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Hi,
For a group analysis, it possible to use 'tractstats2table' to generate a single table that contains all the tracts for multiple subjects?
It's not intuitively obvious looking at the options with the 'tractstats2table' utility.
Jim
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Hi Jim - You can use the --load-pathstats-from-file option, as in the tutorial, to pass a text file that contains the paths to all the stats files that you want to include in the table. These can be from multiple subjects and/or tracts.
http://freesurfer.net/fswiki/FsTutorial/TraculaStatistics
Best,
a.y
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Alexopoulos, Dimitrios dimitriosalexopoulos@wustl.edu Sent: Tuesday, June 12, 2018 5:08:20 PM To: Freesurfer support list Subject: [Freesurfer] tractstats2table - all tracts for multiple subjects
External Email - Use Caution
Hi,
For a group analysis, it possible to use ‘tractstats2table’ to generate a single table that contains all the tracts for multiple subjects?
It’s not intuitively obvious looking at the options with the ‘tractstats2table’ utility.
Jim
“The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email.”
________________________________
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
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Thx Anastasia.
This the command I used and the error:
[hellerml@login01 processed_data]$ tractstats2table --load-pathstats-from-file /scratch/jimalex/freesurfer6_0_chd_auck_6yr/processed_data/test.list --overall --tablefile test.table Parsing the .stats files Building the table.. ERROR: all stats files need to have the same pathwayname. try verbose option These are the pathwaynames found: ['fmajor', 'fminor', 'lh.atr', 'lh.cab', 'lh.ccg', 'lh.cst', 'lh.ilf', 'lh.slfp', 'lh.slft', 'lh.unc', 'rh.atr', 'rh.cab', 'rh.ccg', 'rh.cst', 'rh.ilf', 'rh.slfp', 'rh.slft', 'rh.unc']
For example, the test .list input file I used for a single subject is below: -------------------------------- $SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/fmajor_PP_avg33_mni_bbr/pathstats.overall.txt $SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/fminor_PP_avg33_mni_bbr/pathstats.overall.txt $SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/lh.atr_PP_avg33_mni_bbr/pathstats.overall.txt $SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/lh.cab_PP_avg33_mni_bbr/pathstats.overall.txt $SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/lh.ccg_PP_avg33_mni_bbr/pathstats.overall.txt $SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.overall.txt $SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/lh.ilf_AS_avg33_mni_bbr/pathstats.overall.txt $SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/lh.slfp_PP_avg33_mni_bbr/pathstats.overall.txt $SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/lh.slft_PP_avg33_mni_bbr/pathstats.overall.txt $SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/lh.unc_AS_avg33_mni_bbr/pathstats.overall.txt $SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/rh.atr_PP_avg33_mni_bbr/pathstats.overall.txt $SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/rh.cab_PP_avg33_mni_bbr/pathstats.overall.txt $SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/rh.ccg_PP_avg33_mni_bbr/pathstats.overall.txt $SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/rh.cst_AS_avg33_mni_bbr/pathstats.overall.txt $SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/rh.ilf_AS_avg33_mni_bbr/pathstats.overall.txt $SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/rh.slfp_PP_avg33_mni_bbr/pathstats.overall.txt $SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/rh.slft_PP_avg33_mni_bbr/pathstats.overall.txt $SUBJECTS_DIR/chd_auck_BS44_6yr/dpath/rh.unc_AS_avg33_mni_bbr/pathstats.overall.txt
"The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email."
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia Sent: Tuesday, June 12, 2018 4:30 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] tractstats2table - all tracts for multiple subjects
Hi Jim - You can use the --load-pathstats-from-file option, as in the tutorial, to pass a text file that contains the paths to all the stats files that you want to include in the table. These can be from multiple subjects and/or tracts.
http://freesurfer.net/fswiki/FsTutorial/TraculaStatistics
Best,
a.y
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Alexopoulos, Dimitrios <dimitriosalexopoulos@wustl.edumailto:dimitriosalexopoulos@wustl.edu> Sent: Tuesday, June 12, 2018 5:08:20 PM To: Freesurfer support list Subject: [Freesurfer] tractstats2table - all tracts for multiple subjects
External Email - Use Caution
Hi,
For a group analysis, it possible to use 'tractstats2table' to generate a single table that contains all the tracts for multiple subjects?
It's not intuitively obvious looking at the options with the 'tractstats2table' utility.
Jim
"The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email."
________________________________
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
freesurfer@nmr.mgh.harvard.edu
-
Alexopoulos, Dimitrios -
Yendiki, Anastasia