Dear freesurfers,
I am trying to convert a label that I have hand drawn into tksurfer into a volume file using mri_label2volume and succeed in transforming into a volume file but the volume looks splotchy and the ends are not connected , i.e. instead of a smooth bit of cortex I get disjointed bits in the cortex.. I found a similar problem being discussed previously in the archives (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg01999.htm l) but I can't seem to find the solution to it myself.
The steps I've used are:
Draw label in tksurfer, and save it and then use the following command.
mri_label2vol --label test.label --temp norm.mgz -- reg mni152.register.dat -- proj abs 0 1 0.1 --subject --hemi lh --o test.label.mgz
When I load the resultant volume file, the surface is not smooth and there are holes in the surface. I've tried changing the delta values to quite small as well as setting the thickness at 2 with - - proj abs option, but this hasn't made things better..
Has anyone encountered this problem before and knows how to solve it ? Am I missing something in the syntax?
Thanks very much in advance,
Prapti
The problem is that mri_label2volume just does not work all that well on surface labels. Another way to do this is to create an annotation from the single label using mris_label2annot, then create a segmentation/mask volume using mri_aparc2aseg.
doug
Prapti Gautam wrote:
Dear freesurfers,
I am trying to convert a label that I have hand drawn into tksurfer into a volume file using mri_label2volume and succeed in transforming into a volume file but the volume looks splotchy and the ends are not connected , i.e. instead of a smooth bit of cortex I get disjointed bits in the cortex.. I found a similar problem being discussed previously in the archives (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg01999.html) but I can’t seem to find the solution to it myself.
The steps I’ve used are:
Draw label in tksurfer, and save it and then use the following command.
mri_label2vol --label test.label --temp norm.mgz -- reg mni152.register.dat -- proj abs 0 1 0.1 --subject --hemi lh --o test.label.mgz
When I load the resultant volume file, the surface is not smooth and there are holes in the surface. I’ve tried changing the delta values to quite small as well as setting the thickness at 2 with - - proj abs option, but this hasn’t made things better..
Has anyone encountered this problem before and knows how to solve it ? Am I missing something in the syntax?
Thanks very much in advance,
Prapti
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
Thanks for the reply. I have tried using the method you've suggested, however, I'm stuck because mri_label2annot which I use to turn my label into a annot file only works in one hemisphere while mri_aparc2aseg works for the whole brain. Do you know a work around for this?
Can I merge the annot files created from each hemisphere so that I can pass it to mri_aparc2aseg?
Thanks,
Prapti
-----Original Message----- From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Thursday, 16 September 2010 1:34 AM To: Prapti Gautam Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_label2volume issues
The problem is that mri_label2volume just does not work all that well on
surface labels. Another way to do this is to create an annotation from the single label using mris_label2annot, then create a segmentation/mask
volume using mri_aparc2aseg.
doug
Prapti Gautam wrote:
Dear freesurfers,
I am trying to convert a label that I have hand drawn into tksurfer into a volume file using mri_label2volume and succeed in transforming into a volume file but the volume looks splotchy and the ends are not connected , i.e. instead of a smooth bit of cortex I get disjointed bits in the cortex.. I found a similar problem being discussed previously in the archives
(http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg01999.htm l)
but I can't seem to find the solution to it myself.
The steps I've used are:
Draw label in tksurfer, and save it and then use the following
command.
mri_label2vol --label test.label --temp norm.mgz -- reg mni152.register.dat -- proj abs 0 1 0.1 --subject --hemi lh --o test.label.mgz
When I load the resultant volume file, the surface is not smooth and there are holes in the surface. I've tried changing the delta values to quite small as well as setting the thickness at 2 with - - proj abs
option, but this hasn't made things better..
Has anyone encountered this problem before and knows how to solve it ?
Am I missing something in the syntax?
Thanks very much in advance,
Prapti
------------------------------------------------------------------------
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Right, I see, mri_aparc2aseg is hard-coded to expect both lh and rh. The easiest thing is to make a dummy label for the other hemisphere. In the final segmentation, left hemisphere will have an index of 1000+something, the right will have 2000+something. You can then use mri_binarize with --match create a new binary volume with just your hemisphere.
doug
Prapti Gautam wrote:
Hi Doug,
Thanks for the reply. I have tried using the method you've suggested, however, I'm stuck because mri_label2annot which I use to turn my label into a annot file only works in one hemisphere while mri_aparc2aseg works for the whole brain. Do you know a work around for this?
