Hi,
I'd like to know where I can find a detailed description of the sub-cortical segmentation stages
thanks
Valentina
Hi Valentina,
they are described in:
Fischl B, Salat DH, van der Kouwe AJW, Makris N, Sonne F, Dale AM. Sequence-Independent Segmentation of Magnetic Resonance Images. NeuroImage 2004, 23 Suppl 1, S69-84.
Fischl B, Salat D, Busa E, Albert M, Dieterich M, Haselgrove C, van der Kouwe A, Killiany R, Kennedy D, Klaveness S, Montillo A, Makris N, Rosen B, Dale A.M.. Whole brain segmentation. Automated labeling of neuroanatomical structures in the human brain. Neuron. 2002; 33(3): 341-355
you can get reprints at:
http://www.nmr.mgh.harvard.edu/~fischl/reprints.html
cheers, Bruce
On Fri, 20 Oct 2006, Durastanti, Valentina (NIH/NINDS) [F] wrote:
Hi,
I'd like to know where I can find a detailed description of the sub-cortical segmentation stages
thanks
Valentina
Hi, I used the statistical parametric map provided by Freesurfer to evaluate the differences in mean cortical thickness and the software marked an area (in red) located under the corpus callosum, in a region the does not correspond to any of the 34 regions of the atlas (unlabeled sub-cortical region). How I have to interpreter this result? thanks Valentina
Hi Valentina,
you should ignore the noncortical regions like this one. The thickness maps are meaningless there.
cheers, Bruce
On Sun, 22 Oct 2006, Durastanti, Valentina (NIH/NINDS) [F] wrote:
Hi, I used the statistical parametric map provided by Freesurfer to evaluate the differences in mean cortical thickness and the software marked an area (in red) located under the corpus callosum, in a region the does not correspond to any of the 34 regions of the atlas (unlabeled sub-cortical region). How I have to interpreter this result? thanks Valentina
Ok, but can you explain me why it marks those regions? Just to know because I need to explain the meaning of this results and I really don't know how! thanks Valentina
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Sunday, October 22, 2006 10:50 AM To: Durastanti, Valentina (NIH/NINDS) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: regional cortical thickness
Hi Valentina,
you should ignore the noncortical regions like this one. The thickness maps are meaningless there.
cheers, Bruce
On Sun, 22 Oct 2006, Durastanti, Valentina (NIH/NINDS) [F] wrote:
Hi, I used the statistical parametric map provided by Freesurfer to
evaluate
the differences in mean cortical thickness and the software marked an area (in red) located under the corpus callosum, in a region the does not correspond to any of the 34 regions of the atlas (unlabeled sub-cortical region). How I have to interpreter this result? thanks Valentina
usually we mask them out so they are zero. What version are you using? In the most recent versions they shouldn't be an effect there, but it's something we fixed relatively recently.
On Sun, 22 Oct 2006, Durastanti, Valentina (NIH/NINDS) [F] wrote:
Ok, but can you explain me why it marks those regions? Just to know because I need to explain the meaning of this results and I really don't know how! thanks Valentina
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Sunday, October 22, 2006 10:50 AM To: Durastanti, Valentina (NIH/NINDS) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: regional cortical thickness
Hi Valentina,
you should ignore the noncortical regions like this one. The thickness maps are meaningless there.
cheers, Bruce
On Sun, 22 Oct 2006, Durastanti, Valentina (NIH/NINDS) [F] wrote:
Hi, I used the statistical parametric map provided by Freesurfer to
evaluate
the differences in mean cortical thickness and the software marked an area (in red) located under the corpus callosum, in a region the does not correspond to any of the 34 regions of the atlas (unlabeled sub-cortical region). How I have to interpreter this result? thanks Valentina
I'm using the Version 20060418 that should be the last one right?
Valentina
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Sunday, October 22, 2006 11:13 AM To: Durastanti, Valentina (NIH/NINDS) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: regional cortical thickness
usually we mask them out so they are zero. What version are you using? In the most recent versions they shouldn't be an effect there, but it's something we fixed relatively recently.
On Sun, 22 Oct 2006, Durastanti, Valentina (NIH/NINDS) [F] wrote:
Ok, but can you explain me why it marks those regions? Just to know because I need to explain the meaning of this results and I really
don't
know how! thanks Valentina
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Sunday, October 22, 2006 10:50 AM To: Durastanti, Valentina (NIH/NINDS) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: regional cortical thickness
Hi Valentina,
you should ignore the noncortical regions like this one. The thickness maps are meaningless there.
cheers, Bruce
On Sun, 22 Oct 2006, Durastanti, Valentina (NIH/NINDS) [F] wrote:
Hi, I used the statistical parametric map provided by Freesurfer to
evaluate
the differences in mean cortical thickness and the software marked an area (in red) located under the corpus callosum, in a region the does not correspond to any of the 34 regions of the atlas (unlabeled sub-cortical region). How I have to interpreter this result? thanks Valentina
What tool are you using? If mri_glmfit, you can add
--label $SUBJECTS_DIR/fsaverage/$hemi.Medial_wall.label --mask-inv
If you're using something other than fsaverage and you don't have a medial wall label, then you can create one by mapping all the labels in aparc.a2005 to label files with mri_annotation2label.
doug
On Sun, 22 Oct 2006, Durastanti, Valentina (NIH/NINDS) [F] wrote:
I'm using the Version 20060418 that should be the last one right?
Valentina
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Sunday, October 22, 2006 11:13 AM To: Durastanti, Valentina (NIH/NINDS) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: regional cortical thickness
usually we mask them out so they are zero. What version are you using? In the most recent versions they shouldn't be an effect there, but it's something we fixed relatively recently.
