One more thing I noticed... When I run mri_anatomical_stats on the annot file, it tells me this:
reading colortable from annotation file... colortable with 207 entries read (originally /home/leila/freesurfer/mycolortables/original_color_P1_16_R.txt)
I don't find this txt file anywhere though. Is this important?
Thanks,
David
-----Original Message----- From: Douglas Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Monday, October 31, 2011 7:40 PM To: David Grayson Cc: 'freesurfer@nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] propagating labels to gray matter
Hi David, you can use mri_label2vol with the --proj option. This works ok, but it is often not great. Another way (the way that aparc+aseg) is created is to convert your label into an annotation, then use mri_aparc2aseg.
doug
On 10/31/11 7:22 PM, David Grayson wrote:
Hi Doug,
Although in principle, yes this is the idea, we have a set of labels that aren't actually in the aparc+aseg file (basically a set of high-density subdivisions of those regions). The only problem is that the labels I have are just in "surface-land." I am wondering, once I have the surface labels, is there a way to re-propagate them back into the gray matter?
Thanks again,
David
-----Original Message----- From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Monday, October 31, 2011 2:38 PM To: David Grayson Cc: 'freesurfer@nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] propagating labels to gray matter
Do you just want the label in the orig volume space? If so, just use the labels in aparc+aseg.mgz doug
David Grayson wrote:
Hi Doug,
/path/to/FREESURFER/label/regenerated_lh_36$ mri_label2vol --label lh.bankssts.label --temp ../../mri/orig.mgz --identity --o TEST.nii.gz
Thanks,
David
-----Original Message----- From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Monday, October 31, 2011 2:04 PM To: David Grayson Cc: 'freesurfer@nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] propagating labels to gray matter
what was your label2vol command line? doug
David Grayson wrote:
Hi freesurfer experts,
I currently have a set of cortical labels that are the result of a high-resolution parcellation of the standard aparc.annot labels (via the ‘connectomemapper’ software). I would like to extract the gray matter ROIs that correspond to these labels, and I understand that this requires a method to ‘propagate’ these labels through the gray matter. I have so far been unsuccessful – ‘mri_label2vol’ seems to only give me that pial or white surfaces, as opposed to the gray matter bodies. Does anyone know how to accomplish this?
Thank you very much,
David Grayson
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.