thanks, Doug. I am still extremely confused, however. *Am I meant to run recon-all first? *I was told in a previous email that I should do this first, however, I thought that Freesurfer takes the volumes and does a linear registration to MNI305 template, which would not work for my scans that are linearly registered to ICBM152 nonlinear 2006 template...
When you have a moment, could you please outline in a step by step manner the steps I should run to take my labels.mnc and my volumes such that I can generate surfaces for those 50 volumes, overlay the labels (for which I thought I was using mri_vol2surf) and then edit those labels to make them more accurate? *The idea is that I want to generate some sulcal probability maps using surface-based registration, as I can already generate probability maps using volumetric registration quite easily.*
many thanks
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Wed, Apr 6, 2016 at 2:43 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
For the 152, you can run mni152reg --s subject, then specify $SUBJECTS_DIR/subject/mri/transform/mni152reg.dat (or .lta) for the argument to --reg. I'll need to figure out how to generate a .dat/.lta for the 305.
On 4/6/16 12:50 PM, Trisanna Sprung-Much wrote:
Any ideas?
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Tue, Apr 5, 2016 at 9:37 PM, Trisanna Sprung-Much < trisanna.sprung-much@mail.mcgill.catrisanna.sprung-much@mail.mcgill.ca> wrote:
Hi Dr. Fischl
I have a mixture - some of the labels were painted in the MNI305 space (older ones) and the more recent ones are registered to the ICBM152 nonlinear symmetric VI (2006) template.
Best
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Tue, Apr 5, 2016 at 6:34 PM, Bruce Fischl < fischl@nmr.mgh.harvard.edufischl@nmr.mgh.harvard.edu> wrote:
Hi Trisanna
what space are your labels in?
cheers Bruce On Tue, 5 Apr 2016, Trisanna Sprung-Much wrote:
Hi Freesurfer
I have some labels (.mnc) that are painted voxels generated from a
Montreal
Neurological Institute software. I am trying to project the labels
onto the
surfaces generated from recon-all that I applied to the corresponding
MRI
volumes.
I used mri_vol2surf:
mri_vol2surf --src labels.mnc --out test.mgz --srcreg
talairach.auto.xfm
--hemi lh
and got the following error:
Error reading inplaneres from talairach.auto.xfm
Do I need a .dat file? If so, how can I attain it? Essentially, what
is the
registration file that I am supposed to be using?
Many thanks!
Trisanna
-- Ph.D. CandidateMcGill University Integrated Program in Neuroscience Psychology
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