Dear Experts: I am trying to create a cortical mask of M1 (Precentral cortex) for each hemisphere to use it for tractography in FSL. First I register the subject to the space I am using (Talairach or MNI), then I save the label from tksurfer and then use mri_vol2roi to create the ROI which is all the precentral motor area. Finally I am downsampling the output from vol2roi in order to use it as an FSL target mask in ProbtrackX. When checking the output in FSL, the mask seems to be missaligned with the original T1 image, is it beacuse an error in the header or is it because I am doing something wrong in the process? Thenk you for your help, let me know if you need anything else.
Hi Natalia,
at what stage is it misaligned? Note that we do everything in native space, so unless you apply a transform to the ROI it will not be in tal coords. Also, you might consider using our estimate of M1 from the Zilles/Amunts data instead of drawing it (e.g. lh.BA4a.label).
cheers, Bruce
On Tue, 7 Jul 2009, Natalia Sanchez wrote:
Dear Experts: I am trying to create a cortical mask of M1 (Precentral cortex) for each hemisphere to use it for tractography in FSL. First I register the subject to the space I am using (Talairach or MNI), then I save the label from tksurfer and then use mri_vol2roi to create the ROI which is all the precentral motor area. Finally I am downsampling the output from vol2roi in order to use it as an FSL target mask in ProbtrackX. When checking the output in FSL, the mask seems to be missaligned with the original T1 image, is it beacuse an error in the header or is it because I am doing something wrong in the process? Thenk you for your help, let me know if you need anything else.
Sounds like there are a lot of places where something could have gone wrong. Have you checked the output each step of the way or just the final result?
doug
Natalia Sanchez wrote:
Dear Experts: I am trying to create a cortical mask of M1 (Precentral cortex) for each hemisphere to use it for tractography in FSL. First I register the subject to the space I am using (Talairach or MNI), then I save the label from tksurfer and then use mri_vol2roi to create the ROI which is all the precentral motor area. Finally I am downsampling the output from vol2roi in order to use it as an FSL target mask in ProbtrackX. When checking the output in FSL, the mask seems to be missaligned with the original T1 image, is it beacuse an error in the header or is it because I am doing something wrong in the process? Thenk you for your help, let me know if you need anything else.
-- Natalia Sanchez
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Bruce Fischl -
Douglas N Greve -
Natalia Sanchez