I'd like to retrieve information wrt XYZ coordinates of vertices within aparc labels.
I have tried the following command: [<subjid>] $ mri_annotation2label --subject EC --hemi lh --outdir ./test_labels --table ../../surface_labels.txt --annotation aparc.a2005s
A total of 57 labels are returned (expecting 94 after looking at the surface_labels.txt file?)
Reading a single label file [test_labels] $ more lh.S_temporalis_transveralis.label
Returns the following structure #!ascii label , from subject EC 394 64599 -35.192 -31.784 11.805 0.000000 64600 -35.842 -31.799 11.554 0.000000 ....etc
1) What is the name & location of the table file I should be specifying to return all 94 labels? Or do I need to include additional flags in my command line? 2) How are the columns ordered within each output file generated by the mri_annotation2label command?
I'm running FSv3.0.5 on linux (Centos 4). The table specified in the wiki help pages (Simple_surface_labels.txt) does not appear to be located in my $FREESURFER_HOME directory...instead, the file <surface_labels.txt> appears in my $FREESURFER_HOME dir.
Many Thanks, Jenifer
Hi Jennifer,
do you need a table file? I thought not, since the color table is embedded in the .annot file. If you give it an output directory it should extract a label for every different structure in the .annot file. The label file columns are:
<1> vertex index <2>-<5> surface RAS coordinates of the vertex, I believe from the orig surface (could be white, I'm not positive) <6> a slot to assocate a statistic with that vertex (e.g. fMRI p-value)
Does that answer your questions? I'm not sure...
cheers, Bruce
On Mon, 1 Oct 2007, Juranek, Jenifer wrote:
I'd like to retrieve information wrt XYZ coordinates of vertices within aparc labels.
I have tried the following command: [<subjid>] $ mri_annotation2label --subject EC --hemi lh --outdir ./test_labels --table ../../surface_labels.txt --annotation aparc.a2005s
A total of 57 labels are returned (expecting 94 after looking at the surface_labels.txt file?)
Reading a single label file [test_labels] $ more lh.S_temporalis_transveralis.label
Returns the following structure #!ascii label , from subject EC 394 64599 -35.192 -31.784 11.805 0.000000 64600 -35.842 -31.799 11.554 0.000000 ....etc
- What is the name & location of the table file I should be specifying
to return all 94 labels? Or do I need to include additional flags in my command line? 2) How are the columns ordered within each output file generated by the mri_annotation2label command?
I'm running FSv3.0.5 on linux (Centos 4). The table specified in the wiki help pages (Simple_surface_labels.txt) does not appear to be located in my $FREESURFER_HOME directory...instead, the file <surface_labels.txt> appears in my $FREESURFER_HOME dir.
Many Thanks, Jenifer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Bruce, Many thanks for the information. Yes, I'd like a table file for each aparc label in each hemisphere. Whether the annotation file is the ?h.aparc.a2005s.annot variety or the ?h.aparc.annot variety is not crucial at this point.
My goal is to map the XYZ vertex coordinates for each aparc label back to the scanner XYZ coordinates. Is this possible?
Jenifer
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Monday, October 01, 2007 10:25 AM To: Juranek, Jenifer Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] XYZ coordinates of vertices within aparc labels
Hi Jennifer,
do you need a table file? I thought not, since the color table is embedded in the .annot file. If you give it an output directory it should extract a label for every different structure in the .annot file. The label file columns are:
<1> vertex index <2>-<5> surface RAS coordinates of the vertex, I believe from the orig surface (could be white, I'm not positive) <6> a slot to assocate a statistic with that vertex (e.g. fMRI p-value)
Does that answer your questions? I'm not sure...
cheers, Bruce
On Mon, 1 Oct 2007, Juranek, Jenifer wrote:
I'd like to retrieve information wrt XYZ coordinates of vertices
within
aparc labels.
I have tried the following command: [<subjid>] $ mri_annotation2label --subject EC --hemi lh --outdir ./test_labels --table ../../surface_labels.txt --annotation aparc.a2005s
A total of 57 labels are returned (expecting 94 after looking at the surface_labels.txt file?)
Reading a single label file [test_labels] $ more lh.S_temporalis_transveralis.label
Returns the following structure #!ascii label , from subject EC 394 64599 -35.192 -31.784 11.805 0.000000 64600 -35.842 -31.799 11.554 0.000000 ....etc
- What is the name & location of the table file I should be
specifying
to return all 94 labels? Or do I need to include additional flags in
my
command line? 2) How are the columns ordered within each output file generated by
the
mri_annotation2label command?
