mri_vol2surf resulting in different dimensions for two different images in the same space
Dear Surfers,
I (successfully) resampled a functional data on the surface map using mri_vol2surf:
mri_vol2surf --mov func.nii --reg register.dat --projfrac 0.5 --interp nearest --hemi lh --o lh.func.mgh
Then, I normalized this image to a standard space (fsaverage) using mri_surf2surf:
mri_surf2surf --srcsubject sub1 --trgsubject fsaverage --sval sub1/lh.func.mgh --tval sub1/lh.func.norm.mgh --fwhm 5 --cortex --hemi lh
The dimension of the output file, lh.func.norm.mgh, was 163842 x 1 x 1 (identified from mri_info). This file can be opened from Matlab, and I can successfully get access to 163842 vertices. What I want now is to take the aparc+aseg information from the average brain (fsaverage) and be able identify which vertex falls under which ROI label. I decided to resample aparc+aseg.mgz in fsaverage on the surface map, hoping to get label information at the dimension of 163842 x 1 x 1. So I ran:
mri_vol2surf --mov fsaverage/mri/aparc+aseg.mgz --regheader fsaverage --projfrac 0.5 --interp nearest --hemi lh --o fsaverage/surf/lh.roi.mgh mri_vol2surf --mov fsaverage/mri/aparc+aseg.mgz --regheader fsaverage --projfrac 0.5 --interp nearest --hemi rh --o fsaverage/surf/rh.roi.mgh
The resulting mgh files, however, had a dimension of 23406 x 1 x 7.
1. As I said, I wanted to get label information (roi number from the FreeSurferColorLUT) for each vertex of the surface image in the fsaverage space. Is this the right approach? And did I do this correctly (I'm concerned about many options above)?
2. If so, why is the resulting dimension different from the other one? I assume that it's probably a reshape issue, but how I can reshape the dimension to match 163842 x 1 x 1?
Thanks in advance.
Joon
-- Joonkoo Park Ph.D. Candidate, Cognition & Cognitive Neuroscience Department of Psychology, University of Michigan
You're better off loading in the surface annotation directly rather than dealing with aparc+aseg. To make surf2surf output the right dimensions, add --noreshape.
doug
Joonkoo Park wrote:
Dear Surfers,
I (successfully) resampled a functional data on the surface map using mri_vol2surf:
mri_vol2surf --mov func.nii --reg register.dat --projfrac 0.5 --interp nearest --hemi lh --o lh.func.mgh
Then, I normalized this image to a standard space (fsaverage) using mri_surf2surf:
mri_surf2surf --srcsubject sub1 --trgsubject fsaverage --sval sub1/lh.func.mgh --tval sub1/lh.func.norm.mgh --fwhm 5 --cortex --hemi lh
The dimension of the output file, lh.func.norm.mgh, was 163842 x 1 x 1 (identified from mri_info). This file can be opened from Matlab, and I can successfully get access to 163842 vertices. What I want now is to take the aparc+aseg information from the average brain (fsaverage) and be able identify which vertex falls under which ROI label. I decided to resample aparc+aseg.mgz in fsaverage on the surface map, hoping to get label information at the dimension of 163842 x 1 x 1. So I ran:
mri_vol2surf --mov fsaverage/mri/aparc+aseg.mgz --regheader fsaverage --projfrac 0.5 --interp nearest --hemi lh --o fsaverage/surf/lh.roi.mgh mri_vol2surf --mov fsaverage/mri/aparc+aseg.mgz --regheader fsaverage --projfrac 0.5 --interp nearest --hemi rh --o fsaverage/surf/rh.roi.mgh
The resulting mgh files, however, had a dimension of 23406 x 1 x 7.
- As I said, I wanted to get label information (roi number from the
FreeSurferColorLUT) for each vertex of the surface image in the fsaverage space. Is this the right approach? And did I do this correctly (I'm concerned about many options above)?
- If so, why is the resulting dimension different from the other one?
I assume that it's probably a reshape issue, but how I can reshape the dimension to match 163842 x 1 x 1?
Thanks in advance.
Joon
-- Joonkoo Park Ph.D. Candidate, Cognition & Cognitive Neuroscience Department of Psychology, University of Michigan _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks Doug,
Where can I find the surface annotation for the fsaverage (or any other template) data? I will need to import the data into matlab eventually, so I'm thinking that the surface annotation file should be readable using load_mgh.m (and writable using save_mgh.m). I'm very new to FreeSurfer so I'd really appreciate if you can describe each step for me.
Thank you.
