Dear Doug and all,
I have already done two things: (1) 'recon-all’ to the segmentation for 140 subjects; (2) surface registration to fsaverage template for 1 subject using: mri_surf2surf --hemi lh --srcsubject sub001 --srcsurfval thickness --src_type curv --trgsubject fsaverage --trgsurfval ./sub001-thickness-lh.mgz
Now I have got the 'sub001-thickness-lh.mgz' file.
I have two questions: (1) Is this 'sub001-thickness-lh.mgz’ a surface file or a volume file? How can I read it? I used ‘freeview sub001-thickness-lh.mgz’ to read it, but a dark scene was shown, nothing can be found. I also used ‘mris_convert -c $SUBJECTS_DIR/sub001/sub001-thickness-lh.mgz $SUBJECTS_DIR/sub001/surf/lh.orig lh.thickness.asc’, an error occurred like ‘ERROR: number of vertices in /disk250/data_analysis/sub001/sub001-thickness-lh.mgz does not match surface (163842, 132230)’. (2) After the registration, I want to flatten the surface of curvature or thickness into a full plane. The wiki says we should first specify 5 vertices and cut the whole area without the midline region, then ‘kris_flatten’ can be used. Indeed, this procedure requires quite a lot manually operation. I am wondering if there are some automatically commands that can do this flatten projects for 140 subject?
Any reply would be really appreciated!
Qiongmin
Hi Qiongmin
1) The command you ran resamples the thickness from being a scalar field over the subject surface to being a scalar field over the fsaverage surface. If you load fsaverage (say inflated) in tksurfer or freeview you should then be able to load the overlay onto it.
2) We provide pre-flattened patches named ?h.cortex.patch.flat for fsaverage so if you have mapped the data there, there is no need to cut and flatten again
cheers Bruce On Wed, 14 May 2014, Caka wrote:
Dear Doug and all,
I have already done two things: (1) 'recon-all’ to the segmentation for 140 subjects; (2) surface registration to fsaverage template for 1 subject using: mri_surf2surf --hemi lh --srcsubject sub001 --srcsurfval thickness --src_type curv --trgsubject fsaverage --trgsurfval ./sub001-thickness-lh.mgz
Now I have got the 'sub001-thickness-lh.mgz' file.
I have two questions: (1) Is this 'sub001-thickness-lh.mgz’ a surface file or a volume file? How can I read it? I used ‘freeview sub001-thickness-lh.mgz’ to read it, but a dark scene was shown, nothing can be found. I also used ‘mris_convert -c $SUBJECTS_DIR/sub001/sub001-thickness-lh.mgz $SUBJECTS_DIR/sub001/surf/lh.orig lh.thickness.asc’, an error occurred like ‘ERROR: number of vertices in /disk250/data_analysis/sub001/sub001-thickness-lh.mgz does not match surface (163842, 132230)’. (2) After the registration, I want to flatten the surface of curvature or thickness into a full plane. The wiki says we should first specify 5 vertices and cut the whole area without the midline region, then ‘kris_flatten’ can be used. Indeed, this procedure requires quite a lot manually operation. I am wondering if there are some automatically commands that can do this flatten projects for 140 subject?
Any reply would be really appreciated!
Qiongmin _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
On 05/13/2014 11:19 PM, Caka wrote:
Dear Doug and all, I have already done two things: (1) 'recon-all’ to the segmentation for 140 subjects; (2) surface registration to fsaverage template for 1 subject using: mri_surf2surf --hemi lh --srcsubject sub001 --srcsurfval thickness --src_type curv --trgsubject fsaverage --trgsurfval ./sub001-thickness-lh.mgz Now I have got the 'sub001-thickness-lh.mgz' file. I have two questions: (1) Is this 'sub001-thickness-lh.mgz’ a surface file or a volume file? How can I read it? I used ‘freeview sub001-thickness-lh.mgz’ to read it, but a dark scene was shown, nothing can be found. I also used ‘mris_convert -c $SUBJECTS_DIR/sub001/sub001-thickness-lh.mgz $SUBJECTS_DIR/sub001/surf/lh.orig lh.thickness.asc’, an error occurred like ‘ERROR: number of vertices in /disk250/data_analysis/sub001/sub001-thickness-lh.mgz does not match surface (163842, 132230)’.
Try tksurfer fsaverage lh inflated -aparc -overlay sub001-thickness-lh.mgz -fminmax .01 4
(2) After the registration, I want to flatten the surface of curvature or thickness into a full plane. The wiki says we should first specify 5 vertices and cut the whole area without the midline region, then ‘kris_flatten’ can be used. Indeed, this procedure requires quite a lot manually operation. I am wondering if there are some automatically commands that can do this flatten projects for 140 subject? Any reply would be really appreciated! Qiongmin _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I don't think so, though I think bruce was working on something. You could just flatten fsaverage and then map everyone to fsaverage (as you have already done). Why do you want to map everyone to a flat map?
doug
-- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Caka -
Douglas N Greve