Hi Amy, Good point. You can first use mri_vol2vol to upsample to 1mm:
mri_vol2vol --mov yourROIs.nii --targ $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz --regheader --o yourROIs_1mm.nii --interp nearest then mri_vol2surf --mov yourROIs_1mm.nii --mni152reg --hemi rh --surf white --o rh.ROIs.mgh You can then visualize with freeview: freeview -f $FREESURFER_HOME/subjects/fsaverage/surf/rh.inflated:overlay=rh.ROIs.mgh By default it uses a heatmap, so you have to adjust the overlay accordingly. Cheers, Thomas On Mon, Mar 2, 2015 at 7:39 PM, Amy Lin <amylin0...@gmail.com> wrote: > hi, of course. The result look strange too. Please see the attached file > with -mni152reg command and this transformation matrix is not for the 2mm > resolution image. lets me know if you have any other suggestion. thanks. > > Amy > > > On Mon, Mar 2, 2015 at 12:26 PM, Thomas Yeo <ytho...@csail.mit.edu> wrote: >> >> Hi Amy, >> >> Have you tried the "--mni152reg" flag instead of "--reg >> /usr/local/freesurfer/subjects/fsaverage/mri.2mm/reg.2mm.dat". Is the >> attached picture from your original command or mni152reg flag? >> >> p.s. Can you please reply all to the freesurfer list? >> >> Cheers, >> Thomas >> >> On Mon, Mar 2, 2015 at 6:54 PM, Amy Lin <amylin0...@gmail.com> wrote: >> > Hello Thomas, thanks for the tips but the result still look strange. >> > please >> > help me to take a look as the attached picture. Another question is how >> > to >> > adjust the color bar and assign by my define look up table. >> > >> > This is my command: >> > >> > amy@ubuntu:~/Downloads$ 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 >> >> >> > >> >> >> > >> > >> > > > _______________________________________________ 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 . 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