Re: [Freesurfer] propagating labels to gray matter
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:gr...@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:gr...@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:gr...@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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] propagating labels to gray matter
Hi David, an easy way is to load the segmentation as both a segmentation and as the auxiliary volume (not aux segmentation). When you click on a point, you'll see the number of the segmentation in the aux field of the control window. doug David Grayson wrote: Hi Doug, I made good progress based on your suggestion of using mri_aparc2aseg. The last piece is that I need to understand what the index values of my output volume file correspond to. Here's the command I used: mri_aparc2aseg --s subID --annot myaparc --o TEST.nii.gz Although I did notice that the index values in TEST.nii.gz for the cortical ROIs in the RH are just above 2000, and just above 1000 for the LH, the values don't seem to match the labels in FreeSurferColorLUT.txt. Then again, that makes sense, because this is a custom label set, so they don't really exist in FreeSurferColorLUT.txt. How can I learn more about how the index values are being assigned? Thanks very much for your help, David P.S. I don't know if it will work, but I attached the aparc and volume files if it's necessary for you to look that those -Original Message- From: Douglas Greve [mailto:gr...@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:gr...@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:gr...@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. -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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
Re: [Freesurfer] propagating labels to gray matter
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:gr...@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:gr...@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:gr...@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. -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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
[Freesurfer] propagating labels to gray matter
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.
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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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.
Re: [Freesurfer] propagating labels to gray matter
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:gr...@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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 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
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:gr...@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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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.
Re: [Freesurfer] propagating labels to gray matter
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:gr...@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:gr...@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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 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
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:gr...@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:gr...@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 ___ 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.
