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Freesurfer Experts,
thanks for the response! There was no command for projabs, but looking through the help I think projdist was about what I needed?
I was also curious though if there were a way to get it into an annotation--like the one available for the Yeo parcellations on the freesurfer webpage. Is there any way to convert a lookup nifti to an annotation, or one of these surface overlays into one? I can't seem to figure it out from the documentation, but it's almost surely user error...
Quentin Funk, PhD Houston Methodist Research Institute 713-363-9003tel:713-363-9003
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Message: 13 Date: Fri, 25 May 2018 11:06:15 -0400 From: Douglas Greve dgreve@mgh.harvard.edu Subject: Re: [Freesurfer] Lookup table to surface overlay To: freesurfer@nmr.mgh.harvard.edu Message-ID: 5cb3e6da-99cb-8365-c4f5-4f1cb17f7150@mgh.harvard.edu Content-Type: text/plain; charset="windows-1252"
You might be sampling outside of the brain. Try adding
--projabs -2
To sample 2mm below the pial surface
On 5/25/18 10:32 AM, Funk, Quentin wrote:
Freesurfer experts,
I have some lookup table volume files in MNI space that I'd like to overlay on a surface (say, fsaverage's lh.pial). Currently I'm using this command:
mri_vol2surf --mov look_up_table.nii --regheader fsaverage --interp nearest --hemi lh --surf pial --o lh_lookup_overlay.mgh
Then I choose "color wheel" as the overlay option in freeview. This works OK, but it's a bit imperfect. There are voxels that somehow don't get a value (and show up in the configuration window as 0's (even though the entire MNI brain is covered by the LUT), and it's a bit 'edgy' and not smooth.
Are there any better ways to do this?
Thanks for any help!
Quentin Funk, PhD Houston Methodist Research Institute 713-363-9003 tel:713-363-9003
Houston Methodist. Leading Medicine.
Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S. News & World Report as the No. 1 hospital in Texas for patient care. Houston Methodist is nationally ranked in 8 specialties and is designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.
On 06/01/2018 10:34 AM, Funk, Quentin wrote:
Freesurfer Experts,
thanks for the response! There was no command for projabs, but looking through the help I think projdist was about what I needed?
Sorry, yes, my bad.
I was also curious though if there were a way to get it into an annotation--like the one available for the Yeo parcellations on the freesurfer webpage. Is there any way to convert a lookup nifti to an annotation, or one of these surface overlays into one? I can't seem to figure it out from the documentation, but it's almost surely user error...
Try mris_seg2annot
Quentin Funk, PhD Houston Methodist Research Institute 713-363-9003 tel:713-363-9003
Message: 13 Date: Fri, 25 May 2018 11:06:15 -0400 From: Douglas Greve dgreve@mgh.harvard.edu Subject: Re: [Freesurfer] Lookup table to surface overlay To: freesurfer@nmr.mgh.harvard.edu Message-ID: 5cb3e6da-99cb-8365-c4f5-4f1cb17f7150@mgh.harvard.edu Content-Type: text/plain; charset="windows-1252"
You might be sampling outside of the brain. Try adding
--projabs -2
To sample 2mm below the pial surface
On 5/25/18 10:32 AM, Funk, Quentin wrote:
Freesurfer experts,
I have some lookup table volume files in MNI space that I'd like to overlay on a surface (say, fsaverage's lh.pial). Currently I'm using this command:
mri_vol2surf --mov look_up_table.nii --regheader fsaverage --interp nearest --hemi lh --surf pial --o lh_lookup_overlay.mgh
Then I choose "color wheel" as the overlay option in freeview. This works OK, but it's a bit imperfect. There are voxels that somehow don't get a value (and show up in the configuration window as 0's (even though the entire MNI brain is covered by the LUT), and it's a bit 'edgy' and not smooth.
Are there any better ways to do this?
Thanks for any help!
Quentin Funk, PhD Houston Methodist Research Institute 713-363-9003 tel:713-363-9003
Houston Methodist. Leading Medicine.
Houston Methodist. Leading Medicine.
Houston Methodist is ranked by /U.S. News & World Report/ as the No. 1 hospital in Texas for patient care. Houston Methodist is nationally ranked in 8 specialties and is designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org <houstonmethodist.org>. Follow us at twitter.com/MethodistHosp <twitter.com/MethodistHosp> and facebook.com/HoustonMethodist.
***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.
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Funk, Quentin