Hi Doug, the .dat file that I mention below had already been converted into a fs matrix using tkregister2.
-----Original Message----- From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Monday, July 18, 2011 12:38 PM To: John Richey Cc: 'Bruce Fischl'; 'freesurfer@nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] Problem registering labels to native space
You can't use a flirt matrix with mri_label2label. You can convert a flirt matrix to the proper format with tkregister2 using the --fsl option (this will allow you to check the reg as well).
doug
John Richey wrote:
Hi Bruce,
The labels that I have fsaverage space are 3D/volume-based and not surface-based labels.
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Monday, July 18, 2011 12:00 PM To: John Richey Cc: 'freesurfer@nmr.mgh.harvard.edu' Subject: RE: [Freesurfer] Problem registering labels to native space
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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- 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
How did you create it? What is the actual "fsaverage space"? Is this an FSFAST analysis? doug
John Richey wrote:
Hi Doug, the .dat file that I mention below had already been converted into a fs matrix using tkregister2.
-----Original Message----- From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Monday, July 18, 2011 12:38 PM To: John Richey Cc: 'Bruce Fischl'; 'freesurfer@nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] Problem registering labels to native space
You can't use a flirt matrix with mri_label2label. You can convert a flirt matrix to the proper format with tkregister2 using the --fsl option (this will allow you to check the reg as well).
doug
John Richey wrote:
Hi Bruce,
The labels that I have fsaverage space are 3D/volume-based and not surface-based labels.
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Monday, July 18, 2011 12:00 PM To: John Richey Cc: 'freesurfer@nmr.mgh.harvard.edu' Subject: RE: [Freesurfer] Problem registering labels to native space
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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- 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@nmr.mgh.harvard.edu
-
Douglas N Greve -
John Richey