Hi Freesurfers, I've run reg-feat2anat on several subjects in order to generate binary masks to use in an FSL ppi. For 3 subjects, this completely failed.
When I looked at the fsl's own registration of fsl feat 2 standard (via tkregister2), the registration is fine, but after running reg-feat2anat, the registration of the feat to the freesurfer anatomical and the feat to standard are completely off.
I manually fixed and saved the registration edits via reg-feat2anat --manual, but when I generated the masks again, they were totally wrong still. When looking at freesurfer's feat to standard registration, it looks like all the brains weren't tall enough in the saggital view. Am I supposed to stretch the feat brain to fit?
How can I fix this so that the masks are accurate?
Thanks. Michelle
How are you generating the masks? doug
Michelle Umali wrote:
Hi Freesurfers, I've run reg-feat2anat on several subjects in order to generate binary masks to use in an FSL ppi. For 3 subjects, this completely failed.
When I looked at the fsl's own registration of fsl feat 2 standard (via tkregister2), the registration is fine, but after running reg-feat2anat, the registration of the feat to the freesurfer anatomical and the feat to standard are completely off.
I manually fixed and saved the registration edits via reg-feat2anat --manual, but when I generated the masks again, they were totally wrong still. When looking at freesurfer's feat to standard registration, it looks like all the brains weren't tall enough in the saggital view. Am I supposed to stretch the feat brain to fit?
How can I fix this so that the masks are accurate?
Thanks. Michelle
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug, I am using reg-feat2anat on the feat directory of each run. reg-feat2anat --feat feadir.feat --subject XX Then I checked and adjusted the registration with: reg-feat2anat --feat featdir.feat --manual Next I checked and adjusted the registration to the standard with: reg-feat2anat --feat featdir.feat --manxfm func2std
To generate cortical binary masks I used: aparc2feat --feat featdir.feat --annot BA fslmaths featdir.feat/reg/freesurfer/lh.BA.nii.gz -thr 10 -uthr 10 featdir.feat/reg/freesurfer/V1_l.nii.gz
To generate subcortical binary masks I did: aseg2feat --feat featdir.feat --aseg aparc+aseg fslmaths featdir.feat/reg/freesurfer/aparc+aseg.nii.gz -thr 54 -uthr 54 featdir.feat/reg/freesurfer/amygdala_r.nii.gz
When I looked at the masks in FSLview and checked the masks against the other atlases, everything was off even after painstakingly editing the registrations.
Is there something I am doing wrong?
Thanks. Michelle
On Mon, Oct 17, 2011 at 1:36 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
How are you generating the masks? doug
Michelle Umali wrote:
Hi Freesurfers, I've run reg-feat2anat on several subjects in order to generate binary masks to use in an FSL ppi. For 3 subjects, this completely failed.
When I looked at the fsl's own registration of fsl feat 2 standard (via tkregister2), the registration is fine, but after running reg-feat2anat, the registration of the feat to the freesurfer anatomical and the feat to standard are completely off.
I manually fixed and saved the registration edits via reg-feat2anat --manual, but when I generated the masks again, they were totally wrong still. When looking at freesurfer's feat to standard registration, it looks like all the brains weren't tall enough in the saggital view. Am I supposed to stretch the feat brain to fit?
How can I fix this so that the masks are accurate?
Thanks. Michelle
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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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/**compliancelinehttp://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.
The registration that should be used for all of these is anat2exf.register.dat found in feat/reg/freesurfer. Can you verify that that was the one that you manually changed? Look at the time stamp as compared to the other files in that folder. doug
Michelle Umali wrote:
Hi Doug, I am using reg-feat2anat on the feat directory of each run. reg-feat2anat --feat feadir.feat --subject XX Then I checked and adjusted the registration with: reg-feat2anat --feat featdir.feat --manual Next I checked and adjusted the registration to the standard with: reg-feat2anat --feat featdir.feat --manxfm func2std
To generate cortical binary masks I used: aparc2feat --feat featdir.feat --annot BA fslmaths featdir.feat/reg/freesurfer/lh.BA.nii.gz -thr 10 -uthr 10 featdir.feat/reg/freesurfer/V1_l.nii.gz
To generate subcortical binary masks I did: aseg2feat --feat featdir.feat --aseg aparc+aseg fslmaths featdir.feat/reg/freesurfer/aparc+aseg.nii.gz -thr 54 -uthr 54 featdir.feat/reg/freesurfer/amygdala_r.nii.gz
When I looked at the masks in FSLview and checked the masks against the other atlases, everything was off even after painstakingly editing the registrations.
Is there something I am doing wrong?
Thanks. Michelle
On Mon, Oct 17, 2011 at 1:36 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
How are you generating the masks? doug Michelle Umali wrote: Hi Freesurfers, I've run reg-feat2anat on several subjects in order to generate binary masks to use in an FSL ppi. For 3 subjects, this completely failed. When I looked at the fsl's own registration of fsl feat 2 standard (via tkregister2), the registration is fine, but after running reg-feat2anat, the registration of the feat to the freesurfer anatomical and the feat to standard are completely off. I manually fixed and saved the registration edits via reg-feat2anat --manual, but when I generated the masks again, they were totally wrong still. When looking at freesurfer's feat to standard registration, it looks like all the brains weren't tall enough in the saggital view. Am I supposed to stretch the feat brain to fit? How can I fix this so that the masks are accurate? Thanks. Michelle ------------------------------------------------------------------------ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel: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> 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
freesurfer@nmr.mgh.harvard.edu
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Michelle Umali