After reading the paper I am still a little confused about how the Subcortical Parcellation labels the parasingulate gyri when some people have one and others have two? Can anyone shed a little light on this issue?
-Eric
Presumably you mean cortical parcellation? It depends on whether the variant is represented in the training set. It certainly can label it properly as the prior will label it as ambiguous but the geometry will distinguish it.
cheers, Bruce
On Wed, 21 Dec 2005, Faden, Eric (NIH/NIMH) [F] wrote:
After reading the paper I am still a little confused about how the Subcortical Parcellation labels the parasingulate gyri when some people have one and others have two? Can anyone shed a little light on this issue?
-Eric
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi all,
From my understanding, ?h.sulc can be used to measure sulcal depth.
I'm wandering if it is possible to use this to get the depth of a sulcus within an ROI, and if so, how you would extract the relevant measures, i.e.., would it be obtainable through mris_anatomical_stats? Thanks, Alex
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au
________________________________
not all that easily, although I guess we could write out something from mris_inflate that has the units of mm.
On Fri, 23 Dec 2005, Fornito, Alexander wrote:
Hi all,
From my understanding, ?h.sulc can be used to measure sulcal depth.
I'm wandering if it is possible to use this to get the depth of a sulcus within an ROI, and if so, how you would extract the relevant measures, i.e.., would it be obtainable through mris_anatomical_stats? Thanks, Alex
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
What it require a lot of work? What would be the odds of somehting like that happening in the near future? :)
On another issue, if the .sulc file encodes dinsitguises between sulcal and gyral regions with positive and negative signs, is it possible to extract the thickness of sulcal and gyral regions separately? I remember seeing a posting about this some time ago, bu can't seem to find it again.
Thanks again.
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Fri 23/12/2005 9:30 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Sulcal depth
not all that easily, although I guess we could write out something from mris_inflate that has the units of mm.
On Fri, 23 Dec 2005, Fornito, Alexander wrote:
Hi all,
From my understanding, ?h.sulc can be used to measure sulcal depth.
I'm wandering if it is possible to use this to get the depth of a sulcus within an ROI, and if so, how you would extract the relevant measures, i.e.., would it be obtainable through mris_anatomical_stats? Thanks, Alex
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
you might be able to use mri_segstats. Give it the thickness file as --in, and use the sulc as the mask and use a threshold of 0 (or close to 0). Note, you might have to convert the thickness and sulc from curv format to mgh (use mri_surf2surf).
doug
What it require a lot of work? What would be the odds of somehting like that happening in the near future? :)
On another issue, if the .sulc file encodes dinsitguises between sulcal and gyral regions with positive and negative signs, is it possible to extract the thickness of sulcal and gyral regions separately? I remember seeing a posting about this some time ago, bu can't seem to find it again.
Thanks again.
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Fri 23/12/2005 9:30 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Sulcal depth
not all that easily, although I guess we could write out something from mris_inflate that has the units of mm.
On Fri, 23 Dec 2005, Fornito, Alexander wrote:
Hi all,
From my understanding, ?h.sulc can be used to measure sulcal depth.
I'm wandering if it is possible to use this to get the depth of a sulcus within an ROI, and if so, how you would extract the relevant measures, i.e.., would it be obtainable through mris_anatomical_stats? Thanks, Alex
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au
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
Hi Doug, I tried what you suggested but don't think sure I've got it right. I'm trying to extract thickness for gyri and sulci separately in labels that I have created and saved as an annotation. I began by using mri_surf2surf to convert the thickness and sulc files to mgh - no errors, although trying to load either in tkmedit just brings up a straight, coloured line running ear to ear (not sure if this is what to expect) . I then comverted the annot file to mgh using mri_label2vol - seemed ok (although one of the labels in the annot did not seem to appear in the resulting volume). I then ran mri_segstats and got the following:
mri_segstats --seg annot_vol.mgh --sum ./annot_stats.txt --in 1000001_thickness_conv.mgh --ctab /usr/local/freesurfer-dev20050905/alex_ACC_colour_LUT.txt --mask 1000001_sulc_conv.mgh --masksign pos Loading annot_vol.mgh Loading 1000001_thickness_conv.mgh Loading 1000001_sulc_conv.mgh NOT INVERTING There were 28632 voxels in the mask Segmentation fault
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au
-----Original Message----- From: greve@nmr.mgh.harvard.edu [mailto:greve@nmr.mgh.harvard.edu] Sent: Fri 23/12/2005 10:33 AM To: Fornito, Alexander Cc: Bruce Fischl; freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Sulcal depth
you might be able to use mri_segstats. Give it the thickness file as --in, and use the sulc as the mask and use a threshold of 0 (or close to 0). Note, you might have to convert the thickness and sulc from curv format to mgh (use mri_surf2surf).
doug
What it require a lot of work? What would be the odds of somehting like that happening in the near future? :)
On another issue, if the .sulc file encodes dinsitguises between sulcal and gyral regions with positive and negative signs, is it possible to extract the thickness of sulcal and gyral regions separately? I remember seeing a posting about this some time ago, bu can't seem to find it again.
