Merge pull request #29 from UCL-ARC/paul/output-mni-registered-images

Add MNI registered images to results zip files

Author: p-j-smith

README.md

@@ -138,12 +138,19 @@ repository.
 To run the analysis using Apptainer:
 
 ```bash
-apptainer run --bind "${PWD}":/data hh-enigmapd-2025/enigma-pd-wml/enigma-pd-wml:<tag>
+apptainer run --bind "${PWD}":/data library://hh-enigmapd-2025/enigma-pd-wml/enigma-pd-wml:<tag>
 ```
 
 where `<tag>` is the version of the image you would like to pull.
 
-Note, the image will be downloaded from Sylabs Cloud the first time you run a particular version of the
+It can sometime be slow to pull the image from Sylabs Cloud. If you would prefer to pull the Docker image
+from Docker Hub and build and run a local Apptainer image, you can run the following command:
+
+```bash
+apptainer run --bind "${PWD}":/data docker://hamiedaharoon24/enigma-pd-wml:<tag>
+```
+
+Note, the image will be downloaded from Sylabs Cloud (or Docker Hub) the first time you run a particular version of the
 image.
 
 ### Options
@@ -216,11 +223,19 @@ These zip files should contain six files:
 
 - `results2min_lin_perivent.nii.gz`: WML segmentations (periventricular) linearly transformed to MNI space.
 
-- `results2mni_nonlin.nii.gz`: WML segmentations non-linearly transformed to MNI space.
+- `results2mni_nonlin.nii.gz`: WML segmentations non-linearly warped to MNI space.
+
+- `results2min_nonlin_deep.nii.gz`: WML segmentations (deep white matter) non-linearly warped to MNI space.
+
+- `results2mni_nonlin_perivent.nii.gz`: WML segmentations (periventricular) non-linearly warped to MNI space.
+
+- `T1_biascorr_brain_to_MNI_lin.nii.gz`: T1 bias-corrected brain linearly transformed to MNI space.
+
+- `FLAIR_biascorr_brain_to_MNI_lin.nii.gz`: FLAIR bias-corrected brain linearly transformed to MNI space.
 
-- `results2min_nonlin_deep.nii.gz`: WML segmentations (deep white matter) non-linearly transformed to MNI space.
+- `T1_biascorr_brain_to_MNI_nonlin.nii.gz`: T1 bias-corrected brain non-linearly warped to MNI space.
 
-- `results2mni_nonlin_perivent.nii.gz`: WML segmentations (periventricular) non-linearly transformed to MNI space.
+- `FLAIR_biascorr_brain_to_MNI_nonlin.nii.gz`: FLAIR bias-corrected brain non-linearly warped to MNI space.
 
 #### Top-level zip file
 

analysis_script.sh

@@ -209,6 +209,10 @@ function processOutputs(){
     "${data_outpath}"/output/results2mni_nonlin.nii.gz
     "${data_outpath}"/output/results2mni_nonlin_deep.nii.gz
     "${data_outpath}"/output/results2mni_nonlin_perivent.nii.gz
+    "${data_outpath}"/output/T1_biascorr_brain_to_MNI_lin.nii.gz
+    "${data_outpath}"/output/FLAIR_biascorr_brain_to_MNI_lin.nii.gz
+    "${data_outpath}"/output/T1_biascorr_brain_to_MNI_nonlin.nii.gz
+    "${data_outpath}"/output/FLAIR_biascorr_brain_to_MNI_nonlin.nii.gz
    )
    if [ "$overwrite" = false ] && allFilesExist "${output_files[@]}"
    then
@@ -232,6 +236,8 @@ function processOutputs(){
    cp ${data_outpath}/input/vent_dist_mapping/dwm_t1brain.nii.gz .
    cp ${data_outpath}/input/vent_dist_mapping/perivent_flairbrain.nii.gz .
    cp ${data_outpath}/input/vent_dist_mapping/dwm_flairbrain.nii.gz .
+   cp ${data_outpath}/input/t1-mni.anat/T1_biascorr_brain.nii.gz .
+   cp ${data_outpath}/input/flair-bet/flairvol2t1brain.nii.gz .
 
 
    tree ${data_outpath}/input/
@@ -279,6 +285,14 @@ function processOutputs(){
      -out results2mni_lin_deep \
      -paddingsize 0.0 -interp nearestneighbour -ref MNI152_T1_1mm_brain.nii.gz
 
+   flirt -in T1_biascorr_brain.nii.gz -applyxfm -init T1_to_MNI_lin.mat \
+     -out T1_biascorr_brain_to_MNI_lin \
+     -paddingsize 0.0 -interp trilinear -ref MNI152_T1_1mm_brain.nii.gz
+
+   flirt -in flairvol2t1brain.nii.gz -applyxfm -init T1_to_MNI_lin.mat \
+     -out FLAIR_biascorr_brain_to_MNI_lin \
+     -paddingsize 0.0 -interp trilinear -ref MNI152_T1_1mm_brain.nii.gz
+
 
    echo "STEP 05"
    # run FSL's applywarp tool to nonlinearly warp WML segmentations with MNI T1
@@ -294,6 +308,14 @@ function processOutputs(){
           --out=results2mni_nonlin_deep \
           --interp=nn --ref=${FSLDIR}/data/standard/MNI152_T1_1mm_brain.nii.gz
 
+   applywarp --in=T1_biascorr_brain.nii.gz --warp=T1_to_MNI_nonlin_coeff.nii.gz \
+          --out=T1_biascorr_brain_to_MNI_nonlin \
+          --interp=trilinear --ref=${FSLDIR}/data/standard/MNI152_T1_1mm_brain.nii.gz
+
+   applywarp --in=flairvol2t1brain.nii.gz --warp=T1_to_MNI_nonlin_coeff.nii.gz \
+          --out=FLAIR_biascorr_brain_to_MNI_nonlin \
+          --interp=trilinear --ref=${FSLDIR}/data/standard/MNI152_T1_1mm_brain.nii.gz
+
    echo all done!
    echo
 }
@@ -347,7 +369,11 @@ function runAnalysis (){
    processOutputs
 
    cd ${data_outpath}/output
-   zip -q ../${subject}_${session}_results.zip results2mni_lin*.nii.gz results2mni_nonlin*.nii.gz
+   zip -q ../${subject}_${session}_results.zip \
+      results2mni_lin*.nii.gz \
+      results2mni_nonlin*.nii.gz \
+      T1_biascorr_brain_to_MNI_*lin.nii.gz \
+      FLAIR_biascorr_brain_to_MNI_*lin.nii.gz
 
 }