hi, of course. The result look strange too. Please see the attached file with -mni152reg command and this transformation matrix is not for the 2mm resolution image. lets me know if you have any other suggestion. thanks.
Amy On Mon, Mar 2, 2015 at 12:26 PM, Thomas Yeo <ytho...@csail.mit.edu> wrote: > Hi Amy, > > Have you tried the "--mni152reg" flag instead of "--reg > /usr/local/freesurfer/subjects/fsaverage/mri.2mm/reg.2mm.dat". Is the > attached picture from your original command or mni152reg flag? > > p.s. Can you please reply all to the freesurfer list? > > Cheers, > Thomas > > On Mon, Mar 2, 2015 at 6:54 PM, Amy Lin <amylin0...@gmail.com> wrote: > > Hello Thomas, thanks for the tips but the result still look strange. > please > > help me to take a look as the attached picture. Another question is how > to > > adjust the color bar and assign by my define look up table. > > > > This is my command: > > > > amy@ubuntu:~/Downloads$ mri_vol2surf --mov my_MNI_ROIs.nii --reg > > /usr/local/freesurfer/subjects/fsaverage/mri.2mm/reg.2mm.dat --hemi lh > > --inflated --o lh.ROIs.mgh > > srcvol = my_MNI_ROIs.nii > > srcreg = /usr/local/freesurfer/subjects/fsaverage/mri.2mm/reg.2mm.dat > > srcregold = 0 > > srcwarp unspecified > > surf = inflated > > hemi = lh > > reshape = 0 > > interp = nearest > > float2int = round > > GetProjMax = 0 > > INFO: float2int code = 0 > > Done loading volume > > Reading surface /usr/local/freesurfer/subjects/fsaverage/surf/lh.inflated > > Done reading source surface > > Mapping Source Volume onto Source Subject Surface > > 1 0 0 0 > > using old > > Done mapping volume to surface > > Number of source voxels hit = 18019 > > Writing to lh.ROIs.mgh > > Dim: 163842 1 1 > > amy@ubuntu:~/Downloads$ tksurfer fsaverage lh inflated -overlay > lh.ROIs.mgh > > subject is fsaverage > > hemi is lh > > surface is inflated > > surfer: current subjects dir: /usr/local/freesurfer/subjects > > surfer: not in "scripts" dir ==> using cwd for session root > > surfer: session root data dir ($session) set to: > > surfer: /home/amy/Downloads > > checking for nofix files in 'inflated' > > Reading image info (/usr/local/freesurfer/subjects/fsaverage) > > Reading /usr/local/freesurfer/subjects/fsaverage/mri/orig.mgz > > surfer: Reading header info from > > /usr/local/freesurfer/subjects/fsaverage/mri/orig.mgz > > surfer: vertices=163842, faces=327680 > > tkmedit: Trying to open lh.ROIs.dat > > surfer: Interpreting overlay volume lh.ROIs.mgh as encoded scalar volume. > > surfer: curvature read: min=-0.673989 max=0.540227 > > surfer: single buffered window > > surfer: tkoInitWindow(fsaverage) > > surfer: using interface /usr/local/freesurfer/tktools/tksurfer.tcl > > Reading /usr/local/freesurfer/tktools/tkm_common.tcl > > Reading /usr/local/freesurfer/tktools/tkm_wrappers.tcl > > Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl > > Reading /usr/local/freesurfer/tktools/tkUtils.tcl > > Successfully parsed tksurfer.tcl > > reading white matter vertex locations... > > > > On Mon, Mar 2, 2015 at 1:15 AM, Thomas Yeo <ytho...@csail.mit.edu> > wrote: > >> > >> Hi Amy, > >> > >> What exactly is the command you use? > >> > >> The command should be something like for the right hemisphere: > >> mri_vol2surf --mov youROIs.nii.gz --mni152reg --hemi rh --surf > >> inflated --o rh.ROIs.mgh > >> > >> You need to repeat for the left hemisphere. I am cc-ing the freesurfer > >> list to keep our conversation on the list. > >> > >> Cheers, > >> Thomas > >> > >> > >> On Mon, Mar 2, 2015 at 3:38 AM, Amy Lin <amylin0...@gmail.com> wrote: > >> > hi, thanks for reply the email. i use command mri_vol2surf try to map > my > >> > define ROI (.nii) to inflated brain. the command work but not so good > in > >> > my > >> > case. My question is how to generate the inflated brain similar as > the > >> > attached picture with my define ROIs. > >> > > >> > Amy > >> > > >> > On Feb 28, 2015 1:02 AM, "Thomas Yeo" <thomas....@nus.edu.sg> wrote: > >> >> > >> >> Hi Amy, > >> >> > >> >> I am confused. Are you trying to run recon-all? From what you said, > >> >> you have some ROIs in MNI space, which you want to map to fsaverage > >> >> space? > >> >> > >> >> p.s. Can you post your question to the freesurfer list instead of > >> >> directly emailing me? > >> >> > >> >> Cheers, > >> >> Thomas > >> >> > >> >> On Sat, Feb 28, 2015 at 12:02 AM, Amy Lin <amylin0...@gmail.com> > wrote: > >> >> > Hello Thomas, > >> >> > > >> >> > I have one quick question for the registration issue from the MNI > >> >> > volume > >> >> > to > >> >> > the freesurfer fsaverage sphere and inflated space. I can not > >> >> > generate > >> >> > the > >> >> > correct .gcs or the .annot file from the my MNI .nifti file . > >> >> > > >> >> > -MNI volume contain several ROIs (see the attached file and the > >> >> > follows > >> >> > link > >> >> > (https://www.dropbox.com/s/f84tm4rwuovyr8p/my_MNI_ROIs.nii?dl=0) > >> >> > > >> >> > Do you have any tips for this? > >> >> > Thanks for the time. > >> >> > > >> >> > Best, > >> >> > Amy Lin > >> >> > > >> >> > > > > > >
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