I'm running FSv3.0.5 on linux (Centos 4). The table specified in the wiki help pages (Simple_surface_labels.txt) does not appear to be located in my $FREESURFER_HOME directory...instead, the file <surface_labels.txt> appears in my $FREESURFER_HOME dir.
Many Thanks, Jenifer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
yes, I think Doug has documented how to do this on our wiki. Doug: can you point jenifer at the right place?
thanks, Bruce
On Mon, 1 Oct 2007, Juranek, Jenifer wrote:
Hi Bruce, Many thanks for the information. Yes, I'd like a table file for each aparc label in each hemisphere. Whether the annotation file is the ?h.aparc.a2005s.annot variety or the ?h.aparc.annot variety is not crucial at this point.
My goal is to map the XYZ vertex coordinates for each aparc label back to the scanner XYZ coordinates. Is this possible?
Jenifer
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Monday, October 01, 2007 10:25 AM To: Juranek, Jenifer Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] XYZ coordinates of vertices within aparc labels
Hi Jennifer,
do you need a table file? I thought not, since the color table is embedded in the .annot file. If you give it an output directory it should extract a label for every different structure in the .annot file. The label file columns are:
<1> vertex index <2>-<5> surface RAS coordinates of the vertex, I believe from the orig surface (could be white, I'm not positive) <6> a slot to assocate a statistic with that vertex (e.g. fMRI p-value)
Does that answer your questions? I'm not sure...
cheers, Bruce
On Mon, 1 Oct 2007, Juranek, Jenifer wrote:
I'd like to retrieve information wrt XYZ coordinates of vertices
within
aparc labels.
I have tried the following command: [<subjid>] $ mri_annotation2label --subject EC --hemi lh --outdir ./test_labels --table ../../surface_labels.txt --annotation aparc.a2005s
A total of 57 labels are returned (expecting 94 after looking at the surface_labels.txt file?)
Reading a single label file [test_labels] $ more lh.S_temporalis_transveralis.label
Returns the following structure #!ascii label , from subject EC 394 64599 -35.192 -31.784 11.805 0.000000 64600 -35.842 -31.799 11.554 0.000000 ....etc
- What is the name & location of the table file I should be
specifying
to return all 94 labels? Or do I need to include additional flags in
my
command line? 2) How are the columns ordered within each output file generated by
the
mri_annotation2label command?
I'm running FSv3.0.5 on linux (Centos 4). The table specified in the wiki help pages (Simple_surface_labels.txt) does not appear to be located in my $FREESURFER_HOME directory...instead, the file <surface_labels.txt> appears in my $FREESURFER_HOME dir.
Many Thanks, Jenifer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I don't have code to do it, but you can look at this doc:
https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems?action=AttachFil...
which explains how to get back to scanner coords
doug
Bruce Fischl wrote:
yes, I think Doug has documented how to do this on our wiki. Doug: can you point jenifer at the right place?
thanks, Bruce
On Mon, 1 Oct 2007, Juranek, Jenifer wrote:
Hi Bruce, Many thanks for the information. Yes, I'd like a table file for each aparc label in each hemisphere. Whether the annotation file is the ?h.aparc.a2005s.annot variety or the ?h.aparc.annot variety is not crucial at this point.
My goal is to map the XYZ vertex coordinates for each aparc label back to the scanner XYZ coordinates. Is this possible?
Jenifer
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Monday, October 01, 2007 10:25 AM To: Juranek, Jenifer Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] XYZ coordinates of vertices within aparc labels
Hi Jennifer,
do you need a table file? I thought not, since the color table is embedded in the .annot file. If you give it an output directory it should extract a label for every different structure in the .annot file. The label file columns are:
<1> vertex index <2>-<5> surface RAS coordinates of the vertex, I believe from the orig surface (could be white, I'm not positive) <6> a slot to assocate a statistic with that vertex (e.g. fMRI p-value)
Does that answer your questions? I'm not sure...
cheers, Bruce
On Mon, 1 Oct 2007, Juranek, Jenifer wrote:
I'd like to retrieve information wrt XYZ coordinates of vertices
within
aparc labels.
