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 Read further if:

  • you develop or run image processing locally in bash;
  • you want to use XNAT as data source and/or remote archive;
  • you want to automate processing of multiple XNAT sessions and want to report your results in spreadsheets.
  • you want to focus on local script development and minimize programming effort to interact with XNAT.

Use case: compute BET whole brain volume for all MPRAGE scans in an MRI project in XNAT and save statistics in a spreadsheet.

1. Write a bash script that computes brain volume on a DICOM brain (assuming FSL v4+ is on the path).

brain_volume.sh
#!/bin/bash
in=$1 #input DICOM scan
dcm2nii $in
cp $in/[0-9]*.nii head.nii
if [ ! -f "head.nii" ]; then exit -1; fi
bet head brain -m
vol=(`fslstats brain_mask -V`); vol=${vol[1]}
#report the volume in mm3 to console.
echo $vol

2. Create a spreadsheet listing all scans that you want to process. In many cases, you'll have such spreadsheet; if not, you can start with the one created using the one generated by XNAT:


Now, modify the spreadsheet so that column names don't contain spaces, empty and irrelevant cells are removed, and change column "Scans" to "T1", with scan numbers that we want to process per each session. If any fields have trailing zeroes, you'll need to modify the csv outside of Excel to add them.



3. Now we are ready to adapt the brain_volume.sh to process all sessions from test.csv.

brain_volume.xt
#!/bin/bash
#this line will convert test.csv to a bash source test.params that assigns corresponding arrays.
rcsv test.csv `pwd`/test.params; source `pwd`/test.params; rm test.params
#as a result, the following arrays are assigned:
#MR_ID=("001_obscured" "002_obscured" ...
#Subject=("001" "002" "003" ...
#Scans=("SPGR" "SPGR" "SPGR" ...
#now, iterate over all MR sessions.
set -x
for ((i=0; i<${#MR_ID[*]}; i++)); do
    #this will create directory named ${MR_ID[i]} and cd to it.
    set_context ${Subject[i]} ${MR_ID[i]}
    #load specified scan from XNAT.
    load_type "${Scans[i]}"
    #find the scan that was created by load_type.
    set -x
    in=`ls -d study*`
    #compute brain volume, similarly to brain_volume.sh
     dcm2nii $in
    #select 
    cp $in/[0-9]*[0-9].nii head.nii
    if [ ! -f "head.nii" ]; then exit -1; fi
    bet head brain -m
    vol=(`fslstats brain_mask -V`); vol=${vol[1]}
    #except, now we use special command to save a variable with this offline session.
    save_vars vol
    break
done
#return to the starting directory.
set_context null 
#this will go through all sessions and generate a spreadsheet summarizing variables saved with "save_vars" command.
summary mpr_vol

  

4. Test the batch processing.

We will run the developed script on a single session to see if it works. For that, uncomment break statement on line 26. Now we are ready to run the script:

running brain_volume.xt
xtolm -sr https://central.xnat.org -u your_xnat_central_user -pr surfmask_smpl -o brain_volume.xt
cat mpr_vol.csv

After making sure that mpr_vol.csv produces correct output, comment the break statement on line 26 and rerun the brain_volume.xt. Now we'll have the BET calculations saved in a single csv file.


















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