Good to know, however I would like to display the volume, not the surface so that I can check to see if the label is covering the entire cortex, not just a small delegation of voxels around the pial surface. Is there a way I can visualize a volume file using tkmedit? I know mri_label2vol can convert the .label file to .mgz, however, I am still getting the same display error and the command is not recognizing the flag --projfrac-max
-----Original Message----- From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Monday, March 12, 2012 1:35 PM To: Tina Jeon Cc: Bruce Fischl; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_vol2surf
tkmedit only displays volumes. Use tksurfer for surfaces, something like tksurfer 3t2234 lh inflated -overlay ./3t2234/label/15yr_lh_A1C_new2.mgh doug
Tina Jeon wrote:
Using tkmedit
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Monday, March 12, 2012 1:01 PM To: Tina Jeon Cc: Douglas N Greve; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_vol2surf
how are you trying to display it? On Mon, 12 Mar 2012, Tina Jeon wrote:
I am still getting the same display error with using an mgh file.
mri_vol2surf --src ./3t2234/label/15yr_lh_A1C_new.mgh --out_type mgh --out ./3t2234/label/15yr_lh_A1C_new2.mgh --regheader 3t2234 --projfrac-max 0 1 .1 --hemi lh
Any suggestions?
Thank you,
Tina Jeon Graduate Student Advanced Imaging Research Center UT Southwestern Medical Center
-----Original Message----- From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Thursday, March 08, 2012 2:01 PM To: Tina Jeon Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_vol2surf
Hi Tina, the problem may be with using nifti. Try an mgh file. Also, you'll probably want to use --projfrac-max 0 1 .1 doug
Tina Jeon wrote:
Hi Freesurfers,
I am trying to use projfrac 1 to threshold my newly created cortical label to include the entire cortical ribbon since only a small number of voxels are being included in my manual tracings.
My input code is:
mri_vol2surf --src ./3t2234/label/15yr_lh_A1C_fs.nii.gz --out_type nifti --out ./3t2234/label/15yr_lh_A1C_new.nii.gz --regheader 3t2234 --projfrac 1 --hemi lh
I open the newly created surface with tkmedit and I get a display error (see below). Does anyone have any suggestions on how to absolve the issue?
Thanks all help appreciated,
Tina Jeon
Graduate Student
Advanced Imaging Research Center
UT Southwestern Medical Center
Error accessing display.
Error accessing display.
while executing"SetSlice $gnVolSlice [set gnVolSlice]"
invoked from within".w.fwToolBar.fwNavBar.fwCurSlice.bwInc invoke"
("uplevel" body line 1) invoked from within"uplevel #0 [list $w invoke]"
(procedure "tk::ButtonUp" line 22) invoked from within"tk::ButtonUp .w.fwToolBar.fwNavBar.fwCurSlice.bwInc"
(command bound to event)
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Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html