I have tried the following command: [<subjid>] $ mri_annotation2label --subject EC --hemi lh --outdir ./test_labels --table ../../surface_labels.txt --annotation aparc.a2005s
A total of 57 labels are returned (expecting 94 after looking at the surface_labels.txt file?)
Reading a single label file [test_labels] $ more lh.S_temporalis_transveralis.label
Returns the following structure #!ascii label , from subject EC 394 64599 -35.192 -31.784 11.805 0.000000 64600 -35.842 -31.799 11.554 0.000000 ....etc
- What is the name & location of the table file I should be
specifying
to return all 94 labels? Or do I need to include additional flags in
my
command line? 2) How are the columns ordered within each output file generated by
the
mri_annotation2label command?
I'm running FSv3.0.5 on linux (Centos 4). The table specified in the wiki help pages (Simple_surface_labels.txt) does not appear to be located in my $FREESURFER_HOME directory...instead, the file <surface_labels.txt> appears in my $FREESURFER_HOME dir.
Many Thanks, Jenifer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks again for the info. However, I'm still not sure how to get an ascii file for each aparc label listing the vertex index, and the RAS coordinates (surface RAS is fine since I can use the fscoordinates.pdf and the wikipage on Coordinate systems to get back to vol coordinates and eventually scanner coordinates.)
Any suggestions how to access this information? From the help pages, I thought mri_annotation2label would do the trick...
Jenifer
-----Original Message----- From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Monday, October 01, 2007 1:05 PM To: Bruce Fischl Cc: Juranek, Jenifer ; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] XYZ coordinates of vertices within aparc labels
I don't have code to do it, but you can look at this doc:
https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems?action=Attac hFile&do=get&target=fscoordinates.pdf
which explains how to get back to scanner coords
doug
Bruce Fischl wrote:
yes, I think Doug has documented how to do this on our wiki. Doug: can
you point jenifer at the right place?
thanks, Bruce
On Mon, 1 Oct 2007, Juranek, Jenifer wrote:
Hi Bruce, Many thanks for the information. Yes, I'd like a table file for each aparc label in each hemisphere. Whether the annotation file is the ?h.aparc.a2005s.annot variety or
the
?h.aparc.annot variety is not crucial at this point.
My goal is to map the XYZ vertex coordinates for each aparc label
back
to the scanner XYZ coordinates. Is this possible?
Jenifer
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Monday, October 01, 2007 10:25 AM To: Juranek, Jenifer Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] XYZ coordinates of vertices within aparc labels
Hi Jennifer,
do you need a table file? I thought not, since the color table is embedded in the .annot file. If you give it an output directory it should extract a label for every different structure in the .annot file. The label file columns are:
<1> vertex index <2>-<5> surface RAS coordinates of the vertex, I believe from the
orig
surface (could be white, I'm not positive)<6> a slot to assocate a statistic with that vertex (e.g. fMRI
p-value)
Does that answer your questions? I'm not sure...
cheers, Bruce
On Mon, 1 Oct 2007, Juranek, Jenifer wrote:
I'd like to retrieve information wrt XYZ coordinates of vertices
within
aparc labels.
I have tried the following command: [<subjid>] $ mri_annotation2label --subject EC --hemi lh --outdir ./test_labels --table ../../surface_labels.txt --annotation aparc.a2005s
A total of 57 labels are returned (expecting 94 after looking at the surface_labels.txt file?)
Reading a single label file [test_labels] $ more lh.S_temporalis_transveralis.label
Returns the following structure #!ascii label , from subject EC 394 64599 -35.192 -31.784 11.805 0.000000 64600 -35.842 -31.799 11.554 0.000000 ....etc
- What is the name & location of the table file I should be
specifying
to return all 94 labels? Or do I need to include additional flags in
my
command line? 2) How are the columns ordered within each output file generated by
the
mri_annotation2label command?
I'm running FSv3.0.5 on linux (Centos 4). The table specified in the wiki help pages
(Simple_surface_labels.txt)
does not appear to be located in my $FREESURFER_HOME directory...instead, the file <surface_labels.txt> appears in my $FREESURFER_HOME dir.
