Hello Freesurfers,
I have developed a pipeline that uses mri_label2vol to take freesurfer parcellations to native fmri space, and uses dilation (within mri_label2vol) to make the ROIs larger since our resolution is only 3.5x3.5x4 we would end up with only a few voxels for some ROIs due to large voxel size and partial voluming wihout the dilation. However, since the lh and rh are done separately by mri_label2vol, I now have overlap on the midline and have to go through a bunch of masking steps to eliminate it.
My question is; is there a tool that will take both lh/rh parcellations to a new coordinate system, do dilation, and most importantly control for lh/rh overlap? Or any other similar suggestions. Thanks!
Basically I am looking to rework my pipeline, and it seems I should be able to find a more parsimonious solution, than my "Rube Goldberg" approach.
Chris
Hi Chris, I don't think there is such a tool. One thing you can do is to use the aparc+aseg.mgz as the source instead of the lh and rh surfaces separately. This might solve all of your problems. doug
On 07/06/2012 12:02 PM, Christopher Bell wrote:
Hello Freesurfers,
I have developed a pipeline that uses mri_label2vol to take freesurfer parcellations to native fmri space, and uses dilation (within mri_label2vol) to make the ROIs larger since our resolution is only 3.5x3.5x4 we would end up with only a few voxels for some ROIs due to large voxel size and partial voluming wihout the dilation. However, since the lh and rh are done separately by mri_label2vol, I now have overlap on the midline and have to go through a bunch of masking steps to eliminate it.
My question is; is there a tool that will take both lh/rh parcellations to a new coordinate system, do dilation, and most importantly control for lh/rh overlap? Or any other similar suggestions. Thanks!
Basically I am looking to rework my pipeline, and it seems I should be able to find a more parsimonious solution, than my "Rube Goldberg" approach.
Chris
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I tried using mri_label2vol with --aparc+aseg instead of --aparc. This works and provides cortical and subcortical with no overlap. It doesn't allow me to do cortical dilation, but that is probably because it wouldn't mesh well with the subcortical ROIs. Thanks.
Chris
On Mon, Jul 16, 2012 at 9:03 AM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
Hi Chris, I don't think there is such a tool. One thing you can do is to use the aparc+aseg.mgz as the source instead of the lh and rh surfaces separately. This might solve all of your problems. doug
On 07/06/2012 12:02 PM, Christopher Bell wrote:
Hello Freesurfers,
I have developed a pipeline that uses mri_label2vol to take freesurfer parcellations to native fmri space, and uses dilation (within mri_label2vol) to make the ROIs larger since our resolution is only 3.5x3.5x4 we would end up with only a few voxels for some ROIs due to large voxel size and partial voluming wihout the dilation. However, since the lh and rh are done separately by mri_label2vol, I now have overlap on the midline and have to go through a bunch of masking steps to eliminate it.
My question is; is there a tool that will take both lh/rh parcellations to a new coordinate system, do dilation, and most importantly control for lh/rh overlap? Or any other similar suggestions. Thanks!
Basically I am looking to rework my pipeline, and it seems I should be able to find a more parsimonious solution, than my "Rube Goldberg" approach.
Chris
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
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.
So you want to make a particular label bigger (more surface area) on cortex? doug
On 07/16/2012 02:51 PM, Christopher Bell wrote:
I tried using mri_label2vol with --aparc+aseg instead of --aparc. This works and provides cortical and subcortical with no overlap. It doesn't allow me to do cortical dilation, but that is probably because it wouldn't mesh well with the subcortical ROIs. Thanks.
Chris
On Mon, Jul 16, 2012 at 9:03 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Hi Chris, I don't think there is such a tool. One thing you can do is to use the aparc+aseg.mgz as the source instead of the lh and rh surfaces separately. This might solve all of your problems. doug On 07/06/2012 12:02 PM, Christopher Bell wrote: > > Hello Freesurfers, > > > I have developed a pipeline that uses mri_label2vol to take freesurfer > parcellations to > native fmri space, and uses dilation (within mri_label2vol) to make > the ROIs larger since our resolution is only > 3.5x3.5x4 we would end up with only a few voxels for some ROIs due to > large voxel > size and partial voluming wihout the dilation. However, since the lh > and rh are done > separately by mri_label2vol, I now have overlap on the midline and > have to go through a bunch > of masking steps to eliminate it. > > My question is; is there a tool that will take both lh/rh > parcellations to a new coordinate > system, do dilation, and most importantly control for lh/rh overlap? > Or any other > similar suggestions. Thanks! > > Basically I am looking to rework my pipeline, and it seems I should be > able > to find a more parsimonious solution, than my "Rube Goldberg" approach. > > Chris > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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
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Douglas N Greve