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add missing singularity --bind paths and add matlab rethrow error #8

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add missing singularity --bind paths and add matlab rethrow error #8

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3afbaf9
add missing --bind paths for singularity commands
epongpipat Dec 11, 2023
e745b05
print error code from matlab
epongpipat Dec 11, 2023
b781450
add missing --bind paths for singularity commands
epongpipat Dec 11, 2023
a466687
add rethrow error to matlab cmd
epongpipat Dec 11, 2023
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31 changes: 18 additions & 13 deletions Functions/MEDI.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -83,8 +83,13 @@ echo "Copying DICOM files from $QSM_Dicom_Dir to $OutFolder/$Subj/QSM/QSM_DICOM"
echo ""


singularity run -e --bind $QSM_Dicom_Dir:/mnt $Path/Functions/QSM_Container.simg find /mnt -mindepth 1 -maxdepth 1 -type f ! \
-regex '.*\(nii\|json\|txt\|nii.gz\|HEAD\|BRIK\|hdr\|img\)$' -exec cp '{}' 'QSM_DICOM/' ';'
singularity run \
-e \
--bind $QSM_Dicom_Dir:/mnt \
--bind $OutFolder/$Subj/QSM \
$Path/Functions/QSM_Container.simg \
find /mnt -mindepth 1 -maxdepth 1 -type f ! \
-regex '.*\(nii\|json\|txt\|nii.gz\|HEAD\|BRIK\|hdr\|img\)$' -exec cp '{}' 'QSM_DICOM/' ';'


echo ""
Expand All @@ -103,8 +108,8 @@ cd QSM_DICOM

#Figure out which nifti file is the Mag and which is the Phase and check if they exist and if correct

File1=$(singularity run -e $Path/Functions/QSM_Container.simg find ${Subj}_QSM_Files*.nii.gz -maxdepth 1 -printf "%s\t%p\n" | sort -nr | sed -n '1p' | awk 'FNR == 1 {print $2}') #presumably phase
File2=$(singularity run -e $Path/Functions/QSM_Container.simg find ${Subj}_QSM_Files*.nii.gz -maxdepth 1 -printf "%s\t%p\n" | sort -nr | sed -n '2p' | awk 'FNR == 1 {print $2}') #presumably magnitude
File1=$(singularity run -e --bind $OutFolder/$Subj/QSM/QSM_DICOM $Path/Functions/QSM_Container.simg find ${Subj}_QSM_Files*.nii.gz -maxdepth 1 -printf "%s\t%p\n" | sort -nr | sed -n '1p' | awk 'FNR == 1 {print $2}') #presumably phase
File2=$(singularity run -e --bind $OutFolder/$Subj/QSM/QSM_DICOM $Path/Functions/QSM_Container.simg find ${Subj}_QSM_Files*.nii.gz -maxdepth 1 -printf "%s\t%p\n" | sort -nr | sed -n '2p' | awk 'FNR == 1 {print $2}') #presumably magnitude

echo ""
echo "Largest .nii.gz file in `pwd` is $File1, possibly the PHASE Scan"
Expand All @@ -116,7 +121,7 @@ echo ""

if [[ $File1 == "${Subj}_QSM_Files"*"_ph".nii.gz ]]; then

QSM_Echos_File1=$(singularity run -e $Path/Functions/QSM_Container.simg 3dinfo -nv $File1)
QSM_Echos_File1=$(singularity run -e --bind $OutFolder/$Subj/QSM/QSM_DICOM $Path/Functions/QSM_Container.simg 3dinfo -nv $File1)
#QSM_Echos_File1=3

echo ""
Expand Down Expand Up @@ -176,7 +181,7 @@ fi

if [[ $File2 == "${Subj}_QSM_Files"*.nii.gz ]]; then

QSM_Echos_File2=$(singularity run -e $Path/Functions/QSM_Container.simg 3dinfo -nv $File2)
QSM_Echos_File2=$(singularity run -e --bind $OutFolder/$Subj/QSM/QSM_DICOM $Path/Functions/QSM_Container.simg 3dinfo -nv $File2)
#QSM_Echos_File2=3

echo ""
Expand Down Expand Up @@ -273,7 +278,7 @@ fi
cd $OutFolder/$Subj/QSM
mv QSM_DICOM/*.nii.gz .

