Where did rh.v1.probl.label come from? The way you call mri_label2vol, it should be in fsaverage space. If it is in an individual space, then the registration is wrong. Try running mni152reg to create a registration from the individual to mni152, then use that reg instead. doug
On 7/4/12 5:32 AM, Anders Hougaard wrote:
Dear Doug,
I have problem similar to this: I am trying to convert V1 labels from the Hinds method to volumes and transform them to MNI152 space for use in FSL. I tried using this command: mri_label2vol --label rh.v1.prob.label --reg $FREESURFER_HOME/average/mni152.register.dat --temp MNI152_T1_2mm.nii.gz --o rh_v1_prob.nii.gz --label-stat rh_v1_prob_stat.nii.gz
...but the output is not registered correctly. It seems to be shift downward as Linda described.
Label conversion using the cmd mri_label2label --srclabel rh.v1.prob.label --s <subject> --regmethod surface --trglabel rh.v1.prob.new.label --hemi rh does not solve it.
Any suggestions?
Best regards, Anders Hougaard
2011/10/18 Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>
The problem appears to be with the label itself. Try this conversion: mri_label2label --srclabel lh.entorhinal.label --s fsaverage --regmethod surface --trglabel lh.entorhinal.new.label --hemi lh Also, you might want to use the entorhinal label define in the aparc+aseg since it fills in the ribbon: mri_binarize --i aparc+aseg.mgz --match 1006 --o lh_entorhinal.nii.gz 1006 comes from $FREESURFER_HOME/FreeSurferColorLUT.txt doug Linda Douw wrote: > Hi Doug, > Thanks for the reply. This cmd makes it slightly better I guess, but still > definetely off target. It seems to be shift downward, towards inferior, > and therefore sometimes outside the skull. Any other ideas? > Linda > > >> The way the reg is set up, the targ is your mask. Try this cmd: >> mri_vol2vol --targ lh_entorhinal.nii.gz --mov MNI152_T1_2mm.brain.nii.gz >> --o lh_entorhinal_MNI.nii.gz --reg >> $FREESURFER_HOME/average/mni152.register.dat --inv >> >> doug >> >> Linda Douw wrote: >> >>> Hi all, >>> >>> I am trying to transform some labels from the aparc to masks in MNI >>> space. >>> Ideally, I would like to do this for each subject in my study >>> individually >>> (using their own rawavg.mgz and labels), but for now I started out with >>> fsaverage. I first converted the label file into a nifti: >>> >>> mri_label2vol --label ./fsaverage/label/lh.entorhinal.label --subject >>> fsaverage --temp ./fsaverage/mri/brainmask.mgz --o lh_entorhinal.nii.gz >>> --identity >>> >>> And then put the nifti file containing the label into MNI space: >>> >>> mri_vol2vol --mov lh_entorhinal.nii.gz --targ MNI152_T1_2mm.brain.nii.gz >>> --o lh_entorhinal_MNI.nii.gz --reg >>> $FREESURFER_HOME/average/mni152.register.dat >>> >>> But when I open lh_entorhinal_MNI.nii.gz with fslview, the location is >>> completely wrong. I checked the location with tkregister as well: >>> >>> tkregister2 --mov lh_entorhinal_MNI.nii.gz --reg >>> /$FREESURFER_HOME/average/mni152.register.dat >>> >>> But here the entorhinal was also in the wrong place. >>> >>> Do you know how to fix this? >>> >>> Thanks, >>> >>> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> >> >> >> > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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.