Hi Doug
I've actually tried both inclusive and exclusive and have failed - just checked again in tkmedit that the label was coming up correctly and it was.
Just to double-check - the label should be in the space of the --mov, right?
Thanks!
Fred
Hi Fred, that mask is an inclusive mask, not an exclusive mask. Try inverting you mask. doug
On 4/14/13 4:31 PM, Fred Dick wrote: Dear all
I am painting some higher-res anatomical data from a volume to a surface, and want to use a mask that excludes the vessels. (The same data but 1x1x1 conformed were used to create the surface). I've created a binary label in the same space
mri_cor2label --i ./R2Mask.nii.gz --l ./R2s.label --id 1
made sure that it looks ok when I read in hi-res to tkmedit and display label, then ran mri_vol2surf
mri_vol2surf --mov ./sPQ07082012-0009-00001-000208-01_R1.nii --regregister.dat --surf-fwhm 4 --hemi $hemi --projfrac $frac --interp trilinear --out_type w --mask R2s.label --o ./dancar-0.5-lh.w
And got the output (pasted below), showing that the output is all zero.
Output is fine without label, or with -cortex.
I've also tried this with a conformed version of the label (also verified in tkmedit) and have had the same thing. (I thought maybe it was applying it to orig vol, which I admit would be strange). (I noticed someone had a similar issue a couple of years ago, but it involved a surface rather than volume label, and looked like it had been resolved). Am running current stable version on Mountain Lion.
Thanks for any pointers,
best, Fred
########################################################## masking output with label R2s.label INFO: output format is paint srcvol = ./sPQ07082012-0009-00001-000208-01_R1.nii srcreg = register.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Loading label R2s.label Reading surface /Applications/freesurfer/subjects/dancar-synth-handnorm/surf/lh.white Done reading source surface Reading thickness /Applications/freesurfer/subjects/dancar-synth-handnorm/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 108676 Surface smoothing by fwhm = 4 (n=10) Masking with R2s.label Warning: all vertex values are zero
Oh, the label should be a surface label. mri_cor2label creates a volume label (basically it just means that each label point corresponds to a 1mm3 cube instead of a verex -- the vertex numbers should all be -1). Try running vol2surf on the mask (using nearest interp) to create a surface mask. Then create a surface label with mri_cor2label using the --surf option. doug
On 4/14/13 5:01 PM, Fred Dick wrote:
Hi Doug
I've actually tried both inclusive and exclusive and have failed - just checked again in tkmedit that the label was coming up correctly and it was.
Just to double-check - the label should be in the space of the --mov, right?
Thanks!
Fred
Hi Fred, that mask is an inclusive mask, not an exclusive mask. Try inverting you mask. doug On 4/14/13 4:31 PM, Fred Dick wrote:
Dear all I am painting some higher-res anatomical data from a volume to a surface, and want to use a mask that excludes the vessels. (The same data but 1x1x1 conformed were used to create the surface). I've created a binary label in the same space >> mri_cor2label --i ./R2Mask.nii.gz --l ./R2s.label --id 1 made sure that it looks ok when I read in hi-res to tkmedit and display label, then ran mri_vol2surf >> mri_vol2surf --mov ./sPQ07082012-0009-00001-000208-01_R1.nii --regregister.dat --surf-fwhm 4 --hemi $hemi --projfrac $frac --interp trilinear --out_type w --mask R2s.label --o ./dancar-0.5-lh.w And got the output (pasted below), showing that the output is all zero. Output is fine without label, or with -cortex. I've also tried this with a conformed version of the label (also verified in tkmedit) and have had the same thing. (I thought maybe it was applying it to orig vol, which I admit would be strange).(I noticed someone had a similar issue a couple of years ago, but it involved a surface rather than volume label, and looked like it had been resolved). Am running current stable version on Mountain Lion. Thanks for any pointers, best, Fred ########################################################## masking output with label R2s.label INFO: output format is paint srcvol = ./sPQ07082012-0009-00001-000208-01_R1.nii srcreg = register.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Loading label R2s.label Reading surface /Applications/freesurfer/subjects/dancar-synth-handnorm/surf/lh.white Done reading source surface Reading thickness /Applications/freesurfer/subjects/dancar-synth-handnorm/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 108676 Surface smoothing by fwhm = 4 (n=10) Masking with R2s.label Warning: all vertex values are zero
Ah, OK, makes sense - should have guessed, sorry, vol2surf behaved so agreeably with the vertex-free mask!
