Hi
If you use multiple seed masks with the GUI, a text file is created with the list of seed masks and stored inside the output folder.
If you want to use the command line, you need to create that text file (using full paths to each seed mask) and pass that on as the -x option.
The xfm option should be fine, you don’t need to change that compared to what the GUI does.
Cheers,
Saad
> On 5 May 2017, at 13:17, Joe Harding <[log in to unmask]> wrote:
>
> Hello,
>
> I was wondering if you could help me run a probtractX analysis from the command line. I’ve run the process numerous times successfully from the GUI:
>
> On the ProbtractX tab of the FSL GUI, I input the BedpostX directory, select Multiple masks for seed space, add two masks to the mask list, select the option seed space is not diffusion, select the patient's xfms/standard2diff.mat file, select a termination mask and then define the output directory.
>
> Now I want to run exactly the same type of analysis (with the same masks - left thalamus and left PSC, and left PSC as the termination mask) but from the command line. This would allow me to write out all the commands and leave the computer for ages to run each patient in turn, rather than having to come back every day. However I just can’t seem to get my command right.
>
> When I run the GUI as explained above, the following command line appears in the terminal:
>
> rm -rf /Users/Dinesh/Documents/JoeNewDTI/Tractography/136799.probtrackX_left_BA1
> mkdir -p /Users/Dinesh/Documents/JoeNewDTI/Tractography/136799.probtrackX_left_BA1
> /usr/local/fsl/bin/probtrackx2 --network -x /Users/Dinesh/Documents/JoeNewDTI/Tractography/136799.probtrackX_left_BA1/masks.txt -l --onewaycondition -c 0.2 -S 2000 --steplength=0.5 -P 5000 --fibthresh=0.01 --distthresh=0.0 --sampvox=0.0 --xfm=/Users/Dinesh/Documents/JoeNewDTI/Tractography/136799.bedpostX/xfms/standard2diff.mat --stop=/Users/Dinesh/Documents/JoeNewDTI/Tractography/PSC_Left_BA1.nii.gz --forcedir --opd -s /Users/Dinesh/Documents/JoeNewDTI/Tractography/136799.bedpostX/merged -m /Users/Dinesh/Documents/JoeNewDTI/Tractography/136799.bedpostX/nodif_brain_mask --dir=/Users/Dinesh/Documents/JoeNewDTI/Tractography/136799.probtrackX_left_BA1
>
> However when I try to copy and paste this same command (and just change all the patient numbers) it give me the error message,
> “load seeds
> /Users/Dinesh/Documents/JoeNewDTI/Tractography/136805.probtrackX_left_BA1/masks.txt does not exist”
>
> I've tried saving the two masks as a list (so it's just one file) but that hasn't worked either.
>
> The bit I'm most confused about is the -s and the -x options. I don't know how to specify to the command that the seed space is multiple masks (and what these masks are), or that the seed space is not diffusion (and where the xfms/standard2diff.mat file is).
>
> Please could you help me? What command line would you use?
>
> Thank you in advance
>
> Joe (medical student, Sheffield)
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