Many Thanks, Jenifer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
use mri_annotation2label to create a text label file for each annotation. These have the surface xyz in them.
doug
Juranek, Jenifer wrote:
Thanks again for the info. However, I'm still not sure how to get an ascii file for each aparc label listing the vertex index, and the RAS coordinates (surface RAS is fine since I can use the fscoordinates.pdf and the wikipage on Coordinate systems to get back to vol coordinates and eventually scanner coordinates.)
Any suggestions how to access this information? From the help pages, I thought mri_annotation2label would do the trick...
Jenifer
-----Original Message----- From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Monday, October 01, 2007 1:05 PM To: Bruce Fischl Cc: Juranek, Jenifer ; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] XYZ coordinates of vertices within aparc labels
I don't have code to do it, but you can look at this doc:
https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems?action=Attac hFile&do=get&target=fscoordinates.pdf
which explains how to get back to scanner coords
doug
Bruce Fischl wrote:
yes, I think Doug has documented how to do this on our wiki. Doug: can
you point jenifer at the right place?
thanks, Bruce
On Mon, 1 Oct 2007, Juranek, Jenifer wrote:
Hi Bruce, Many thanks for the information. Yes, I'd like a table file for each aparc label in each hemisphere. Whether the annotation file is the ?h.aparc.a2005s.annot variety or
the
?h.aparc.annot variety is not crucial at this point.
My goal is to map the XYZ vertex coordinates for each aparc label
back
to the scanner XYZ coordinates. Is this possible?
Jenifer
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Monday, October 01, 2007 10:25 AM To: Juranek, Jenifer Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] XYZ coordinates of vertices within aparc labels
Hi Jennifer,
do you need a table file? I thought not, since the color table is embedded in the .annot file. If you give it an output directory it should extract a label for every different structure in the .annot file. The label file columns are:
<1> vertex index <2>-<5> surface RAS coordinates of the vertex, I believe from the
orig
surface (could be white, I'm not positive)<6> a slot to assocate a statistic with that vertex (e.g. fMRI
p-value)
Does that answer your questions? I'm not sure...
cheers, Bruce
On Mon, 1 Oct 2007, Juranek, Jenifer wrote:
I'd like to retrieve information wrt XYZ coordinates of vertices
within
aparc labels.
I have tried the following command: [<subjid>] $ mri_annotation2label --subject EC --hemi lh --outdir ./test_labels --table ../../surface_labels.txt --annotation aparc.a2005s
A total of 57 labels are returned (expecting 94 after looking at the surface_labels.txt file?)
Reading a single label file [test_labels] $ more lh.S_temporalis_transveralis.label
Returns the following structure #!ascii label , from subject EC 394 64599 -35.192 -31.784 11.805 0.000000 64600 -35.842 -31.799 11.554 0.000000 ....etc
- What is the name & location of the table file I should be
specifying
to return all 94 labels? Or do I need to include additional flags in
my
command line? 2) How are the columns ordered within each output file generated by
the
mri_annotation2label command?
I'm running FSv3.0.5 on linux (Centos 4). The table specified in the wiki help pages
(Simple_surface_labels.txt)
does not appear to be located in my $FREESURFER_HOME directory...instead, the file <surface_labels.txt> appears in my $FREESURFER_HOME dir.
Many Thanks, Jenifer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks, Doug. I have tried the following command: [<subjid>] $ mri_annotation2label --subject EC --hemi lh --outdir ./test_labels --table ../../surface_labels.txt --annotation aparc.a2005s A total of 57 labels are returned (expecting 94 after looking at the surface_labels.txt file?) Reading a single label file [test_labels] $ more lh.S_temporalis_transveralis.label Returns the following structure #!ascii label , from subject EC 394 64599 -35.192 -31.784 11.805 0.000000 64600 -35.842 -31.799 11.554 0.000000 The table specified in the wiki help pages (Simple_surface_labels.txt) does not appear to be located in my $FREESURFER_HOME directory...instead, the file <surface_labels.txt> appears in my $FREESURFER_HOME dir.
Have I missed something in the command line and/or specified table?
