diff --git a/handler/ezBIDS_core/ezBIDS_core.py b/handler/ezBIDS_core/ezBIDS_core.py
index dbe29c3e..f1bea8fa 100755
--- a/handler/ezBIDS_core/ezBIDS_core.py
+++ b/handler/ezBIDS_core/ezBIDS_core.py
@@ -504,9 +504,11 @@ def modify_uploaded_dataset_list(uploaded_img_list):
elif any(x.endswith(tuple(['.v', '.v.gz'])) for x in grouped_files):
grouped_files = [x for x in grouped_files if not x.endswith(tuple(['.v', '.v.gz']))]
- # If imaging file comes with additional data (JSON, bval/bvec) add them to list for processing
- if len(grouped_files) > 1:
- uploaded_files_list.append(grouped_files)
+ # Don't want this section is we're allowing only NIfTI files to be uploaded (group length will only be 1).
+ # # If imaging file comes with additional data (JSON, bval/bvec) add them to list for processing
+ # if len(grouped_files) > 1:
+ # uploaded_files_list.append(grouped_files)
+ uploaded_files_list.append(grouped_files)
# Flatten uploaded_files_list
uploaded_files_list = natsorted([file for sublist in uploaded_files_list for file in sublist])
@@ -913,7 +915,9 @@ def generate_dataset_list(uploaded_files_list, exclude_data):
for img_file in img_list:
# Find file extension
if img_file.endswith('.nii.gz'):
- ext = 'nii.gz'
+ ext = '.nii.gz'
+ elif img_file.endswith('.v.gz'):
+ ext = '.v.gz'
else:
ext = Path(img_file).suffix
diff --git a/handler/find_img_data.py b/handler/find_img_data.py
index a047f6a5..5f54cd55 100755
--- a/handler/find_img_data.py
+++ b/handler/find_img_data.py
@@ -64,8 +64,8 @@ def find_img_data(dir):
# PET
+# TODO - These two lines take several seconds to complete, maybe can be sped up?
pet_folders = [str(folder) for folder in is_pet.pet_folder(Path(root).resolve())]
-
pet_folders = [os.path.relpath(x, root) for x in pet_folders if x != '']
pet_folders = [os.path.join('.', x) for x in pet_folders]
diff --git a/handler/preprocess.sh b/handler/preprocess.sh
index 6d24eca1..bb4815f8 100755
--- a/handler/preprocess.sh
+++ b/handler/preprocess.sh
@@ -92,9 +92,13 @@ if [ $bids_compliant == "true" ]; then
touch $root/dcm2niix_output
touch $root/dcm2niix_error
+
+ touch $root/pet2bids_output
+ touch $root/pet2bids_error
# find products (NIfTI files)
- (cd $root && find . -maxdepth 9 -type f \( -name "*.nii.gz" \) > list)
+ (cd $root && find . -maxdepth 9 -type f \( -name "*.nii.gz" \) > $root/list)
+ (cd $root && find . -maxdepth 9 -type f \( -name "*blood.json" \) >> $root/list)
echo "running ezBIDS_core (may take several minutes, depending on size of data)"
python3 "./ezBIDS_core/ezBIDS_core.py" $root
@@ -142,13 +146,15 @@ else
# determine which uploaded files/folders are PET directories or ECAT files
echo "Finding imaging directories and files"
- if [ ! -f $root/list]; then
- mkdir -p $root/list
+ if [ ! -f $root/list ]; then
+ touch $root/list
fi
./find_img_data.py $root
# sort $root/pet2bids_dcm.list, $root/pet2bids_ecat.list, and $root/dcm2niix.list for comm.
# Then, remove pet directories from dcm2niix list
+ touch $root/pet2bids_output
+
if [ -f $root/pet2bids_dcm.list ]; then
sort -o $root/pet2bids_dcm.list $root/pet2bids_dcm.list
echo "Removing PET directories from dcm2niix list"
@@ -216,17 +222,41 @@ else
done
fi
- # Let's add the transformed raw data (i.e. to NIfTI or MEG formats) to the list file
-
- (cd $root && find . -maxdepth 9 -type f \( -name "*.nii.gz" \) > list)
- (cd $root && find . -maxdepth 9 -type f \( -name "*blood.json" \) >> list)
+ # Check for pet2bids errors
+ if [[ $PET2BIDS_RUN -eq "true" ]]; then
+ # pull pet2bids error information to log file
+ { grep -B 1 --group-separator=$'\n\n' Error $root/pet2bids_output || true; } > $root/pet2bids_error
+ # # remove error message(s) about not finding any DICOMs in folder
+ line_nums=$(grep -n 'Error: Unable to find any DICOM images' $root/pet2bids_error | cut -d: -f1)
+
+ for line_num in ${line_nums[*]}
+ do
+ sed -i "$((line_num-1)), $((line_num+1))d" $root/pet2bids_error
+ done
+ fi
+
+ # Add all transformed data (e.g. NIfTI or MEG formats) to the list file
+ (cd $root && find . -maxdepth 9 -type f \( -name "*.nii.gz" \) > $root/list)
+ (cd $root && find . -maxdepth 9 -type f \( -name "*blood.json" \) >> $root/list)
if [ -f $root/meg.list ]; then
cat $root/meg.list >> $root/list
fi
if [ ! -s $root/list ]; then
- echo "Could not find any MRI, PET, or MEG imaging files in upload, aborting"
+ err_file=''
+ if [ `grep 'Error' $root/dcm2niix_error | wc -l` -ne 0 ]; then
+ err_file='dcm2niix_error'
+ fi
+
+ if [ `grep 'Error' $root/pet2bids_error | wc -l` -ne 0 ]; then
+ err_file='pet2bids_error'
+ fi
+
+ echo ""
+ echo "Error: Could not find any MRI, PET, or MEG imaging files in upload."
+ echo "Please click the Debug section below and select Download ${err_file}"
+ echo "We recommend reaching out to the dcm2niix team for assistance: https://github.com/rordenlab/dcm2niix/issues"
exit 1
fi
diff --git a/ui/src/Upload.vue b/ui/src/Upload.vue
index 848cd232..4c94c122 100644
--- a/ui/src/Upload.vue
+++ b/ui/src/Upload.vue
@@ -149,7 +149,8 @@
<div v-if="session.status == 'failed'">
<el-alert type="error"
- >ezBIDS failed.. Please check the Debug logs and contact ezBIDS team (dlevitas@iu.edu).</el-alert
+ >ezBIDS failed.. Please check the Debug logs and contact the ezBIDS team
+ (dlevitas@iu.edu).</el-alert
>
<br />
<pre class="status">{{ session.status_msg }}</pre>
@@ -190,7 +191,7 @@
<div v-if="!ezbids.notLoaded && !ezbids.objects.length">
<el-alert type="error"
>We couldn't find any objects. Please upload data that contains at least 1 object. Contact the
- ezBIDS team (dlevitas@iu.edu) or https://github.com/brainlife/ezbids/issues for
+ ezBIDS team (dlevitas@iu.edu or https://github.com/brainlife/ezbids/issues) for
support</el-alert
>
</div>
@@ -213,6 +214,9 @@
<el-button type="warning" size="mini" @click="downloadFile('dcm2niix_error')"
>Download dcm2niix_error</el-button
>
+ <el-button type="warning" size="mini" @click="downloadFile('pet2bids_error')"
+ >Download pet2bids_error</el-button
+ >
<el-button type="warning" size="mini" @click="downloadFile('list')">Download list</el-button>
<el-button type="warning" size="mini" @click="downloadFile('ezBIDS_core.json')"
>Download ezBIDS_core.json</el-button