Hi Bruce - thanks for the reply.
Here is my command line:
mri_label2label --srcsubject fsaverage \ --trgsubject ${SUBJECT} --srclabel $SUBJECTS_DIR/group_analysis/${CONTRAST}/${LABEL} \ --trglabel $SUBJECTS_DIR/${SUBJECT}/label/${CONTRAST}_${LABEL} \ --regmethod volume \ --reg $SUBJECTS_DIR/$SUBJECT/mri/brain_reg.dat
Where "brain_reg.dat" is the subject-specific matrix I created through FLIRT. However, as I mentioned, disincluding this matrix does not seem to change the result much.
One other problem I encounter... Occasionally when I view the label in native space, the label itself seems to be eroded on a voxel-wise basis. That is, the label essentially appears as a series of non-contiguous dots (which if dialated would become contiguous).
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Monday, July 18, 2011 11:20 AM To: John Richey Cc: 'freesurfer@nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] Problem registering labels to native space
Hi John
can you email us your label2label cmdline?
cheers Bruce
On Mon, 18 Jul 2011, John Richey wrote:
Dear freesurfer experts,
I have a series of labels corresponding to clusters of significant activation in fsaverage space.
I want to map these back to native space using mri_label2label, however when I view the individual (native) labels, the registration is way off and the labels do not map into plausible space.
I have tried using talairach space as an intemediary (by omitting the --reg flag in mri_label2label), as well as using fsl tools (FLIRT) to create a registration matrix but unfortunately I cannot seem to get the label into the right space to query my ces maps in funcroi-sess.
Have others encountered this problem? And how might I create a more robust registration between fsaverage and native space to facilitate the spatial transformation of my labels?
Thanks very much in advance, John _______________________________________________ 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.
Hi John
why are you using an affine volume registration for fsaverage? Why not use surface registration?
Bruce
On Mon, 18 Jul 2011, John Richey wrote:
Hi Bruce - thanks for the reply.
Here is my command line:
mri_label2label --srcsubject fsaverage \ --trgsubject ${SUBJECT} --srclabel $SUBJECTS_DIR/group_analysis/${CONTRAST}/${LABEL} \ --trglabel $SUBJECTS_DIR/${SUBJECT}/label/${CONTRAST}_${LABEL} \ --regmethod volume \ --reg $SUBJECTS_DIR/$SUBJECT/mri/brain_reg.dat
Where "brain_reg.dat" is the subject-specific matrix I created through FLIRT. However, as I mentioned, disincluding this matrix does not seem to change the result much.
One other problem I encounter... Occasionally when I view the label in native space, the label itself seems to be eroded on a voxel-wise basis. That is, the label essentially appears as a series of non-contiguous dots (which if dialated would become contiguous).
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Monday, July 18, 2011 11:20 AM To: John Richey Cc: 'freesurfer@nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] Problem registering labels to native space
Hi John
can you email us your label2label cmdline?
cheers Bruce
On Mon, 18 Jul 2011, John Richey wrote:
Dear freesurfer experts,
I have a series of labels corresponding to clusters of significant activation in fsaverage space.
I want to map these back to native space using mri_label2label, however when I view the individual (native) labels, the registration is way off and the labels do not map into plausible space.
I have tried using talairach space as an intemediary (by omitting the --reg flag in mri_label2label), as well as using fsl tools (FLIRT) to create a registration matrix but unfortunately I cannot seem to get the label into the right space to query my ces maps in funcroi-sess.
Have others encountered this problem? And how might I create a more robust registration between fsaverage and native space to facilitate the spatial transformation of my labels?
Thanks very much in advance, John _______________________________________________ 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
-
Bruce Fischl -
John Richey