Shall make that surf mask now, thanks much,
Fred
On 14 Apr 2013, at 22:56, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
Oh, the label should be a surface label. mri_cor2label creates a volume label (basically it just means that each label point corresponds to a 1mm3 cube instead of a verex -- the vertex numbers should all be -1). Try running vol2surf on the mask (using nearest interp) to create a surface mask. Then create a surface label with mri_cor2label using the --surf option. doug
On 4/14/13 5:01 PM, Fred Dick wrote:
Hi Doug
I've actually tried both inclusive and exclusive and have failed - just checked again in tkmedit that the label was coming up correctly and it was.
Just to double-check - the label should be in the space of the --mov, right?
Thanks!
Fred
Hi Fred, that mask is an inclusive mask, not an exclusive mask. Try inverting you mask. doug On 4/14/13 4:31 PM, Fred Dick wrote: Dear all
I am painting some higher-res anatomical data from a volume to a surface, and want to use a mask that excludes the vessels. (The same data but 1x1x1 conformed were used to create the surface). I've created a binary label in the same space
mri_cor2label --i ./R2Mask.nii.gz --l ./R2s.label --id 1
made sure that it looks ok when I read in hi-res to tkmedit and display label, then ran mri_vol2surf
mri_vol2surf --mov ./sPQ07082012-0009-00001-000208-01_R1.nii --regregister.dat --surf-fwhm 4 --hemi $hemi --projfrac $frac --interp trilinear --out_type w --mask R2s.label --o ./dancar-0.5-lh.w
And got the output (pasted below), showing that the output is all zero.
Output is fine without label, or with -cortex.
I've also tried this with a conformed version of the label (also verified in tkmedit) and have had the same thing. (I thought maybe it was applying it to orig vol, which I admit would be strange).(I noticed someone had a similar issue a couple of years ago, but it involved a surface rather than volume label, and looked like it had been resolved). Am running current stable version on Mountain Lion.
Thanks for any pointers,
best, Fred
########################################################## masking output with label R2s.label INFO: output format is paint srcvol = ./sPQ07082012-0009-00001-000208-01_R1.nii srcreg = register.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Loading label R2s.label Reading surface /Applications/freesurfer/subjects/dancar-synth-handnorm/surf/lh.white Done reading source surface Reading thickness /Applications/freesurfer/subjects/dancar-synth-handnorm/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 108676 Surface smoothing by fwhm = 4 (n=10) Masking with R2s.label Warning: all vertex values are zero
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.
Hey again
sorry, I seem not to be able to accomplish this very simple thing!
First wrote out mask as .w file using vol2surf, but mri_cor2label couldn't read ('mri_read(): couldn't determine type of file ./rh.R2MaskBrain.w').
Then tried writing out as curv using the following command:
mri_vol2surf --mov R2MaskBrain.nii.gz --reg register.dat --hemi $hemi --interp nearest --o ./$hemi.R2MaskBrain --out_type curv --projfrac 0.5
and got this error,
################ Writing to ./lh.R2MaskBrain Dim: 152308 1 1 MRIwriteType(): code inconsistency (file type recognized but not caught) ERROR: saving ./lh.R2MaskBrain #####################
Bug, or user stupidity???
cheers, Fred
On 14 Apr 2013, at 22:56, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
Oh, the label should be a surface label. mri_cor2label creates a volume label (basically it just means that each label point corresponds to a 1mm3 cube instead of a verex -- the vertex numbers should all be -1). Try running vol2surf on the mask (using nearest interp) to create a surface mask. Then create a surface label with mri_cor2label using the --surf option. doug
On 4/14/13 5:01 PM, Fred Dick wrote:
Hi Doug
I've actually tried both inclusive and exclusive and have failed - just checked again in tkmedit that the label was coming up correctly and it was.
Just to double-check - the label should be in the space of the --mov, right?
Thanks!
