Dan > > > > 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 > > > > > > > > _______________________________________________ > > 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 > > > > _______________________________________________ > 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
