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 dougOn 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
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