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- #!/bin/tcsh
- # January, 2014.
- # An example of using DSI-Studio (Yeh et al., 2010) to reconstruct
- # HARDI models for use in tracking. Note: this is *NOT* a tutorial on
- # using DSI-Studio, but merely a simple example in using it to make
- # some examples for HARDI-tracking with AFNI-FATCAT-3dTrackID. Please
- # refer to the DSI-Studio website/poster/papers/etc. for more
- # information. Key to this enterprise has been the recent DSI-Studio
- # addition of enabling NIFTI file outputs (many thanks), so that
- # AFNI-FATCAT can use the results.
- # This script was run from the $maindir, defined just below
- #*********************************************************************
- # Just setting some names/locations of things-- user can adjust
- # appropriately for own usage
- # 1) where DSI-Studio has been installed
- set whereprog = "/usr/local/pkg/dsistudio/20120919"
- # 2) where the demo is-- for some reason, I needed to put full path of
- # 'home', and couldn't use '~' abbreviation
- set maindir = "/home/paul/FATCAT_DEMO"
- # 3) where I want my output to go
- set whereto = "$maindir/HARDI"
- #*********************************************************************
- # DSI-Studio start: make source file; b_table was made using
- # AFNI-1dDW_Grad_o_Mat-- note its columnar structure including
- # b-values.
- $whereprog/dsi_studio \
- --action=src \
- --source="$maindir/AVEB0_DWI.nii.gz" \
- --b_table="$whereto/b_table.txt" \
- --output="$whereto/output.src"
- # * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
- # GQI
- # * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
- # Make use of GQI to construct directions (<=3 per vox);
- # makes a 'fib' file called: output.src.odf8.f3rec.gqi.1.25.fib.gz
- $whereprog/dsi_studio \
- --action=rec \
- --source="$whereto/output.src" \
- --thread=4 \
- --method=4 \
- --param0=1.25 \
- --record_odf=1 \
- --odf_order=8 \
- --num_fiber=3
- # Export data from 'fib' file to NIFTI; for tracking, we need dirs
- # and a WM-proxy map. Here, I'm outputting both FA and GFA (will
- # just use latter, probably)
- $whereprog/dsi_studio \
- --action=exp \
- --source="$whereto/output.src.odf8.f3rec.gqi.1.25.fib.gz" \
- --export=dirs,fa0,gfa
- # * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
- # QBALL
- # * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
- # Make use of QBall to construct directions (<=3 per vox)
- # makes a 'fib' file called: output.src.odf8.f3rec.qbi.sh8.1.25.fib.gz
- $whereprog/dsi_studio \
- --action=rec \
- --source="$whereto/output.src" \
- --thread=4 \
- --method=3 \
- --param0=1.25 \
- --record_odf=1 \
- --odf_order=8 \
- --num_fiber=3
- # Export data from 'fib' file to NIFTI; for tracking, we need dirs
- # and a WM-proxy map. Here, I'm outputting both FA and GFA (will
- # just use latter, probably)
- $whereprog/dsi_studio \
- --action=exp \
- --source="$whereto/output.src.odf8.f3rec.qbi.sh8.1.25.fib.gz" \
- --export=dirs,fa0,gfa
- # bit of copying to shorter file names:
- 3dcopy \
- $whereto/output.src.odf8.f3rec.qbi.sh8.1.25.fib.gz.gfa.nii.gz \
- $whereto/QBALL_GFA.nii.gz
- 3dcopy \
- $whereto/output.src.odf8.f3rec.qbi.sh8.1.25.fib.gz.dirs.nii.gz \
- $whereto/QBALL_DIRS.nii.gz
- 3dcopy \
- $whereto/output.src.odf8.f3rec.qbi.sh8.1.25.fib.gz.fa0.nii.gz \
- $whereto/QBALL_FA.nii.gz
- printf "\nDONE.\n"
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