Dear FS experts
When using mris_make_face_parcellation is it possible to restrict the face parcellation to a parcellation found in aparc.a2005s, e.g. to the precentral gyrus.
Or is there another way to decide which micro-parcellation produced by mris_make_face_parcellation belong to which parcellation in aparc.a2005s?
Thanks in advance Regards Jürgen
---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website)
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Hi all I am relatively unfamiliar with the structural side of analysis and am curious about how aseg.stats is created during recon. I have 2 subjects with the same ICV but volumes for other structures are different. What are the chances that this is just a coincidence and not an issue with the data? Assuming there is a mistake, how is it possible for there to be a mistake with ICV but not other structures?
Thanks, Becca
aseg.stats is created by counting the number of voxels in the aseg.mgz. Actually, it includes partial volume correction, so it won't be exactly the same as the voxel count. The ICV is an estimate only based on the talairach transform. It's hard to say why two subjects would have the same ICV. Maybe they have the same ICV or it might be an artifact of the transform. Try checking the transforms on both of them to make sure they are accurate.
doug
Rebecca Dautoff wrote:
Hi all I am relatively unfamiliar with the structural side of analysis and am curious about how aseg.stats is created during recon. I have 2 subjects with the same ICV but volumes for other structures are different. What are the chances that this is just a coincidence and not an issue with the data? Assuming there is a mistake, how is it possible for there to be a mistake with ICV but not other structures?
Thanks, Becca _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Assuming the results of -subcortseg should be corrected for whole brain volume (for group comparison or use as covariate), what number should be used: ICV, BrainSegVol, total number of voxels? Should it be obtained from an image file (e.g., aseg.mgz) or stats (e.g., aseg.stats) file?
Thank-you,
Julie
Julie E. McEntee, MA, CCRP Senior Research Program Coordinator Department of Psychiatry- Neuroimaging Johns Hopkins University School of Medicine 600 N. Wolfe St./Phipps 300 Baltimore, MD 21287 Phone: 410-502-0468 Fax: 410-614-3676
On 12/15/09 12:49 PM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
aseg.stats is created by counting the number of voxels in the aseg.mgz. Actually, it includes partial volume correction, so it won't be exactly the same as the voxel count. The ICV is an estimate only based on the talairach transform. It's hard to say why two subjects would have the same ICV. Maybe they have the same ICV or it might be an artifact of the transform. Try checking the transforms on both of them to make sure they are accurate.
doug
Rebecca Dautoff wrote:
Hi all I am relatively unfamiliar with the structural side of analysis and am curious about how aseg.stats is created during recon. I have 2 subjects with the same ICV but volumes for other structures are different. What are the chances that this is just a coincidence and not an issue with the data? Assuming there is a mistake, how is it possible for there to be a mistake with ICV but not other structures?
Thanks, Becca _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
It's probably a bit of an open question, but check out Randy Buckner's paper on ICV.
doug
Julie McEntee wrote:
Assuming the results of -subcortseg should be corrected for whole brain volume (for group comparison or use as covariate), what number should be used: ICV, BrainSegVol, total number of voxels? Should it be obtained from an image file (e.g., aseg.mgz) or stats (e.g., aseg.stats) file?
Thank-you,
Julie
Julie E. McEntee, MA, CCRP Senior Research Program Coordinator Department of Psychiatry- Neuroimaging Johns Hopkins University School of Medicine 600 N. Wolfe St./Phipps 300 Baltimore, MD 21287 Phone: 410-502-0468 Fax: 410-614-3676
On 12/15/09 12:49 PM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
aseg.stats is created by counting the number of voxels in the aseg.mgz. Actually, it includes partial volume correction, so it won't be exactly the same as the voxel count. The ICV is an estimate only based on the talairach transform. It's hard to say why two subjects would have the same ICV. Maybe they have the same ICV or it might be an artifact of the transform. Try checking the transforms on both of them to make sure they are accurate.
doug
Rebecca Dautoff wrote:
Hi all I am relatively unfamiliar with the structural side of analysis and am curious about how aseg.stats is created during recon. I have 2 subjects with the same ICV but volumes for other structures are different. What are the chances that this is just a coincidence and not an issue with the data? Assuming there is a mistake, how is it possible for there to be a mistake with ICV but not other structures?
Thanks, Becca _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Jurgen,
you might try using mris_divide_parcellation instead, which divides up a specified set of annotation units (if you give it a configuration file).
cheers Bruce On Tue, 15 Dec 2009, Jürgen Hänggi wrote:
Dear FS experts
When using mris_make_face_parcellation is it possible to restrict the face parcellation to a parcellation found in aparc.a2005s, e.g. to the precentral gyrus.
Or is there another way to decide which micro-parcellation produced by mris_make_face_parcellation belong to which parcellation in aparc.a2005s?
Thanks in advance Regards Jürgen
Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website)
This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden.
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Rebecca Dautoff