Does "masks.txt" exist? Because you create the directory immediately before running probtrackx2, in which you use that file as input.
Are there supposed to be square brackets around the file for "--targetmasks"?

What error message(s) do you get?

On 05/30/2013 03:26 PM, Thushini Manuweera wrote:

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Hello!

I am trying to create a script to run probtrackx to generate tractography between two masks. However, I have not been able to successfully run the script. Shown below is the script that I created. I would really appreciate it if someone could please help me out, to try understand what I am doing wrong.

subjs="sub1 sub2" 


cd ~/Documents/DTI/ecc/

for s in ${subjs}  
do
echo "Tractography for subject ${s}"

mkdir -p /home/fsl/Documents/DTI/Masks/${s}_prec
probtrackx2 --network -x /home/fsl/Documents/DTI/Masks/${s}_prec/masks.txt  -l --onewaycondition -c 0.2 -S 2000 --steplength=0.5 -P 5000 --fibthresh=0.01 --distthresh=0.0 --sampvox=0.0 --xfm=/home/fsl/Documents/DTI/ecc/${s}.bedpostX/xfms/standard2diff.mat --targetmasks=[/home/fsl/Documents/DTI_stroke/Masks/masks.txt] --forcedir --opd -s /home/fsl/Documents/DTI/ecc/${s}.bedpostX/merged -m /home/fsl/Documents/DTI/ecc/${s}.bedpostX/nodif_brain_mask.nii.gz  --dir=/home/fsl/Documents/DTI/Masks/${s}_prec
mv /home/fsl/Documents/DTI/Masks/${s}_prec/fdt_log.tcl /home/fsl/Documents/DTI/Masks/${s}_prec/fdt.log

done 

I have created a text file that has the directory of the two masks.

thanks in advance!

Thushini