Jenifer
-----Original Message----- From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Monday, October 01, 2007 1:20 PM To: Juranek, Jenifer Cc: Bruce Fischl; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] XYZ coordinates of vertices within aparc labels
use mri_annotation2label to create a text label file for each annotation. These have the surface xyz in them.
doug
Juranek, Jenifer wrote:
Thanks again for the info. However, I'm still not sure how to get an ascii file for each aparc label listing the vertex index, and the RAS coordinates (surface RAS is fine since I can use the fscoordinates.pdf and the wikipage on Coordinate systems to get back to vol coordinates and eventually scanner coordinates.) Any suggestions how to access this information? From the help pages, I thought mri_annotation2label would do the trick... Jenifer -----Original Message----- From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Monday, October 01, 2007 1:05 PM To: Bruce Fischl Cc: Juranek, Jenifer ; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] XYZ coordinates of vertices within aparc labels I don't have code to do it, but you can look at this doc: https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems?action=Attac hFile&do=get&target=fscoordinates.pdf which explains how to get back to scanner coords doug Bruce Fischl wrote:
yes, I think Doug has documented how to do this on our wiki. Doug: can
you point jenifer at the right place? thanks, Bruce On Mon, 1 Oct 2007, Juranek, Jenifer wrote:
Hi Bruce, Many thanks for the information. Yes, I'd like a table file for each aparc label in each hemisphere. Whether the annotation file is the ?h.aparc.a2005s.annot variety or
the
?h.aparc.annot variety is not crucial at this point. My goal is to map the XYZ vertex coordinates for each aparc label
back
to the scanner XYZ coordinates. Is this possible? Jenifer -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Monday, October 01, 2007 10:25 AM To: Juranek, Jenifer Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] XYZ coordinates of vertices within aparc labels Hi Jennifer, do you need a table file? I thought not, since the color table is embedded in the .annot file. If you give it an output directory it should extract a label for every different structure in the .annot file. The label file columns are: <1> vertex index <2>-<5> surface RAS coordinates of the vertex, I believe from the
orig
surface (could be white, I'm not positive) <6> a slot to assocate a statistic with that vertex (e.g. fMRI
p-value)
Does that answer your questions? I'm not sure... cheers, Bruce On Mon, 1 Oct 2007, Juranek, Jenifer wrote:
I'd like to retrieve information wrt XYZ coordinates of vertices
within
aparc labels. I have tried the following command: [<subjid>] $ mri_annotation2label --subject EC --hemi lh --outdir ./test_labels --table ../../surface_labels.txt --annotation aparc.a2005s A total of 57 labels are returned (expecting 94 after looking at the surface_labels.txt file?) Reading a single label file [test_labels] $ more lh.S_temporalis_transveralis.label Returns the following structure #!ascii label , from subject EC 394 64599 -35.192 -31.784 11.805 0.000000 64600 -35.842 -31.799 11.554 0.000000 ....etc 1) What is the name & location of the table file I should be
specifying
to return all 94 labels? Or do I need to include additional flags in
my
command line? 2) How are the columns ordered within each output file generated by
the
mri_annotation2label command? I'm running FSv3.0.5 on linux (Centos 4). The table specified in the wiki help pages
(Simple_surface_labels.txt)
does not appear to be located in my $FREESURFER_HOME directory...instead, the file <surface_labels.txt> appears in my $FREESURFER_HOME dir. Many Thanks, Jenifer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Try it without --table
Juranek, Jenifer wrote:
Thanks, Doug. I have tried the following command: [<subjid>] $ mri_annotation2label --subject EC --hemi lh --outdir ./test_labels --table ../../surface_labels.txt --annotation aparc.a2005s A total of 57 labels are returned (expecting 94 after looking at the surface_labels.txt file?) Reading a single label file [test_labels] $ more lh.S_temporalis_transveralis.label Returns the following structure #!ascii label , from subject EC 394 64599 -35.192 -31.784 11.805 0.000000 64600 -35.842 -31.799 11.554 0.000000 The table specified in the wiki help pages (Simple_surface_labels.txt) does not appear to be located in my $FREESURFER_HOME directory...instead, the file <surface_labels.txt> appears in my $FREESURFER_HOME dir.
Have I missed something in the command line and/or specified table?
Jenifer
-----Original Message----- From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Monday, October 01, 2007 1:20 PM To: Juranek, Jenifer Cc: Bruce Fischl; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] XYZ coordinates of vertices within aparc labels
use mri_annotation2label to create a text label file for each annotation. These have the surface xyz in them.
doug
Juranek, Jenifer wrote:
Thanks again for the info. However, I'm still not sure how to get an ascii file for each aparc label listing the vertex index, and the RAS coordinates (surface RAS is fine since I can use the fscoordinates.pdf and the wikipage on Coordinate systems to get back to vol coordinates and eventually scanner coordinates.)