Joon
On Fri, Feb 19, 2010 at 11:47 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
You're better off loading in the surface annotation directly rather than dealing with aparc+aseg. To make surf2surf output the right dimensions, add --noreshape.
doug
Joonkoo Park wrote:
Dear Surfers,
I (successfully) resampled a functional data on the surface map using mri_vol2surf:
mri_vol2surf --mov func.nii --reg register.dat --projfrac 0.5 --interp nearest --hemi lh --o lh.func.mgh
Then, I normalized this image to a standard space (fsaverage) using mri_surf2surf:
mri_surf2surf --srcsubject sub1 --trgsubject fsaverage --sval sub1/lh.func.mgh --tval sub1/lh.func.norm.mgh --fwhm 5 --cortex --hemi lh
The dimension of the output file, lh.func.norm.mgh, was 163842 x 1 x 1 (identified from mri_info). This file can be opened from Matlab, and I can successfully get access to 163842 vertices. What I want now is to take the aparc+aseg information from the average brain (fsaverage) and be able identify which vertex falls under which ROI label. I decided to resample aparc+aseg.mgz in fsaverage on the surface map, hoping to get label information at the dimension of 163842 x 1 x 1. So I ran:
mri_vol2surf --mov fsaverage/mri/aparc+aseg.mgz --regheader fsaverage --projfrac 0.5 --interp nearest --hemi lh --o fsaverage/surf/lh.roi.mgh mri_vol2surf --mov fsaverage/mri/aparc+aseg.mgz --regheader fsaverage --projfrac 0.5 --interp nearest --hemi rh --o fsaverage/surf/rh.roi.mgh
The resulting mgh files, however, had a dimension of 23406 x 1 x 7.
- As I said, I wanted to get label information (roi number from the
FreeSurferColorLUT) for each vertex of the surface image in the fsaverage space. Is this the right approach? And did I do this correctly (I'm concerned about many options above)?
- If so, why is the resulting dimension different from the other one?
I assume that it's probably a reshape issue, but how I can reshape the dimension to match 163842 x 1 x 1?
Thanks in advance.
Joon
-- Joonkoo Park Ph.D. Candidate, Cognition & Cognitive Neuroscience Department of Psychology, University of Michigan _______________________________________________ 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 greve@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
It is in the fsaverage/label dir. Use $FREESURFER_HOME/matlab/read_annotation.m
doug
Joonkoo Park wrote:
Thanks Doug,
Where can I find the surface annotation for the fsaverage (or any other template) data? I will need to import the data into matlab eventually, so I'm thinking that the surface annotation file should be readable using load_mgh.m (and writable using save_mgh.m). I'm very new to FreeSurfer so I'd really appreciate if you can describe each step for me.
Thank you.
Joon
On Fri, Feb 19, 2010 at 11:47 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
You're better off loading in the surface annotation directly rather than dealing with aparc+aseg. To make surf2surf output the right dimensions, add --noreshape.
doug
Joonkoo Park wrote:
Dear Surfers,
I (successfully) resampled a functional data on the surface map using mri_vol2surf:
mri_vol2surf --mov func.nii --reg register.dat --projfrac 0.5 --interp nearest --hemi lh --o lh.func.mgh
Then, I normalized this image to a standard space (fsaverage) using mri_surf2surf:
mri_surf2surf --srcsubject sub1 --trgsubject fsaverage --sval sub1/lh.func.mgh --tval sub1/lh.func.norm.mgh --fwhm 5 --cortex --hemi lh
The dimension of the output file, lh.func.norm.mgh, was 163842 x 1 x 1 (identified from mri_info). This file can be opened from Matlab, and I can successfully get access to 163842 vertices. What I want now is to take the aparc+aseg information from the average brain (fsaverage) and be able identify which vertex falls under which ROI label. I decided to resample aparc+aseg.mgz in fsaverage on the surface map, hoping to get label information at the dimension of 163842 x 1 x 1. So I ran:
mri_vol2surf --mov fsaverage/mri/aparc+aseg.mgz --regheader fsaverage --projfrac 0.5 --interp nearest --hemi lh --o fsaverage/surf/lh.roi.mgh mri_vol2surf --mov fsaverage/mri/aparc+aseg.mgz --regheader fsaverage --projfrac 0.5 --interp nearest --hemi rh --o fsaverage/surf/rh.roi.mgh
The resulting mgh files, however, had a dimension of 23406 x 1 x 7.
- As I said, I wanted to get label information (roi number from the
FreeSurferColorLUT) for each vertex of the surface image in the fsaverage space. Is this the right approach? And did I do this correctly (I'm concerned about many options above)?
- If so, why is the resulting dimension different from the other one?
I assume that it's probably a reshape issue, but how I can reshape the dimension to match 163842 x 1 x 1?
Thanks in advance.
Joon
-- Joonkoo Park Ph.D. Candidate, Cognition & Cognitive Neuroscience Department of Psychology, University of Michigan _______________________________________________ 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 greve@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
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Joonkoo Park