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)
________________________________
UT Southwestern Medical Center The future of medicine, today.
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)
UT Southwestern Medical Center The future of medicine, today.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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)
--
UT Southwestern Medical Center The future of medicine, today.
--
Freesurfer mailing list 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 Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: 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.
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)
--
UT Southwestern Medical Center The future of medicine, today.
--
Freesurfer mailing list 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 Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: 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
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)
--
UT Southwestern Medical Center The future of medicine, today.
--
Freesurfer mailing list 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 Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: 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
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)
--
UT Southwestern Medical Center The future of medicine, today.
--
Freesurfer mailing list 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 Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: 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
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)
--
UT Southwestern Medical Center The future of medicine, today.
--
Freesurfer mailing list 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 Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: 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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Hi Tina, I think I'm missing something. If you want a volume, why are you converting it to the surface? Also, make sure to send command-lines of commands that are failing. doug
Tina Jeon wrote:
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)
--
UT Southwestern Medical Center The future of medicine, today.
--
Freesurfer mailing list 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 Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: 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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
I want both the surface and volume. Sorry about the confusion. The command line is:
mri_label2vol --label ./3t2234/label/15yr_lh_A1C_fs.label --temp ./3t2234/mri/brainmask.mgz --regheader 3t2234 --projfracmax 0 1 .1 --subject 3t2234 --hemi lh --o ./3t2234/label/15yr_lh_A1C_fs.mgz
I am using a linux centos.
I can send you my files if need be. Basically I would like my manual roi edits to project to the entire cortical ribbon.
Thanks, Tina
-----Original Message----- From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Monday, March 12, 2012 4:12 PM To: Tina Jeon Cc: Bruce Fischl; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_vol2surf
Hi Tina, I think I'm missing something. If you want a volume, why are you converting it to the surface? Also, make sure to send command-lines of commands that are failing. doug
Tina Jeon wrote:
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)
--
UT Southwestern Medical Center The future of medicine, today.
--
Freesurfer mailing list 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 Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: 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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
How did you create the manual ROIs? How is the label2vol command failing? Usually good to send the terminal output of a failing command too. doug
Tina Jeon wrote:
I want both the surface and volume. Sorry about the confusion. The command line is:
mri_label2vol --label ./3t2234/label/15yr_lh_A1C_fs.label --temp ./3t2234/mri/brainmask.mgz --regheader 3t2234 --projfracmax 0 1 .1 --subject 3t2234 --hemi lh --o ./3t2234/label/15yr_lh_A1C_fs.mgz
I am using a linux centos.
I can send you my files if need be. Basically I would like my manual roi edits to project to the entire cortical ribbon.
Thanks, Tina
-----Original Message----- From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Monday, March 12, 2012 4:12 PM To: Tina Jeon Cc: Bruce Fischl; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_vol2surf
Hi Tina, I think I'm missing something. If you want a volume, why are you converting it to the surface? Also, make sure to send command-lines of commands that are failing. doug
Tina Jeon wrote:
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)
--
UT Southwestern Medical Center The future of medicine, today.
--
Freesurfer mailing list 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 Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: 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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
I created the manual ROIs in tksurfer. Then saved them as label files, however, I ran into a problem when the manual ROI's only include a small number of voxels lining the cortical ribbon.
The commands mri_label2vol and mri_vol2surf are NOT failing however when I try to visualize the volume with tkmedit I get this Application error when I try to scroll through slices:
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)
What I think happened was the predefined label created in tksurfer is not a surface label, therefore does not work when I add projfrac-max. Can you suggest a work around based on my objectives of: 1). Creating a manual drawn surface label in volume and surface format 2). Having the surface label project to the entire cortical surface, not just a tiny sliver of voxels surrounding the white matter.
Thank you for your help,
Tina Graduate student Advanced Imaging Research Center UT Southwestern Medical Center
-----Original Message----- From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Monday, March 12, 2012 5:01 PM To: Tina Jeon Cc: Bruce Fischl; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_vol2surf
How did you create the manual ROIs? How is the label2vol command failing? Usually good to send the terminal output of a failing command too. doug
Tina Jeon wrote:
I want both the surface and volume. Sorry about the confusion. The command line is:
mri_label2vol --label ./3t2234/label/15yr_lh_A1C_fs.label --temp ./3t2234/mri/brainmask.mgz --regheader 3t2234 --projfracmax 0 1 .1 --subject 3t2234 --hemi lh --o ./3t2234/label/15yr_lh_A1C_fs.mgz
I am using a linux centos.
I can send you my files if need be. Basically I would like my manual roi edits to project to the entire cortical ribbon.
Thanks, Tina
-----Original Message----- From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Monday, March 12, 2012 4:12 PM To: Tina Jeon Cc: Bruce Fischl; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_vol2surf
Hi Tina, I think I'm missing something. If you want a volume, why are you converting it to the surface? Also, make sure to send command-lines of commands that are failing. doug
Tina Jeon wrote:
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)
--
UT Southwestern Medical Center The future of medicine, today.
--
Freesurfer mailing list 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 Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: 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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Douglas N Greve -
Tina Jeon