Any suggestions how to access this information? From the help pages, I thought mri_annotation2label would do the trick...
Jenifer
-----Original Message----- From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Monday, October 01, 2007 1:05 PM To: Bruce Fischl Cc: Juranek, Jenifer ; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] XYZ coordinates of vertices within aparc labels
I don't have code to do it, but you can look at this doc:
https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems?action=Attac hFile&do=get&target=fscoordinates.pdf
which explains how to get back to scanner coords
doug
Bruce Fischl wrote:
yes, I think Doug has documented how to do this on ourwiki. Doug: can
you point jenifer at the right place?thanks, Bruce On Mon, 1 Oct 2007, Juranek, Jenifer wrote:
Hi Bruce, Many thanks for the information. Yes, I'd like a table file for each aparc labelin each hemisphere. Whether the annotation file is the ?h.aparc.a2005s.annot variety or
the
?h.aparc.annot variety is not crucial at thispoint. My goal is to map the XYZ vertex coordinates for each aparc label
back
to the scanner XYZ coordinates. Is thispossible? Jenifer -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Monday, October 01, 2007 10:25 AM To: Juranek, Jenifer Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] XYZ coordinates of vertices within aparc labels Hi Jennifer, do you need a table file? I thought not, since the color table is embedded in the .annot file. If you give it an output directory it should extract a label for every different structure in the .annot file. The label file columns are: <1> vertex index <2>-<5> surface RAS coordinates of the vertex, I believe from the
orig
surface (could be white, I'm notpositive) <6> a slot to assocate a statistic with that vertex (e.g. fMRI
p-value)
Does that answer your questions? I'm not sure... cheers, Bruce On Mon, 1 Oct 2007, Juranek, Jenifer wrote: I'd like to retrieve information wrt XYZcoordinates of vertices
within aparc labels. I have tried the following command: [<subjid>] $ mri_annotation2label --subject EC--hemi lh --outdir ./test_labels --table ../../surface_labels.txt --annotation aparc.a2005s A total of 57 labels are returned (expecting 94 after looking at the surface_labels.txt file?) Reading a single label file [test_labels] $ more lh.S_temporalis_transveralis.label Returns the following structure #!ascii label , from subject EC 394 64599 -35.192 -31.784 11.805 0.000000 64600 -35.842 -31.799 11.554 0.000000 ....etc 1) What is the name & location of the table file I should be
specifying to return all 94 labels? Or do I need toinclude additional flags in
my command line? 2) How are the columns ordered withineach output file generated by
the mri_annotation2label command? I'm running FSv3.0.5 on linux (Centos4). The table specified in the wiki help pages
(Simple_surface_labels.txt)
does not appear to be located in my$FREESURFER_HOME directory...instead, the file <surface_labels.txt> appears in my $FREESURFER_HOME dir. Many Thanks, Jenifer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Jennifer,
The --table option is obsolete, as the table is found in the .annot file. Refer to $FREESURFER_HOME/FreeSurferColorLUT.txt for labels.
Nick
On Mon, 2007-10-01 at 09:45 -0500, Juranek, Jenifer wrote:
I'd like to retrieve information wrt XYZ coordinates of vertices within aparc labels.
I have tried the following command: [<subjid>] $ mri_annotation2label --subject EC --hemi lh --outdir ./test_labels --table ../../surface_labels.txt --annotation aparc.a2005s
A total of 57 labels are returned (expecting 94 after looking at the surface_labels.txt file?)
Reading a single label file [test_labels] $ more lh.S_temporalis_transveralis.label
Returns the following structure #!ascii label , from subject EC 394 64599 -35.192 -31.784 11.805 0.000000 64600 -35.842 -31.799 11.554 0.000000 ....etc
- What is the name & location of the table file I should be specifying
to return all 94 labels? Or do I need to include additional flags in my command line? 2) How are the columns ordered within each output file generated by the mri_annotation2label command?
I'm running FSv3.0.5 on linux (Centos 4). The table specified in the wiki help pages (Simple_surface_labels.txt) does not appear to be located in my $FREESURFER_HOME directory...instead, the file <surface_labels.txt> appears in my $FREESURFER_HOME dir.
Many Thanks, Jenifer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Doug Greve -
Juranek, Jenifer -
Nick Schmansky