Merge pull request KUL-Radneuron#5 from treanus/dev

Dev
treanus · Nov 11, 2021 · 27443a9 · 27443a9
2 parents ceb9896 + caf4cb4
commit 27443a9
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Showing 4 changed files with 58 additions and 5 deletions.
diff --git a/KUL_VBG.sh b/KUL_VBG.sh
@@ -323,7 +323,11 @@ if [[ "$bids_flag" -eq 1 ]] && [[ "$s_flag" -eq 0 ]]; then
 
 		# now we need to search for the images
 		# then also find which modalities are available and set wf accordingly
-
+
+        ### STEFAN NEED TO DO: check what is the best input T1w: with or whitout Gd?
+        ### to select use something like:
+        ### find_T1w=($(find ${cwd}/BIDS/sub-${participant}/anat/ -name "*_T1w.nii.gz" ! -name "*gadolinium*"))
+
 		search_T1=($(find $search_sessions -type f | grep T1w.nii.gz));
 		# search_T2=($(find $search_sessions -type f | grep T2w.nii.gz));
 		# search_FLAIR=($(find $search_sessions -type f | grep FLAIR.nii.gz));
@@ -371,8 +375,12 @@ elif [[ "$bids_flag" -eq 1 ]] && [[ "$s_flag" -eq 1 ]]; then
 	if [[ "$num_sessions" -eq 1 ]]; then 
 
 		echo " One session " $ses " specified in BIDS dir, good."
+
+		### STEFAN NEED TO DO: check what is the best input T1w: with or whitout Gd?
+        ### to select use something like:
+        ### find_T1w=($(find ${cwd}/BIDS/sub-${participant}/anat/ -name "*_T1w.nii.gz" ! -name "*gadolinium*"))
 
-		search_T1=($(find $search_sessions -type f | grep T1w.nii.gz));
+        search_T1=($(find $search_sessions -type f | grep T1w.nii.gz));
 		# search_T2=($(find $search_sessions -type f | grep T2w.nii.gz));
 		# search_FLAIR=($(find $search_sessions -type f | grep flair.nii.gz));
 
@@ -392,6 +400,9 @@ elif [[ "$bids_flag" -eq 1 ]] && [[ "$s_flag" -eq 1 ]]; then
 
     fi
 
+
+
+    ### STEFAN NEED TO DO: prefer to set KUL_compute/sub-participant/VBG as default output?
     if [[ "$o_flag" -eq 0 ]]; then
 
         output_d="${cwd}/BIDS/derivatives/output_VBG/${subj}${ses_long}"
@@ -1086,6 +1097,7 @@ function task_exec {
 
     wait ${pid}
 
+    ### STEFAN NEED TO DO: is the sleep needed, or can it be shorter?
     sleep 5
 
     if [ $? -eq 0 ]; then
@@ -1155,6 +1167,11 @@ function KUL_antsBETp {
 
     # task_exec
 
+    ### STEFAN NEED TO DO: nvcc is not always installed even if you have a working nvidia GPU
+    ### it would be better to check the available free GPU mem
+    ### This can be done with, outputs kb
+    ### nvidia-smi --query-gpu=memory.free --format=csv
+    ### and if more the 4096 continue with GPU
     nvd_cu=$(nvcc --version)
 
     if [[ ${BET_m} -eq 1 ]]; then

diff --git a/README.md b/README.md
@@ -1,17 +1,53 @@
 # KUL_VBG
-A workflow to allow Freesurfer recon-all to run on brain images with large lesions.
-VBG is a bash script tested in Mac OSX, Ubuntu 18.0 and CentOS. 
 
-The first commit on this repository corresponds to the version of the workflow used in the preprint "Virtual brain grafting: Enabling whole brain parcellation in the presence of large lesions. Radwan et al., 2020, DOI: https://doi.org/10.1101/2020.09.30.20204701, available via: https://www.medrxiv.org/content/10.1101/2020.09.30.20204701v1). This work was published in Neuroimage, 2021 available here: https://doi.org/10.1016/j.neuroimage.2021.117731
+KUL_VBG or "KULeuven - Virtual brain grafting" enables whole brain parcellation in the presence of large lesions.
+
+Whole brain parcellation means labeling the brain in parts, gyri, etc...
+Many parcellation software packages fail in the presence of large brain lesions.
+
+The approach taken here is to:
+
+- extract the gross brain lesion using a mask
+- replace the brain lesion with normal looking tissue (hence virtual brain grafting)
+- run parellation software like freesufer or fastsurfer (which only work well on non-lesioned brains)
+- reinsert the lesion mask into the parcellation 
+
+## Introduction 
+
+For reference we point to the paper published in Neuroimage, 2021 available here: https://doi.org/10.1016/j.neuroimage.2021.117731
+
+## Posing the problem and solution
+
+An image to explain the problem: Freesurfer will not parcellate these brains
+
+![VBG fig1](figs4readme/fig1.jpg)
+
+The graphical solution of the VBG workflow is show here:
+
+![VBG fig1](figs4readme/fig2.jpg)
+
+
+## Using VBG
+
+VBG was tested in Mac OSX, WSL2 on WIN11, Ubuntu 18.0, 20.04 and CentOS. 
 
 **Updated Dependencies:**
+
 a) ANTs v2.3.1 and ANTsX scripts
+
 b) FSL v6.0
+
 c) MRtrix3 v3.0.2-64-g3eadb340
+
 d) HD-BET
+
 f) Freesurfer v6.0
+
 e) FastSurfer
 
+
+## Examples
+
 Inputs:
 
 Obligatory: 

diff --git a/figs4readme/fig1.jpg b/figs4readme/fig1.jpg
diff --git a/figs4readme/fig2.jpg b/figs4readme/fig2.jpg