Commit 38854dd6 authored by Shaun Warrington's avatar Shaun Warrington
Browse files

Updated xtract_data location to FSLDIR/data

parent 75d52faa
...@@ -56,7 +56,7 @@ NeuroImage, 76(1), 400-411. DOI: 10.1016/j.neuroimage.2013.03.015 ...@@ -56,7 +56,7 @@ NeuroImage, 76(1), 400-411. DOI: 10.1016/j.neuroimage.2013.03.015
Optional arguments: Optional arguments:
-list List the tract names used in XTRACT -list List the tract names used in XTRACT
-str <file> Structures file (format: <tractName> per line OR format: <tractName> [samples=1], 1 means 1000, '#' to skip lines) -str <file> Structures file (format: <tractName> per line OR format: <tractName> [samples=1], 1 means 1000, '#' to skip lines)
-p <folder> Protocols folder (all masks in same standard space) (Default=$FSLDIR/etc/xtract_data/<SPECIES>) -p <folder> Protocols folder (all masks in same standard space) (Default=$FSLDIR/data/xtract_data/<SPECIES>)
-stdwarp <std2diff> <diff2std> Standard2diff and Diff2standard transforms (Default=bedpostx_dir/xfms/{standard2diff,diff2standard}) -stdwarp <std2diff> <diff2std> Standard2diff and Diff2standard transforms (Default=bedpostx_dir/xfms/{standard2diff,diff2standard})
-gpu Use GPU version -gpu Use GPU version
-res <mm> Output resolution (Default=same as in protocol folders unless '-native' used) -res <mm> Output resolution (Default=same as in protocol folders unless '-native' used)
...@@ -108,19 +108,19 @@ Prior to running XTRACT, you must complete the FDT processing pipeline: ...@@ -108,19 +108,19 @@ Prior to running XTRACT, you must complete the FDT processing pipeline:
3. Eddy current distortion and motion correction using eddy 3. Eddy current distortion and motion correction using eddy
4. Fit the crossing fibre model using bedpostx 4. Fit the crossing fibre model using bedpostx
5. Registration to standard space (MNI152), see the FDT pipeline 5. Registration to standard space (MNI152), see the FDT pipeline
6. Your data should now be ready to run XTRACT!
Your data should now be ready to run XTRACT!
--------------------------------------------------------------------- ---------------------------------------------------------------------
## Atlases: ## Atlases:
- For HUMAN, XTRACT uses the MNI152 standard space in $FSLDIR/etc/standard - For HUMAN, XTRACT uses the MNI152 standard space in $FSLDIR/data/standard
- For MACAQUE, XTRACT uses the F99 atlas in Caret - see http://brainvis.wustl.edu/wiki/index.php/Caret:Atlases - For MACAQUE, XTRACT uses the F99 atlas in Caret - see http://brainvis.wustl.edu/wiki/index.php/Caret:Atlases
We also provide a copy of the F99 atlas in $FSLDIR/etc/xtract_data/standard/F99. This We also provide a copy of the F99 atlas in $FSLDIR/data/xtract_data/standard/F99. This
includes a helper script for registering your own diffusion/structural data to the F99 altas includes a helper script for registering your own diffusion/structural data to the F99 altas
When running XTRACT with the '-species' option, a predefined list of tracts is automatically extracted. Currently the following tracts are available: When running XTRACT with the '-species' option, a predefined list of tracts is automatically extracted. Currently the following tracts are available:
...@@ -159,7 +159,7 @@ OR ...@@ -159,7 +159,7 @@ OR
tractName nsamples, per line tractName nsamples, per line
For an example, see $FSLDIR/etc/xtract_data/Human/structureList For an example, see $FSLDIR/data/xtract_data/Human/structureList
--------------------------------------------------------------------- ---------------------------------------------------------------------
...@@ -240,8 +240,8 @@ stats to get such summary statistics in a quick and simple way. ...@@ -240,8 +240,8 @@ stats to get such summary statistics in a quick and simple way.
You can use XTRACT stats with any modelled diffusion data, e.g. DTI, bedpostx, DKI. You can use XTRACT stats with any modelled diffusion data, e.g. DTI, bedpostx, DKI.
