RE: [Freesurfer] Re: ventral cingulate sulcus labeled 'corpuscallosum' with skull-stripped orig data
Hi, I'm using stable 3.0 with the recon-all -all command (so whichever atlas is the default for lh.aparc.annot). I'm not sure if this is what your 2nd question is asking, but the pial outlines do tend to "cross under" the orig slightly (as shown above). I kind of assumed this was normal though.
Anyway, I've looked at some more, and when I look at the orig surface I think most of ours look like the image Greg posted. Were you able to answer his question (if so, I don't think it went to the list)? Thanks,
Aaron
-----Original Message----- From: Rahul Desikan [mailto:rahul@nmr.mgh.harvard.edu] Sent: Monday, March 20, 2006 2:20 PM To: Goldman, Aaron (NIH/NIMH) [C] Cc: Greg Harris; Freesurfer Mailing List; Karl Helmer Subject: RE: [Freesurfer] Re: ventral cingulate sulcus labeled 'corpuscallosum' with skull-stripped orig data
Hi Aaron,
Which version of Freesurfer and which version of the parc atlas are you using? Also have you checked your surfaces along the midline to see if they are acting in a strange way (i.e. self-intersecting, crossing the midline, etc.)?
thanks,
Rahul
On Mon, 20 Mar 2006, Goldman, Aaron (NIH/NIMH) [C] wrote:
Hi, I think I may have observed the same issue he's talking about. What I've attached is possibly an extreme example (I haven't inspected many yet, to be honest), but it seems typical for at least a bit of this to happen in our subjects. I was also curious if the black "unknown" label was expected to extend into the temporal lobe as it does here.
Thanks,
-Aaron-
-----Original Message----- From: Rahul Desikan [mailto:rahul@nmr.mgh.harvard.edu] Sent: Saturday, March 18, 2006 5:51 PM To: Greg Harris Cc: Freesurfer Mailing List; Karl Helmer Subject: [Freesurfer] Re: ventral cingulate sulcus labeled 'corpuscallosum' with skull-stripped orig data
Hi Greg,
Could you send along jpegs or rgbs detailing what excactly the parcellation atlas is doing in the cingulate region? Also have you looked at both the white and pial surfaces in this area?
Hope you are well othwerwise,
Rahul
On Sat, 18 Mar 2006, Greg Harris wrote:
Dear Karl,
Has anybody had any success with the midline rois given by the atlas curvature.buckner40.filled.desikan_killiany that is automatically applied by autorecon3 under the newest stable release, version 3.0?
Our trouble lies in the regions labeled corpuscallosum and <anything>cingulate: this atlas is giving us a corpus callosum that is exactly the ventral cingulate sulcus, and the 4 cingulate gyrus segments, which is what we are interested in in this case, incorrectly exclude their ventral portion.
I presume this has been made to work at mgh, because Rahul Desikan's paper contains an illustration that is anatomically correctly labeled for these regions.
We are providing an orig/001.mgz image to the autorecon1 step that is talairach aligned, skull stripped, and resampled to 1.0 mm voxels, but otherwise is a signed 16-bit T1-weighted MRI scan. We have thousands of them, collected over the past 15 years. We are writing a nifti .nii file, and converting it with
mri_convert -it nii -ic 128 128 96 -oc 128 128 96 -iid -1.0 0.0 0.0 /raid1/structural/MR/9517294/0036195/10_ACPC/0036195_10_T1_brain.nii /raid1/data/methods/atlas/parcel/lobes/cloud_study/clipped_atlas_hand_masks/iowa_cortex_atlas/FreeSurfer_Subjects/IowaFifty_2005_0036195/mri/orig/001.mgz
We actually mean to numerically measure the extent -- the area and thickness, say -- of anatomical regions of interest including <anything>cingulate and apply statistical tests to these data. A line of guff about Type I and Type II errors and what is only presumable when identifying anatomical rois would be of no interest, and considered needlessly defensive. After all, the other 29 regions of Desikan's really great atlas are in working order!
Do we need to convince Rahul Desikan to release the "correct" *h.curvature.buckner40.filled.desikan_killiany.gcs files with FreeSurfer 3.0 that correspond to his paper?
Greg Harris The University of Iowa College of Medicine Psychiatry NeuroImaging Lab
Hi Aaron,
don't bother looking at the orig - look at the white and pial instead. The pial in your image looks fine.