On Sun, 22 Oct 2006, Durastanti, Valentina (NIH/NINDS) [F] wrote:
Ok, but can you explain me why it marks those regions? Just to know because I need to explain the meaning of this results and I really
don't
know how! thanks Valentina
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Sunday, October 22, 2006 10:50 AM To: Durastanti, Valentina (NIH/NINDS) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: regional cortical thickness
Hi Valentina,
you should ignore the noncortical regions like this one. The thickness maps are meaningless there.
cheers, Bruce
On Sun, 22 Oct 2006, Durastanti, Valentina (NIH/NINDS) [F] wrote:
Hi, I used the statistical parametric map provided by Freesurfer to
evaluate
the differences in mean cortical thickness and the software marked an area (in red) located under the corpus callosum, in a region the does not correspond to any of the 34 regions of the atlas (unlabeled sub-cortical region). How I have to interpreter this result? thanks Valentina
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug, I didn't understand very well how to create a medial wall label. Where I can find I more detailed explanation? thanks
Valentina
-----Original Message----- From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Sunday, October 22, 2006 1:03 PM To: Durastanti, Valentina (NIH/NINDS) [F] Cc: Bruce Fischl; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] RE: regional cortical thickness
What tool are you using? If mri_glmfit, you can add
--label $SUBJECTS_DIR/fsaverage/$hemi.Medial_wall.label --mask-inv
If you're using something other than fsaverage and you don't have a medial wall label, then you can create one by mapping all the labels in aparc.a2005 to label files with mri_annotation2label.
doug
On Sun, 22 Oct 2006, Durastanti, Valentina (NIH/NINDS) [F] wrote:
I'm using the Version 20060418 that should be the last one right?
Valentina
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Sunday, October 22, 2006 11:13 AM To: Durastanti, Valentina (NIH/NINDS) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: regional cortical thickness
usually we mask them out so they are zero. What version are you using? In the most recent versions they shouldn't be an effect there, but it's something we fixed relatively recently.
On Sun, 22 Oct 2006, Durastanti, Valentina (NIH/NINDS) [F] wrote:
Ok, but can you explain me why it marks those regions? Just to know because I need to explain the meaning of this results and I really
don't
know how! thanks Valentina
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Sunday, October 22, 2006 10:50 AM To: Durastanti, Valentina (NIH/NINDS) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: regional cortical thickness
Hi Valentina,
you should ignore the noncortical regions like this one. The
thickness
maps are meaningless there.
cheers, Bruce
On Sun, 22 Oct 2006, Durastanti, Valentina (NIH/NINDS) [F] wrote:
Hi, I used the statistical parametric map provided by Freesurfer to
evaluate
the differences in mean cortical thickness and the software marked
an
area (in red) located under the corpus callosum, in a region the
does
not correspond to any of the 34 regions of the atlas (unlabeled sub-cortical region). How I have to interpreter this result? thanks Valentina
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
cd $subjecct/label Then run mri_annotation2label on the ?h.aparc.a2005.annot (run it with --help for more docs)
doug
On Mon, 23 Oct 2006, Durastanti, Valentina (NIH/NINDS) [F] wrote:
Hi Doug, I didn't understand very well how to create a medial wall label. Where I can find I more detailed explanation? thanks
Valentina
-----Original Message----- From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Sunday, October 22, 2006 1:03 PM To: Durastanti, Valentina (NIH/NINDS) [F] Cc: Bruce Fischl; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] RE: regional cortical thickness
What tool are you using? If mri_glmfit, you can add
--label $SUBJECTS_DIR/fsaverage/$hemi.Medial_wall.label --mask-inv
If you're using something other than fsaverage and you don't have a medial wall label, then you can create one by mapping all the labels in aparc.a2005 to label files with mri_annotation2label.
doug
On Sun, 22 Oct 2006, Durastanti, Valentina (NIH/NINDS) [F] wrote:
I'm using the Version 20060418 that should be the last one right?
Valentina
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Sunday, October 22, 2006 11:13 AM To: Durastanti, Valentina (NIH/NINDS) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: regional cortical thickness
usually we mask them out so they are zero. What version are you using? In the most recent versions they shouldn't be an effect there, but it's something we fixed relatively recently.
On Sun, 22 Oct 2006, Durastanti, Valentina (NIH/NINDS) [F] wrote:
Ok, but can you explain me why it marks those regions? Just to know because I need to explain the meaning of this results and I really
don't
know how! thanks Valentina
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Sunday, October 22, 2006 10:50 AM To: Durastanti, Valentina (NIH/NINDS) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: regional cortical thickness
Hi Valentina,
you should ignore the noncortical regions like this one. The
thickness
maps are meaningless there.
cheers, Bruce
On Sun, 22 Oct 2006, Durastanti, Valentina (NIH/NINDS) [F] wrote:
Hi, I used the statistical parametric map provided by Freesurfer to
evaluate
the differences in mean cortical thickness and the software marked
an
area (in red) located under the corpus callosum, in a region the
does
not correspond to any of the 34 regions of the atlas (unlabeled sub-cortical region). How I have to interpreter this result? thanks Valentina
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi, I sent an e-mail few days ago asking for the direction to create a medial wall label by mapping all the labels in aparc.a2005 to label files with mri_annotation2label to mask the non cortical regions on the thickness map. Can someone help me?
Thanks Valentina
Sorry, I've been in and out. Did you try mri_annotation2label ?
doug
Durastanti, Valentina (NIH/NINDS) [F] wrote:
Hi, I sent an e-mail few days ago asking for the direction to create a medial wall label by mapping all the labels in aparc.a2005 to label files with mri_annotation2label to mask the non cortical regions on the thickness map. Can someone help me?
Thanks Valentina
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Doug Greve -
Durastanti, Valentina (NIH/NINDS) [F]