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? dougOn 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 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.