Thanks again.
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Fri 23/12/2005 9:30 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Sulcal depth
not all that easily, although I guess we could write out something from mris_inflate that has the units of mm.
On Fri, 23 Dec 2005, Fornito, Alexander wrote:
Hi all,
From my understanding, ?h.sulc can be used to measure sulcal depth.
I'm wandering if it is possible to use this to get the depth of a sulcus within an ROI, and if so, how you would extract the relevant measures, i.e.., would it be obtainable through mris_anatomical_stats? Thanks, Alex
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au
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
sure, just sum them separately. Would be easy to do in matlab (we did it in our PNAS thickness paper) On Fri, 23 Dec 2005, Fornito, Alexander wrote:
What it require a lot of work? What would be the odds of somehting like that happening in the near future? :)
On another issue, if the .sulc file encodes dinsitguises between sulcal and gyral regions with positive and negative signs, is it possible to extract the thickness of sulcal and gyral regions separately? I remember seeing a posting about this some time ago, bu can't seem to find it again.
Thanks again.
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Fri 23/12/2005 9:30 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Sulcal depth
not all that easily, although I guess we could write out something from mris_inflate that has the units of mm.
On Fri, 23 Dec 2005, Fornito, Alexander wrote:
Hi all,
From my understanding, ?h.sulc can be used to measure sulcal depth.
I'm wandering if it is possible to use this to get the depth of a sulcus within an ROI, and if so, how you would extract the relevant measures, i.e.., would it be obtainable through mris_anatomical_stats? Thanks, Alex
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Famous last words, but seems simple enough. Will give it a try. Would just like to clarify what the columns represent in curvature files after converting to ascii: The first volumn is the vertx id. The next three columns are the xyz co-ords. The rightmost column is the actual 'curvature value', e.g., in thickness file, it's the thickness associated with that vertex, in the sulc file, it's the integrated the distnace the node moves during inflation, etc.. In which case, for extracting sulcal and gyral regions separately, I'd need to split vertices based on the sign of the final column in the sulc file.
Another question: are the xyz coords talairach or native coords? They're not surface coords are they? I would've thought surface coords would be in 2D (although I have been known to get it completely wrong form time to time!).
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Fri 23/12/2005 10:36 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Sulcal depth
sure, just sum them separately. Would be easy to do in matlab (we did it in our PNAS thickness paper) On Fri, 23 Dec 2005, Fornito, Alexander wrote:
What it require a lot of work? What would be the odds of somehting like that happening in the near future? :)
On another issue, if the .sulc file encodes dinsitguises between sulcal and gyral regions with positive and negative signs, is it possible to extract the thickness of sulcal and gyral regions separately? I remember seeing a posting about this some time ago, bu can't seem to find it again.
Thanks again.
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Fri 23/12/2005 9:30 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Sulcal depth
not all that easily, although I guess we could write out something from mris_inflate that has the units of mm.
On Fri, 23 Dec 2005, Fornito, Alexander wrote:
Hi all,
From my understanding, ?h.sulc can be used to measure sulcal depth.
I'm wandering if it is possible to use this to get the depth of a sulcus within an ROI, and if so, how you would extract the relevant measures, i.e.., would it be obtainable through mris_anatomical_stats? Thanks, Alex
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I think they are volume RAS coords, with 0,0,0 at the center of the volume. I think we distribute a read_label.m or load_label.m that can read it into matlab.
On Fri, 23 Dec 2005, Fornito, Alexander wrote:
Famous last words, but seems simple enough. Will give it a try. Would just like to clarify what the columns represent in curvature files after converting to ascii: The first volumn is the vertx id. The next three columns are the xyz co-ords. The rightmost column is the actual 'curvature value', e.g., in thickness file, it's the thickness associated with that vertex, in the sulc file, it's the integrated the distnace the node moves during inflation, etc.. In which case, for extracting sulcal and gyral regions separately, I'd need to split vertices based on the sign of the final column in the sulc file.
Another question: are the xyz coords talairach or native coords? They're not surface coords are they? I would've thought surface coords would be in 2D (although I have been known to get it completely wrong form time to time!).
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Fri 23/12/2005 10:36 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Sulcal depth
sure, just sum them separately. Would be easy to do in matlab (we did it in our PNAS thickness paper) On Fri, 23 Dec 2005, Fornito, Alexander wrote:
What it require a lot of work? What would be the odds of somehting like that happening in the near future? :)
On another issue, if the .sulc file encodes dinsitguises between sulcal and gyral regions with positive and negative signs, is it possible to extract the thickness of sulcal and gyral regions separately? I remember seeing a posting about this some time ago, bu can't seem to find it again.
Thanks again.
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Fri 23/12/2005 9:30 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Sulcal depth
not all that easily, although I guess we could write out something from mris_inflate that has the units of mm.