ObliFile1=$(singularity run -e $Path/Functions/QSM_Container.simg 3dinfo -is_oblique ${Subj}_QSM_Mag.nii.gz)
ObliFile1=$(singularity run -e --bind $OutFolder/$Subj/QSM $Path/Functions/QSM_Container.simg 3dinfo -is_oblique ${Subj}_QSM_Mag.nii.gz)

if (( $ObliFile1 == 1 )); then

Expand All @@ -284,10 +289,10 @@ if (( $ObliFile1 == 1 )); then
mv ${Subj}_QSM_Mag.nii.gz ${Subj}_QSM_Mag_Obli.nii.gz
mv ${Subj}_QSM_PHASE.nii.gz ${Subj}_QSM_PHASE_Obli.nii.gz

singularity run -e $Path/Functions/QSM_Container.simg \
singularity run -e --bind $OutFolder/$Subj/QSM/QSM_DICOM $Path/Functions/QSM_Container.simg \
3dWarp -deoblique -wsinc5 -prefix ${Subj}_QSM_Mag.nii.gz ${Subj}_QSM_Mag_Obli.nii.gz

singularity run -e $Path/Functions/QSM_Container.simg \
singularity run -e --bind $OutFolder/$Subj/QSM/QSM_DICOM $Path/Functions/QSM_Container.simg \
3dWarp -deoblique -wsinc5 -prefix ${Subj}_QSM_PHASE.nii.gz ${Subj}_QSM_PHASE_Obli.nii.gz

fi
Expand Down Expand Up @@ -382,7 +387,7 @@ echo ""
#Run MEDI_QSM.m FILE to create a QSM map
#stty -tostop
#$MatPath -nodisplay -nosplash -nodesktop -batch <-- Matlab 2020 only
$MatPath -nodisplay -nosplash -nodesktop -r "try; Subj_${Subj}_MEDI_QSM; catch warning('*ERROR*ERROR*ERROR*'); end; quit" #> ${Subj}_MEDI_Matlab_Log.txt
$MatPath -nodisplay -nosplash -nodesktop -r "try; Subj_${Subj}_MEDI_QSM; catch ME; warning('*ERROR*ERROR*ERROR*'); rethrow(ME); end; quit" #> ${Subj}_MEDI_Matlab_Log.txt

if (grep -Fq "*ERROR*ERROR*ERROR*" $log_file); then #${Subj}_MEDI_Matlab_Log.txt

Expand Down Expand Up @@ -419,7 +424,7 @@ else
#mv QSM_Orig_Mask_CSF/${Subj}_QSM_Orig_Mask_CSF*.nii.gz QSM_Orig_Mask_CSF/${Subj}_QSM_Orig_Mask_CSF.nii.gz

unset ObliFileQSM
ObliFileQSM=$(singularity run -e $Path/Functions/QSM_Container.simg 3dinfo -is_oblique ${Subj}_QSM_Map.nii.gz)
ObliFileQSM=$(singularity run -e --bind $OutFolder/$Subj/QSM $Path/Functions/QSM_Container.simg 3dinfo -is_oblique ${Subj}_QSM_Map.nii.gz)

if (( $ObliFileQSM == 1 )); then

Expand All @@ -431,10 +436,10 @@ else
mv ${Subj}_RDF.nii.gz ${Subj}_RDF_Obli.nii.gz
mv QSM_Orig_Mask_CSF/${Subj}_QSM_Orig_Mask_CSF*.nii.gz QSM_Orig_Mask_CSF/${Subj}_QSM_Orig_Mask_CSF_Obli.nii.gz