Can I merge the annot files created from each hemisphere so that I can pass it to mri_aparc2aseg?
Thanks,
Prapti
-----Original Message----- From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Thursday, 16 September 2010 1:34 AM To: Prapti Gautam Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_label2volume issues
The problem is that mri_label2volume just does not work all that well on
surface labels. Another way to do this is to create an annotation from the single label using mris_label2annot, then create a segmentation/mask
volume using mri_aparc2aseg.
doug
Prapti Gautam wrote:
Dear freesurfers,
I am trying to convert a label that I have hand drawn into tksurfer into a volume file using mri_label2volume and succeed in transforming into a volume file but the volume looks splotchy and the ends are not connected , i.e. instead of a smooth bit of cortex I get disjointed bits in the cortex.. I found a similar problem being discussed previously in the archives
(http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg01999.htm l)
but I can't seem to find the solution to it myself.
The steps I've used are:
Draw label in tksurfer, and save it and then use the following
command.
mri_label2vol --label test.label --temp norm.mgz -- reg mni152.register.dat -- proj abs 0 1 0.1 --subject --hemi lh --o test.label.mgz
When I load the resultant volume file, the surface is not smooth and there are holes in the surface. I've tried changing the delta values to quite small as well as setting the thickness at 2 with - - proj abs
option, but this hasn't made things better..
Has anyone encountered this problem before and knows how to solve it ?
Am I missing something in the syntax?
Thanks very much in advance,
Prapti
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug, Thanks for the reply. I am sorry, I am a bit confused about what you mean by creating a dummy label. I am also not sure at which step I need to do this.
As I understand it, I use mri_label2annot to transform my label into a annotation file and this will be separate for the two hemispheres. Do I then edit these files ? where exactly do I use mri_binarize?
Thanks,
Prapti
-----Original Message----- From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Friday, 17 September 2010 12:44 AM To: Prapti Gautam Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_label2volume issues
Right, I see, mri_aparc2aseg is hard-coded to expect both lh and rh. The
easiest thing is to make a dummy label for the other hemisphere. In the final segmentation, left hemisphere will have an index of 1000+something, the right will have 2000+something. You can then use mri_binarize with --match create a new binary volume with just your hemisphere.
doug
Prapti Gautam wrote:
Hi Doug,
Thanks for the reply. I have tried using the method you've suggested, however, I'm stuck because mri_label2annot which I use to turn my
label
into a annot file only works in one hemisphere while mri_aparc2aseg works for the whole brain. Do you know a work around for this?
Can I merge the annot files created from each hemisphere so that I can pass it to mri_aparc2aseg?
Thanks,
Prapti
-----Original Message----- From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Thursday, 16 September 2010 1:34 AM To: Prapti Gautam Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_label2volume issues
The problem is that mri_label2volume just does not work all that well
on
surface labels. Another way to do this is to create an annotation from
the single label using mris_label2annot, then create a
segmentation/mask
volume using mri_aparc2aseg.
doug
Prapti Gautam wrote:
Dear freesurfers,
I am trying to convert a label that I have hand drawn into tksurfer into a volume file using mri_label2volume and succeed in transforming
into a volume file but the volume looks splotchy and the ends are not
connected , i.e. instead of a smooth bit of cortex I get disjointed bits in the cortex.. I found a similar problem being discussed previously in the archives
(http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg01999.htm
l)
but I can't seem to find the solution to it myself.
The steps I've used are:
Draw label in tksurfer, and save it and then use the following
command.
mri_label2vol --label test.label --temp norm.mgz -- reg mni152.register.dat -- proj abs 0 1 0.1 --subject --hemi lh --o test.label.mgz
When I load the resultant volume file, the surface is not smooth and there are holes in the surface. I've tried changing the delta values to quite small as well as setting the thickness at 2 with - - proj
abs
option, but this hasn't made things better..
Has anyone encountered this problem before and knows how to solve it
?
Am I missing something in the syntax?
Thanks very much in advance,
Prapti
------------------------------------------------------------------------
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Prapti Gautam