Commit 75d52faa authored by Shaun Warrington's avatar Shaun Warrington
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changes to readme

parent 355cc7ae
......@@ -15,6 +15,7 @@ with help from:
Saad Jbabdi, Kathryn Bryant, Shaun Warrington, Marina Charquero-Ballester, Gwenaelle Douaud
The XTRACT viewer helper script was written by Shaun Warrington
The XTRACT stats helper script was written by Shaun Warrington
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......@@ -22,8 +23,9 @@ The XTRACT stats helper script was written by Shaun Warrington
## Citations:
Warrington S, Bryant K, Charquero-Ballester M, Douaud G, Jbabdi S*, Mars R*, Sotiropoulos SN* (Submitted)
Standardised protocols for automated tractography and connectivity blueprints in the human and macaque brain.
Warrington S, Bryant K, Khrapitchev A, Sallet J, Charquero-Ballester M, Douaud G, Jbabdi S*, Mars R*,
Sotiropoulos SN* (2020) XTRACT - Standardised protocols for automated tractography in the human and
macaque brain. NeuroImage. DOI: 10.1016/j.neuroimage.2020.116923
de Groot M; Vernooij MW. Klein S, Ikram MA, Vos FM, Smith SM, Niessen WJ, Andersson JLR (2013)
Improving alignment in Tract-based spatial statistics: Evaluation and optimization of image registration.
......@@ -83,8 +85,10 @@ Under <outputDir>:
- "<tractName>" - directory per tract, each continaing:
- "waytotal" - txt file continaing the number of valid streamlines
- "density.nii.gz" - nifti file containing the fibre probability distribution
- "density_lenths.nii.gz" - nifti file containing the fibre lengths, i.e. each voxel is the average streamline length - this is the "-ompl" probtrackx option
- "densityNorm.nii.gz" - nifti file continaing the waytotal normalised fibre probability distribution (the "density.nii.gz" divided by the total number of valid streamlines)
- "density_lenths.nii.gz" - nifti file containing the fibre lengths, i.e. each voxel is the
average streamline length - this is the "-ompl" probtrackx option
- "densityNorm.nii.gz" - nifti file continaing the waytotal normalised fibre probability distribution
(the "density.nii.gz" divided by the total number of valid streamlines)
- If the protocol calls for reverse-seeding:
- "tractsInv" - directory continaing the above for the seed-target reversed run
- "sum_waytotal" and "sum_density.nii.gz" - the summed waytotal and fibre probability distribution
......@@ -99,7 +103,8 @@ The primary output is the "densityNorm.nii.gz" file.
Prior to running XTRACT, you must complete the FDT processing pipeline:
1. Brain extraction using BET
2. Susceptibility distortion correction using topup (only if spin-echo fieldmaps have been acquired - if you don't have these, skip to step 3)
2. Susceptibility distortion correction using topup (only if spin-echo fieldmaps have been
acquired - if you don't have these, skip to step 3)
3. Eddy current distortion and motion correction using eddy
4. Fit the crossing fibre model using bedpostx
5. Registration to standard space (MNI152), see the FDT pipeline
......@@ -115,7 +120,8 @@ Prior to running XTRACT, you must complete the FDT processing pipeline:
- 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 includes a helper script for registering your own diffusion/structural data to the F99 altas
We also provide a copy of the F99 atlas in $FSLDIR/etc/xtract_data/standard/F99. This
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:
......@@ -177,15 +183,19 @@ Then create the following NIFTI files (with this exact naming) and copy them int
- invert (empty file to indicate that a seed->target and target->seed run will be added and combined)
if such an option is required a single "target.nii.gz" file is also expected
All the masks above should be in standard space (e.g. MNI152 or F99) if you want to run the same tracking for a collection of subjects.
All the masks above should be in standard space (e.g. MNI152 or F99) if you want to run
the same tracking for a collection of subjects.
Next, make a structure file using the format <tractName> <nsamples> per line and call XTRACT using -species <SPECIES> -str <file> -p <folder>, pointing to your new protocols folder 'mytrack'.
Next, make a structure file using the format <tractName> <nsamples> per line and call XTRACT
using -species <SPECIES> -str <file> -p <folder>, pointing to your new protocols folder 'mytrack'.
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## Visualising results with FSLEYES
The output of XTRACT is a folder that contains tracts in separate folders. We provide a convenient script that can load these tracts (or a subset of the tracts) into FSLEYES using different colours for the different tracts but matching the left/right colours
The output of XTRACT is a folder that contains tracts in separate folders. We provide a
convenient script that can load these tracts (or a subset of the tracts) into FSLEYES using
different colours for the different tracts but matching the left/right colours
```
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......@@ -224,15 +234,21 @@ The output of XTRACT is a folder that contains tracts in separate folders. We pr
## Extracting tract-wise summary statistics
A common usage of the XTRACT output is to summarise tracts in terms of simple summary statistics, such as their volume and microstructural properties (e.g. mean FA). We provide XTRACT stats to get such summary statistics in a quick and simple way.
A common usage of the XTRACT output is to summarise tracts in terms of simple summary
statistics, such as their volume and microstructural properties (e.g. mean FA). We provide XTRACT
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.
Simply provide; the directory (and basename of files, if any) leading to the diffusion 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 provide a reference image in diffusion space (e.g. FA map).
Simply provide; the directory (and basename of files, if any) leading to the diffusion d
ata 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
provide a reference image in diffusion space (e.g. FA map).
e.g. call: xtract_stats -d /home/DTI/dti_ -xtract /home/xtract -w /home/warp/standard2diff -r /home/DTI/dti_FA
The output (a .csv file) by default contains the tract volume (mm3) and the mean, median and standard deviation of the probability, length, FA and MD for each tract.
The output (a .csv file) by default contains the tract volume (mm3) and the mean, median and
standard deviation of the probability, length, FA and MD for each tract.
```
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