singularity run -e $Path/Functions/QSM_Container.simg \
singularity run -e --bind $OutFolder/$Subj/QSM $Path/Functions/QSM_Container.simg \
3dWarp -deoblique -wsinc5 -prefix ${Subj}_QSM_Map.nii.gz ${Subj}_QSM_Map_Obli.nii.gz

singularity run -e $Path/Functions/QSM_Container.simg \
singularity run -e --bind $OutFolder/$Subj/QSM $Path/Functions/QSM_Container.simg \
3dWarp -deoblique -wsinc5 -prefix ${Subj}_RDF.nii.gz ${Subj}_RDF_Obli.nii.gz

singularity run -e --bind $OutFolder/$Subj/QSM $Path/Functions/QSM_Container.simg \
Expand Down
8 changes: 4 additions & 4 deletions Functions/MEDI_QSM_New_Ref.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -424,7 +424,7 @@ echo ""
#Run MEDI_QSM_New_Ref.m FILE to create QSM Maps with new CSF and new WM masks as reference
#stty -tostop
#$MatPath -nodisplay -nosplash -nodesktop -batch <-- Matlab 2020 only
$MatPath -nodisplay -nosplash -nodesktop -r "try; Subj_${Subj}_MEDI_QSM_New_Ref; catch warning('*ERROR*ERROR*ERROR*'); end; quit" #> ${Subj}_MEDI_New_Ref_Matlab_Log.txt
$MatPath -nodisplay -nosplash -nodesktop -r "try; Subj_${Subj}_MEDI_QSM_New_Ref; catch ME; warning('*ERROR*ERROR*ERROR*'); rethrow(ME); end; quit" #> ${Subj}_MEDI_New_Ref_Matlab_Log.txt

if (grep -Fq "*ERROR*ERROR*ERROR*" $log_file); then #${Subj}_MEDI_New_Ref_Matlab_Log.txt

Expand Down Expand Up @@ -464,7 +464,7 @@ else
#mv QSM_New_Mask_WM/${Subj}_QSM_New_Mask_WM*.nii.gz QSM_New_Mask_WM/${Subj}_QSM_New_Mask_WM.nii.gz

unset ObliFileQSM
ObliFileQSM=$(singularity run -e $Path/Functions/QSM_Container.simg 3dinfo -is_oblique ${Subj}_QSM_Map_New_CSF.nii.gz)
ObliFileQSM=$(singularity run -e --bind $OutFolder/$Subj/QSM $Path/Functions/QSM_Container.simg 3dinfo -is_oblique ${Subj}_QSM_Map_New_CSF.nii.gz)

if (( $ObliFileQSM == 1 )); then

Expand All @@ -477,10 +477,10 @@ else
mv QSM_New_Mask_CSF/${Subj}_QSM_New_Mask_CSF*.nii.gz QSM_New_Mask_CSF/${Subj}_QSM_New_Mask_CSF_Obli.nii.gz
mv QSM_New_Mask_WM/${Subj}_QSM_New_Mask_WM*.nii.gz QSM_New_Mask_WM/${Subj}_QSM_New_Mask_WM_Obli.nii.gz

singularity run -e $Path/Functions/QSM_Container.simg \
singularity run -e --bind $OutFolder/$Subj/QSM $Path/Functions/QSM_Container.simg \
3dWarp -deoblique -wsinc5 -prefix ${Subj}_QSM_Map_New_CSF.nii.gz ${Subj}_QSM_Map_New_CSF_Obli.nii.gz

singularity run -e $Path/Functions/QSM_Container.simg \
singularity run -e --bind $OutFolder/$Subj/QSM $Path/Functions/QSM_Container.simg \
3dWarp -deoblique -wsinc5 -prefix ${Subj}_QSM_Map_New_WM.nii.gz ${Subj}_QSM_Map_New_WM_Obli.nii.gz

singularity run -e --bind $OutFolder/$Subj/QSM $Path/Functions/QSM_Container.simg \
Expand Down