Fred
Hi Fred, that mask is an inclusive mask, not an exclusive mask. Try inverting you mask. doug On 4/14/13 4:31 PM, Fred Dick wrote: Dear all
I am painting some higher-res anatomical data from a volume to a surface, and want to use a mask that excludes the vessels. (The same data but 1x1x1 conformed were used to create the surface). I've created a binary label in the same space
mri_cor2label --i ./R2Mask.nii.gz --l ./R2s.label --id 1
made sure that it looks ok when I read in hi-res to tkmedit and display label, then ran mri_vol2surf
mri_vol2surf --mov ./sPQ07082012-0009-00001-000208-01_R1.nii --regregister.dat --surf-fwhm 4 --hemi $hemi --projfrac $frac --interp trilinear --out_type w --mask R2s.label --o ./dancar-0.5-lh.w
And got the output (pasted below), showing that the output is all zero.
Output is fine without label, or with -cortex.
I've also tried this with a conformed version of the label (also verified in tkmedit) and have had the same thing. (I thought maybe it was applying it to orig vol, which I admit would be strange).(I noticed someone had a similar issue a couple of years ago, but it involved a surface rather than volume label, and looked like it had been resolved). Am running current stable version on Mountain Lion.
Thanks for any pointers,
best, Fred
########################################################## masking output with label R2s.label INFO: output format is paint srcvol = ./sPQ07082012-0009-00001-000208-01_R1.nii srcreg = register.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Loading label R2s.label Reading surface /Applications/freesurfer/subjects/dancar-synth-handnorm/surf/lh.white Done reading source surface Reading thickness /Applications/freesurfer/subjects/dancar-synth-handnorm/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 108676 Surface smoothing by fwhm = 4 (n=10) Masking with R2s.label Warning: all vertex values are zero
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.
Hi Fred, why do you want to save it as a wfile? We're trying to phase wfiles out. Can you use mgh format? doug
On 4/15/13 12:56 PM, Fred Dick wrote:
Hey again
sorry, I seem not to be able to accomplish this very simple thing!
First wrote out mask as .w file using vol2surf, but mri_cor2label couldn't read ('mri_read(): couldn't determine type of file ./rh.R2MaskBrain.w').
Then tried writing out as curv using the following command:
mri_vol2surf --mov R2MaskBrain.nii.gz --reg register.dat --hemi $hemi --interp nearest --o ./$hemi.R2MaskBrain --out_type curv --projfrac 0.5
and got this error,
################ Writing to ./lh.R2MaskBrain Dim: 152308 1 1 MRIwriteType(): code inconsistency (file type recognized but not caught) ERROR: saving ./lh.R2MaskBrain #####################
Bug, or user stupidity???
cheers, Fred
On 14 Apr 2013, at 22:56, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Oh, the label should be a surface label. mri_cor2label creates a volume label (basically it just means that each label point corresponds to a 1mm3 cube instead of a verex -- the vertex numbers should all be -1). Try running vol2surf on the mask (using nearest interp) to create a surface mask. Then create a surface label with mri_cor2label using the --surf option. doug
On 4/14/13 5:01 PM, Fred Dick wrote:
Hi Doug
I've actually tried both inclusive and exclusive and have failed - just checked again in tkmedit that the label was coming up correctly and it was.
Just to double-check - the label should be in the space of the --mov, right?
Thanks!
Fred
Hi Fred, that mask is an inclusive mask, not an exclusive mask. Try inverting you mask. doug On 4/14/13 4:31 PM, Fred Dick wrote:
Dear all I am painting some higher-res anatomical data from a volume to a surface, and want to use a mask that excludes the vessels. (The same data but 1x1x1 conformed were used to create the surface). I've created a binary label in the same space >> mri_cor2label --i ./R2Mask.nii.gz --l ./R2s.label --id 1 made sure that it looks ok when I read in hi-res to tkmedit and display label, then ran mri_vol2surf >> mri_vol2surf --mov ./sPQ07082012-0009-00001-000208-01_R1.nii --regregister.dat --surf-fwhm 4 --hemi $hemi --projfrac $frac --interp trilinear --out_type w --mask R2s.label --o ./dancar-0.5-lh.w And got the output (pasted below), showing that the output is all zero. Output is fine without label, or with -cortex. I've also tried this with a conformed version of the label (also verified in tkmedit) and have had the same thing. (I thought maybe it was applying it to orig vol, which I admit would be strange).(I noticed someone had a similar issue a couple of years ago, but it involved a surface rather than volume label, and looked like it had been resolved). Am running current stable version on Mountain Lion. Thanks for any pointers, best, Fred ########################################################## masking output with label R2s.label INFO: output format is paint srcvol = ./sPQ07082012-0009-00001-000208-01_R1.nii srcreg = register.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Loading label R2s.label Reading surface /Applications/freesurfer/subjects/dancar-synth-handnorm/surf/lh.white Done reading source surface Reading thickness /Applications/freesurfer/subjects/dancar-synth-handnorm/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 108676 Surface smoothing by fwhm = 4 (n=10) Masking with R2s.label Warning: all vertex values are zeroThe 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
Hey
I wrote out to .w since I couldn't write to curv. (And I'm old fashioned!)
