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,
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,
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 Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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 Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
This fixed the problem, thanks!
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 Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
-- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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
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 Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
-- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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.
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.
Of course, you are right...It fits perfectly now. Thank you so much!
Best, Anders
2012/7/4 Douglas Greve greve@nmr.mgh.harvard.edu
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
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 Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
-- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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.
freesurfer@nmr.mgh.harvard.edu
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Anders Hougaard -
Douglas Greve -
Douglas N Greve
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Linda Douw