fix for 7T grad correction, and bedpost # of files

Singularity.0.0.7g

@@ -0,0 +1,33 @@
+Bootstrap: shub
+From: khanlab/neuroglia-dwi:v1.3.1
+
+
+%labels
+Maintainer "Ali Khan"
+
+#########
+%setup
+#########
+mkdir -p $SINGULARITY_ROOTFS/opt/prepdwi
+cp -Rv . $SINGULARITY_ROOTFS/opt/prepdwi
+
+
+#########
+%post
+#########
+
+
+echo addpath\(genpath\(\'/opt/prepdwi/octave\'\)\)\; >> /etc/octave.conf 
+apt-get install -y bc
+
+#########
+%environment
+#########
+
+export PATH=/opt/prepdwi/bin:$PATH
+
+#########
+%runscript
+#########
+
+exec /opt/prepdwi/prepdwi $@

bin/importDWI

@@ -5,7 +5,7 @@
 
 if [ "$#" -lt 4 ]
 then
- echo "Command-line Usage: $0 <out folder name - e.g. multiband or singleband> <number of dwi acquisitions> <input DWI blip 1 > <input DWI blip 2 > ..   <subjid> <optional resample resolution>"
+ echo "Command-line Usage: $0 <out folder name - e.g. multiband or singleband> <number of dwi acquisitions> <input DWI blip 1 > <input DWI blip 2 > ..   <subjid>"
  exit 0
 fi
 
@@ -38,13 +38,6 @@ done
 
 subj=$1
 
-resample_res=
-if [ "$#" -gt 1 ]
-then
-    resample_res=$2
-fi
-
-
 
 
 
@@ -76,13 +69,6 @@ cp -v ${in_json[$i]} $uncorr_dir/dwi_$i.json
 cp -v ${in_bvec[$i]} $uncorr_dir/dwi_$i.bvec
 cp -v ${in_bval[$i]} $uncorr_dir/dwi_$i.bval
 
-if [ -n "$resample_res" ]
-then
- echo "Resampling to isotropic resolution $resample_res"
- echo mri_convert $uncorr_dir/dwi_$i.nii.gz $uncorr_dir/dwi_$i.nii.gz -vs $resample_res $resample_res $resample_res
- mri_convert $uncorr_dir/dwi_$i.nii.gz $uncorr_dir/dwi_$i.nii.gz -vs $resample_res $resample_res $resample_res
-fi
-
 
 done
 

bin/processBedpost

@@ -35,9 +35,14 @@ subj_dir=$output_dir/$subj
 dwi_dir=$subj_dir/dwi/${in_dwi}
 out_dir=$subj_dir/dwi/${out_name}
 
-
-bedpost_data=$dwi_dir/bedpost
-mkdir -p $bedpost_data
+    if [ -n "$scratch_dir" ] #if running on compute cluster, use scratch dir
+    then
+        bedpost_data=$scratch_dir/bedpost
+    else
+        bedpost_data=$dwi_dir/bedpost
+    fi
+
+    mkdir -p $bedpost_data
 
 dwi_bvec=$dwi_dir/dwi.bvec
 dwi_bval=$dwi_dir/dwi.bval
@@ -71,7 +76,16 @@ fslmaths $nodif_brain_mask -bin $nodif_brain_mask
 
 bedpostx-parallel  $bedpost_data/ -c -P $n_cpus $gradopt
 
+ #remove unneeded diff_slice files:
+ rm -rf $bedpost_data.bedpostX/diff_slices
+
 
+    if [ -n "$scratch_dir" ] #if running on compute cluster, use scratch dir
+    then
+        final_bedpost_data=$dwi_dir/bedpost
+        mv -v  $bedpost_data $final_bedpost_data
+        mv -v $bedpost_data.bedpostX $final_bedpost_data.bedpostX
+    fi
 
 done
 

bin/processGradUnwarp

@@ -168,8 +168,9 @@ if [ "$do_regT1" = 1 ]
  then
 
 #rotate bvec
-echo rotate_bvecs $dwi_bvec $xfm_b0_t1 $out_dir/dwi.bvec
-rotate_bvecs $dwi_bvec $xfm_b0_t1 $out_dir/dwi.bvec
+echo octave --eval "rotate_bvecs_imgorient('$dwi_bvec','$xfm_b0_t1','$b0','$b0_t1_ref','$out_dir/dwi.bvec')"
+octave --eval "rotate_bvecs_imgorient('$dwi_bvec','$xfm_b0_t1','$b0','$b0_t1_ref','$out_dir/dwi.bvec')"
+
 
 else
 cp -v $dwi_bvec $out_dir/dwi.bvec