But actually it's because I am really behind the times and forgot that .mgh was also used for surface data. And yup, this worked fine.
So in answer to my question 'Bug or stupidity' - the latter!
Thanks Doug, Fred On 15 Apr 2013, at 17:58, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
Hi Fred, why do you want to save it as a wfile? We're trying to phase wfiles out. Can you use mgh format? doug
On 4/15/13 12:56 PM, Fred Dick wrote:
Hey again
sorry, I seem not to be able to accomplish this very simple thing!
First wrote out mask as .w file using vol2surf, but mri_cor2label couldn't read ('mri_read(): couldn't determine type of file ./rh.R2MaskBrain.w').
Then tried writing out as curv using the following command:
mri_vol2surf --mov R2MaskBrain.nii.gz --reg register.dat --hemi $hemi --interp nearest --o ./$hemi.R2MaskBrain --out_type curv --projfrac 0.5
and got this error,
################ Writing to ./lh.R2MaskBrain Dim: 152308 1 1 MRIwriteType(): code inconsistency (file type recognized but not caught) ERROR: saving ./lh.R2MaskBrain #####################
Bug, or user stupidity???
cheers, Fred
On 14 Apr 2013, at 22:56, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
Oh, the label should be a surface label. mri_cor2label creates a volume label (basically it just means that each label point corresponds to a 1mm3 cube instead of a verex -- the vertex numbers should all be -1). Try running vol2surf on the mask (using nearest interp) to create a surface mask. Then create a surface label with mri_cor2label using the --surf option. doug
On 4/14/13 5:01 PM, Fred Dick wrote:
Hi Doug
I've actually tried both inclusive and exclusive and have failed - just checked again in tkmedit that the label was coming up correctly and it was.
Just to double-check - the label should be in the space of the --mov, right?
Thanks!
Fred
Hi Fred, that mask is an inclusive mask, not an exclusive mask. Try inverting you mask. doug On 4/14/13 4:31 PM, Fred Dick wrote: Dear all
I am painting some higher-res anatomical data from a volume to a surface, and want to use a mask that excludes the vessels. (The same data but 1x1x1 conformed were used to create the surface). I've created a binary label in the same space
mri_cor2label --i ./R2Mask.nii.gz --l ./R2s.label --id 1
made sure that it looks ok when I read in hi-res to tkmedit and display label, then ran mri_vol2surf
mri_vol2surf --mov ./sPQ07082012-0009-00001-000208-01_R1.nii --regregister.dat --surf-fwhm 4 --hemi $hemi --projfrac $frac --interp trilinear --out_type w --mask R2s.label --o ./dancar-0.5-lh.w
And got the output (pasted below), showing that the output is all zero.
Output is fine without label, or with -cortex.
I've also tried this with a conformed version of the label (also verified in tkmedit) and have had the same thing. (I thought maybe it was applying it to orig vol, which I admit would be strange).(I noticed someone had a similar issue a couple of years ago, but it involved a surface rather than volume label, and looked like it had been resolved). Am running current stable version on Mountain Lion.
Thanks for any pointers,
best, Fred
########################################################## masking output with label R2s.label INFO: output format is paint srcvol = ./sPQ07082012-0009-00001-000208-01_R1.nii srcreg = register.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Loading label R2s.label Reading surface /Applications/freesurfer/subjects/dancar-synth-handnorm/surf/lh.white Done reading source surface Reading thickness /Applications/freesurfer/subjects/dancar-synth-handnorm/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 108676 Surface smoothing by fwhm = 4 (n=10) Masking with R2s.label Warning: all vertex values are zero
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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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@nmr.mgh.harvard.edu
-
Douglas Greve -
Fred Dick