Bruce On Tue, 21 Mar 2006, Goldman, Aaron (NIH/NIMH) [C] wrote:
Hi, I'm using stable 3.0 with the recon-all -all command (so whichever atlas is the default for lh.aparc.annot). I'm not sure if this is what your 2nd question is asking, but the pial outlines do tend to "cross under" the orig slightly (as shown above). I kind of assumed this was normal though.
Anyway, I've looked at some more, and when I look at the orig surface I think most of ours look like the image Greg posted. Were you able to answer his question (if so, I don't think it went to the list)? Thanks,
Aaron
-----Original Message----- From: Rahul Desikan [mailto:rahul@nmr.mgh.harvard.edu] Sent: Monday, March 20, 2006 2:20 PM To: Goldman, Aaron (NIH/NIMH) [C] Cc: Greg Harris; Freesurfer Mailing List; Karl Helmer Subject: RE: [Freesurfer] Re: ventral cingulate sulcus labeled 'corpuscallosum' with skull-stripped orig data
Hi Aaron,
Which version of Freesurfer and which version of the parc atlas are you using? Also have you checked your surfaces along the midline to see if they are acting in a strange way (i.e. self-intersecting, crossing the midline, etc.)?
thanks,
Rahul
On Mon, 20 Mar 2006, Goldman, Aaron (NIH/NIMH) [C] wrote:
Hi, I think I may have observed the same issue he's talking about. What I've attached is possibly an extreme example (I haven't inspected many yet, to be honest), but it seems typical for at least a bit of this to happen in our subjects. I was also curious if the black "unknown" label was expected to extend into the temporal lobe as it does here.
Thanks,
-Aaron-
-----Original Message----- From: Rahul Desikan [mailto:rahul@nmr.mgh.harvard.edu] Sent: Saturday, March 18, 2006 5:51 PM To: Greg Harris Cc: Freesurfer Mailing List; Karl Helmer Subject: [Freesurfer] Re: ventral cingulate sulcus labeled 'corpuscallosum' with skull-stripped orig data
Hi Greg,
Could you send along jpegs or rgbs detailing what excactly the parcellation atlas is doing in the cingulate region? Also have you looked at both the white and pial surfaces in this area?
Hope you are well othwerwise,
Rahul
On Sat, 18 Mar 2006, Greg Harris wrote:
Dear Karl,
Has anybody had any success with the midline rois given by the atlas curvature.buckner40.filled.desikan_killiany that is automatically applied by autorecon3 under the newest stable release, version 3.0?
Our trouble lies in the regions labeled corpuscallosum and <anything>cingulate: this atlas is giving us a corpus callosum that is exactly the ventral cingulate sulcus, and the 4 cingulate gyrus segments, which is what we are interested in in this case, incorrectly exclude their ventral portion.
I presume this has been made to work at mgh, because Rahul Desikan's paper contains an illustration that is anatomically correctly labeled for these regions.
We are providing an orig/001.mgz image to the autorecon1 step that is talairach aligned, skull stripped, and resampled to 1.0 mm voxels, but otherwise is a signed 16-bit T1-weighted MRI scan. We have thousands of them, collected over the past 15 years. We are writing a nifti .nii file, and converting it with
mri_convert -it nii -ic 128 128 96 -oc 128 128 96 -iid -1.0 0.0 0.0 /raid1/structural/MR/9517294/0036195/10_ACPC/0036195_10_T1_brain.nii /raid1/data/methods/atlas/parcel/lobes/cloud_study/clipped_atlas_hand_masks/iowa_cortex_atlas/FreeSurfer_Subjects/IowaFifty_2005_0036195/mri/orig/001.mgz
We actually mean to numerically measure the extent -- the area and thickness, say -- of anatomical regions of interest including <anything>cingulate and apply statistical tests to these data. A line of guff about Type I and Type II errors and what is only presumable when identifying anatomical rois would be of no interest, and considered needlessly defensive. After all, the other 29 regions of Desikan's really great atlas are in working order!
Do we need to convince Rahul Desikan to release the "correct" *h.curvature.buckner40.filled.desikan_killiany.gcs files with FreeSurfer 3.0 that correspond to his paper?
Greg Harris The University of Iowa College of Medicine Psychiatry NeuroImaging Lab
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Goldman, Aaron (NIH/NIMH) [C]