Dear experts,
I am using aparcstats2table to extract values on a number of measures like thickness, curvature, folding index, and surface area for specific ROIs. Is it possible to create a table (using aparcstats2table) with all these measures included or do I have to run it separately and create a separate table for each measure? Passing --meas flag multiple items did not work.
Thanks for your help! Hamdi
you have to run it separately
On 11/12/2015 11:18 AM, Eryilmaz, H. Hamdi wrote:
Dear experts,
I am using aparcstats2table to extract values on a number of measures like thickness, curvature, folding index, and surface area for specific ROIs. Is it possible to create a table (using aparcstats2table) with all these measures included or do I have to run it separately and create a separate table for each measure? Passing --meas flag multiple items did not work.
Thanks for your help! Hamdi
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks Doug for the quick reply! Is there an option in aparcstats2table that allows to make a table with the folding index measure? If so, what variable should I use in the flag -meas?
Best, Hamdi
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Thursday, November 12, 2015 11:26 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] aparcstats2table -- extracting multiple measures
you have to run it separately
On 11/12/2015 11:18 AM, Eryilmaz, H. Hamdi wrote:
Dear experts,
I am using aparcstats2table to extract values on a number of measures like thickness, curvature, folding index, and surface area for specific ROIs. Is it possible to create a table (using aparcstats2table) with all these measures included or do I have to run it separately and create a separate table for each measure? Passing --meas flag multiple items did not work.
Thanks for your help! Hamdi
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Use foldind
On 11/12/15 12:06 PM, Eryilmaz, H. Hamdi wrote:
Thanks Doug for the quick reply! Is there an option in aparcstats2table that allows to make a table with the folding index measure? If so, what variable should I use in the flag -meas?
Best, Hamdi
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Thursday, November 12, 2015 11:26 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] aparcstats2table -- extracting multiple measures
you have to run it separately
On 11/12/2015 11:18 AM, Eryilmaz, H. Hamdi wrote:
Dear experts,
I am using aparcstats2table to extract values on a number of measures like thickness, curvature, folding index, and surface area for specific ROIs. Is it possible to create a table (using aparcstats2table) with all these measures included or do I have to run it separately and create a separate table for each measure? Passing --meas flag multiple items did not work.
Thanks for your help! Hamdi
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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 get the following error when I use 'foldind' in this command >> aparcstats2table --hemi lh --subjectsfile $SUBJECTS_DIR/RPDR/214_PrePostFort_FSGDorder --parc rostralmiddlefrontal.label --meas foldind --tablefile $SUBJECTS_DIR/Tables/LH_rostralmiddlefrontal_FoldInd.txt
aparcstats2table: error: option --measure: invalid choice: 'foldind' (choose from 'area', 'volume', 'thickness', 'thicknessstd', 'meancurv')
Isn't it an option for aparcstats2table yet? Should I make a matlab or python script to extract it?
Thanks! Hamdi
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] Sent: Friday, November 13, 2015 6:27 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] aparcstats2table -- extracting multiple measures
Use foldind
On 11/12/15 12:06 PM, Eryilmaz, H. Hamdi wrote:
Thanks Doug for the quick reply! Is there an option in aparcstats2table that allows to make a table with the folding index measure? If so, what variable should I use in the flag -meas?
Best, Hamdi
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Thursday, November 12, 2015 11:26 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] aparcstats2table -- extracting multiple measures
you have to run it separately
On 11/12/2015 11:18 AM, Eryilmaz, H. Hamdi wrote:
Dear experts,
I am using aparcstats2table to extract values on a number of measures like thickness, curvature, folding index, and surface area for specific ROIs. Is it possible to create a table (using aparcstats2table) with all these measures included or do I have to run it separately and create a separate table for each measure? Passing --meas flag multiple items did not work.
Thanks for your help! Hamdi
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
what version of FS are you using? When I run
aparcstats2table --hemi lh -s subject --meas foldind --tablefile table.dat
it runs fine
On 11/16/2015 10:24 AM, Eryilmaz, H. Hamdi wrote:
Hi Doug,
I get the following error when I use 'foldind' in this command >> aparcstats2table --hemi lh --subjectsfile $SUBJECTS_DIR/RPDR/214_PrePostFort_FSGDorder --parc rostralmiddlefrontal.label --meas foldind --tablefile $SUBJECTS_DIR/Tables/LH_rostralmiddlefrontal_FoldInd.txt
aparcstats2table: error: option --measure: invalid choice: 'foldind' (choose from 'area', 'volume', 'thickness', 'thicknessstd', 'meancurv')
Isn't it an option for aparcstats2table yet? Should I make a matlab or python script to extract it?
Thanks! Hamdi
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] Sent: Friday, November 13, 2015 6:27 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] aparcstats2table -- extracting multiple measures
Use foldind
On 11/12/15 12:06 PM, Eryilmaz, H. Hamdi wrote:
Thanks Doug for the quick reply! Is there an option in aparcstats2table that allows to make a table with the folding index measure? If so, what variable should I use in the flag -meas?
Best, Hamdi
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Thursday, November 12, 2015 11:26 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] aparcstats2table -- extracting multiple measures
you have to run it separately
On 11/12/2015 11:18 AM, Eryilmaz, H. Hamdi wrote:
Dear experts,
I am using aparcstats2table to extract values on a number of measures like thickness, curvature, folding index, and surface area for specific ROIs. Is it possible to create a table (using aparcstats2table) with all these measures included or do I have to run it separately and create a separate table for each measure? Passing --meas flag multiple items did not work.
Thanks for your help! Hamdi
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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
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
I'm using 5.0. It's a version issue then. Thanks Doug!
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Monday, November 16, 2015 12:28 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] aparcstats2table -- extracting multiple measures
what version of FS are you using? When I run
aparcstats2table --hemi lh -s subject --meas foldind --tablefile table.dat
it runs fine
On 11/16/2015 10:24 AM, Eryilmaz, H. Hamdi wrote:
Hi Doug,
I get the following error when I use 'foldind' in this command >> aparcstats2table --hemi lh --subjectsfile $SUBJECTS_DIR/RPDR/214_PrePostFort_FSGDorder --parc rostralmiddlefrontal.label --meas foldind --tablefile $SUBJECTS_DIR/Tables/LH_rostralmiddlefrontal_FoldInd.txt
aparcstats2table: error: option --measure: invalid choice: 'foldind' (choose from 'area', 'volume', 'thickness', 'thicknessstd', 'meancurv')
Isn't it an option for aparcstats2table yet? Should I make a matlab or python script to extract it?
Thanks! Hamdi
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] Sent: Friday, November 13, 2015 6:27 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] aparcstats2table -- extracting multiple measures
Use foldind
On 11/12/15 12:06 PM, Eryilmaz, H. Hamdi wrote:
Thanks Doug for the quick reply! Is there an option in aparcstats2table that allows to make a table with the folding index measure? If so, what variable should I use in the flag -meas?
Best, Hamdi
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Thursday, November 12, 2015 11:26 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] aparcstats2table -- extracting multiple measures
you have to run it separately
On 11/12/2015 11:18 AM, Eryilmaz, H. Hamdi wrote:
Dear experts,
I am using aparcstats2table to extract values on a number of measures like thickness, curvature, folding index, and surface area for specific ROIs. Is it possible to create a table (using aparcstats2table) with all these measures included or do I have to run it separately and create a separate table for each measure? Passing --meas flag multiple items did not work.
Thanks for your help! Hamdi
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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
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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Douglas Greve -
Douglas N Greve
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Eryilmaz, H. Hamdi