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 >> >> > >> >> > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
