Re: [Freesurfer] Problem registering labels to native space

2011-07-21 Thread John Richey
\ --noedit -Original Message- From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Sent: Monday, July 18, 2011 3:11 PM To: John Richey Cc: 'Bruce Fischl'; 'freesurfer@nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] Problem registering labels to native space How did you create

[Freesurfer] Problem registering labels to native space

2011-07-18 Thread John Richey
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

Re: [Freesurfer] Problem registering labels to native space

2011-07-18 Thread Bruce Fischl
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

Re: [Freesurfer] Problem registering labels to native space

2011-07-18 Thread John Richey
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

Re: [Freesurfer] Problem registering labels to native space

2011-07-18 Thread Bruce Fischl
if dialated would become contiguous). -Original Message- From: Bruce Fischl [mailto:fis...@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

Re: [Freesurfer] Problem registering labels to native space

2011-07-18 Thread John Richey
: [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

Re: [Freesurfer] Problem registering labels to native space

2011-07-18 Thread Douglas N Greve
and not surface-based labels. -Original Message- From: Bruce Fischl [mailto:fis...@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

Re: [Freesurfer] Problem registering labels to native space

2011-07-18 Thread John Richey
@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

Re: [Freesurfer] Problem registering labels to native space

2011-07-18 Thread Douglas N 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

Re: [Freesurfer] Problem registering labels to native space

2011-07-18 Thread John Richey
...@nmr.mgh.harvard.edu] Sent: Monday, July 18, 2011 3:11 PM To: John Richey Cc: 'Bruce Fischl'; 'freesurfer@nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] Problem registering labels to native space How did you create it? What is the actual fsaverage space? Is this an FSFAST analysis? doug John Richey wrote: Hi

Re: [Freesurfer] Problem registering labels to native space

2011-07-18 Thread Douglas N Greve
: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Sent: Monday, July 18, 2011 3:11 PM To: John Richey Cc: 'Bruce Fischl'; 'freesurfer@nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] Problem registering labels to native space How did you create it? What is the actual fsaverage space