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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
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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.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
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