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

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

no, it saves the actual color table in the annot file. doug

David Grayson wrote:

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

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