On Fri, 23 Dec 2005, Fornito, Alexander wrote:
Hi all,
From my understanding, ?h.sulc can be used to measure sulcal depth.
I'm wandering if it is possible to use this to get the depth of a sulcus within an ROI, and if so, how you would extract the relevant measures, i.e.., would it be obtainable through mris_anatomical_stats? Thanks, Alex
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
So, read_label could be used to load the label in, and then that could be used to pull out the relevant vertices from the .thickness and .sulc files? Also, is there a straightforward way of converting the final column in the .sulc file into mm (as in mm sulcal depth)?
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Fri 23/12/2005 11:29 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Sulcal depth
I think they are volume RAS coords, with 0,0,0 at the center of the volume. I think we distribute a read_label.m or load_label.m that can read it into matlab.
On Fri, 23 Dec 2005, Fornito, Alexander wrote:
Famous last words, but seems simple enough. Will give it a try. Would just like to clarify what the columns represent in curvature files after converting to ascii: The first volumn is the vertx id. The next three columns are the xyz co-ords. The rightmost column is the actual 'curvature value', e.g., in thickness file, it's the thickness associated with that vertex, in the sulc file, it's the integrated the distnace the node moves during inflation, etc.. In which case, for extracting sulcal and gyral regions separately, I'd need to split vertices based on the sign of the final column in the sulc file.
Another question: are the xyz coords talairach or native coords? They're not surface coords are they? I would've thought surface coords would be in 2D (although I have been known to get it completely wrong form time to time!).
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Fri 23/12/2005 10:36 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Sulcal depth
sure, just sum them separately. Would be easy to do in matlab (we did it in our PNAS thickness paper) On Fri, 23 Dec 2005, Fornito, Alexander wrote:
What it require a lot of work? What would be the odds of somehting like that happening in the near future? :)
On another issue, if the .sulc file encodes dinsitguises between sulcal and gyral regions with positive and negative signs, is it possible to extract the thickness of sulcal and gyral regions separately? I remember seeing a posting about this some time ago, bu can't seem to find it again.
Thanks again.
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Fri 23/12/2005 9:30 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Sulcal depth
not all that easily, although I guess we could write out something from mris_inflate that has the units of mm.
On Fri, 23 Dec 2005, Fornito, Alexander wrote:
Hi all,
From my understanding, ?h.sulc can be used to measure sulcal depth.
I'm wandering if it is possible to use this to get the depth of a sulcus within an ROI, and if so, how you would extract the relevant measures, i.e.., would it be obtainable through mris_anatomical_stats? Thanks, Alex
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
not as is, sorry On Fri, 23 Dec 2005, Fornito, Alexander wrote:
So, read_label could be used to load the label in, and then that could be used to pull out the relevant vertices from the .thickness and .sulc files? Also, is there a straightforward way of converting the final column in the .sulc file into mm (as in mm sulcal depth)?
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Fri 23/12/2005 11:29 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Sulcal depth
I think they are volume RAS coords, with 0,0,0 at the center of the volume. I think we distribute a read_label.m or load_label.m that can read it into matlab.
On Fri, 23 Dec 2005, Fornito, Alexander wrote:
Famous last words, but seems simple enough. Will give it a try. Would just like to clarify what the columns represent in curvature files after converting to ascii: The first volumn is the vertx id. The next three columns are the xyz co-ords. The rightmost column is the actual 'curvature value', e.g., in thickness file, it's the thickness associated with that vertex, in the sulc file, it's the integrated the distnace the node moves during inflation, etc.. In which case, for extracting sulcal and gyral regions separately, I'd need to split vertices based on the sign of the final column in the sulc file.
Another question: are the xyz coords talairach or native coords? They're not surface coords are they? I would've thought surface coords would be in 2D (although I have been known to get it completely wrong form time to time!).
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Fri 23/12/2005 10:36 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Sulcal depth
sure, just sum them separately. Would be easy to do in matlab (we did it in our PNAS thickness paper) On Fri, 23 Dec 2005, Fornito, Alexander wrote:
What it require a lot of work? What would be the odds of somehting like that happening in the near future? :)
On another issue, if the .sulc file encodes dinsitguises between sulcal and gyral regions with positive and negative signs, is it possible to extract the thickness of sulcal and gyral regions separately? I remember seeing a posting about this some time ago, bu can't seem to find it again.
Thanks again.
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Fri 23/12/2005 9:30 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Sulcal depth
not all that easily, although I guess we could write out something from mris_inflate that has the units of mm.
On Fri, 23 Dec 2005, Fornito, Alexander wrote:
Hi all,
From my understanding, ?h.sulc can be used to measure sulcal depth.
I'm wandering if it is possible to use this to get the depth of a sulcus within an ROI, and if so, how you would extract the relevant measures, i.e.., would it be obtainable through mris_anatomical_stats? Thanks, Alex
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Faden, Eric (NIH/NIMH) [F] -
Fornito, Alexander -
greve＠nmr.mgh.harvard.edu