Simply provide; the directory (and basename of files, if any) leading to the diffusion d Simply provide; the directory (and basename of files, if any) leading to the diffusion
ata of interest, the directory containing the XTRACT output, the warp field (or use 'native' data of interest, the directory containing the XTRACT output, the warp field (or use 'native'
if tracts are already in diffusion space). If tracts are not in diffusion space, you must also if tracts are already in diffusion space). If tracts are not in diffusion space, you must also
provide a reference image in diffusion space (e.g. FA map). provide a reference image in diffusion space (e.g. FA map).
...@@ -254,7 +254,7 @@ standard deviation of the probability, length, FA and MD for each tract. ...@@ -254,7 +254,7 @@ standard deviation of the probability, length, FA and MD for each tract.
__ _______ ____ _ ____ _____ _ _ __ _______ ____ _ ____ _____ _ _
\ \/ /_ _| _ \ / \ / ___|_ _|__| |_ __ _| |_ ___ \ \/ /_ _| _ \ / \ / ___|_ _|__| |_ __ _| |_ ___
\ / | | | |_) | / _ \| | | |/ __| __/ _ | __/ __| \ / | | | |_) | / _ \| | | |/ __| __/ _ | __/ __|
/ \ | | | _ < / ___ \ |___ | |\__ \ || (_| | |_\__ \\ / \ | | | _ < / ___ \ |___ | |\__ \ || (_| | |_\__ \
/_/\_\ |_| |_| \_\/_/ \_\____| |_||___/\__\__ _|\__|___/ /_/\_\ |_| |_| \_\/_/ \_\____| |_||___/\__\__ _|\__|___/
......
...@@ -11,7 +11,7 @@ ...@@ -11,7 +11,7 @@
ptxbin_gpu=$FSLDIR/bin/probtrackx2_gpu ptxbin_gpu=$FSLDIR/bin/probtrackx2_gpu
# Location of xtract data # Location of xtract data
datadir=$FSLDIR/etc/xtract_data datadir=$FSLDIR/data/xtract_data
Usage() { Usage() {
cat << EOF cat << EOF
...@@ -29,7 +29,7 @@ Usage: ...@@ -29,7 +29,7 @@ Usage:
Optional arguments: Optional arguments:
-list List the tract names used in XTRACT -list List the tract names used in XTRACT
-str <file> Structures file (format: <tractName> per line OR format: <tractName> [samples=1], 1 means 1000, '#' to skip lines) -str <file> Structures file (format: <tractName> per line OR format: <tractName> [samples=1], 1 means 1000, '#' to skip lines)
-p <folder> Protocols folder (all masks in same standard space) (Default=$FSLDIR/etc/xtract_data/<SPECIES>) -p <folder> Protocols folder (all masks in same standard space) (Default=$FSLDIR/data/xtract_data/<SPECIES>)
-stdwarp <std2diff> <diff2std> Standard2diff and Diff2standard transforms (Default=bedpostx_dir/xfms/{standard2diff,diff2standard}) -stdwarp <std2diff> <diff2std> Standard2diff and Diff2standard transforms (Default=bedpostx_dir/xfms/{standard2diff,diff2standard})
-gpu Use GPU version -gpu Use GPU version
-res <mm> Output resolution (Default=same as in protocol folders unless '-native' used) -res <mm> Output resolution (Default=same as in protocol folders unless '-native' used)
......
...@@ -99,7 +99,7 @@ if [ "$spec" == "" ];then ...@@ -99,7 +99,7 @@ if [ "$spec" == "" ];then
elif [ $spec == HUMAN ];then elif [ $spec == HUMAN ];then
brain=${FSLDIR}/data/standard/FSL_HCP1065_FA_1mm.nii.gz brain=${FSLDIR}/data/standard/FSL_HCP1065_FA_1mm.nii.gz
elif [ $spec == MACAQUE ];then elif [ $spec == MACAQUE ];then
brain=${FSLDIR}/etc/xtract_data/standard/F99/mri/struct_brain.nii.gz brain=${FSLDIR}/data/xtract_data/standard/F99/mri/struct_brain.nii.gz
elif [ ! "$spec" == "HUMAN" ] && [ ! "$spec" == "MACAQUE" ];then elif [ ! "$spec" == "HUMAN" ] && [ ! "$spec" == "MACAQUE" ];then
echo "Unrecognised option '$spec'. Must set '-species' using HUMAN or MACAQUE" echo "Unrecognised option '$spec'. Must set '-species' using HUMAN or MACAQUE"
errflag=1 errflag=1
......
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