fix reference to fsl src dir in additional pipeline

[jcupitt]

The additional pipeline contains a reference to the src dir of FSL in an invocation of flirt -- this fails on systems with only a binary install.

This patch change this to etc, which is where the .sch files are kept for binary installs.

https://github.com/jcupitt/structural-pipeline/commit/f33e1cd10e1ac61cf7605bed7a15283c7363176d

[jcupitt]

Ooop, the line should be:

    run flirt -in T1/$subj.nii.gz -ref T2/$subj.nii.gz -omat dofs/$subj-T2-T1-r.mat -dof 6 -cost bbr -wmseg dofs/${subj}_wmseg.nii.gz -init dofs/$subj-T2-T1-init-r.mat -schedule $FSLDIR/etc/flirtsch/bbr.sch -bbrslope -0.5 -bbrtype signed -verbose 0 -usesqform

ie. flirtsch/bbr.sch, not flirt/flirtsch/bbr.sch

[zeydabadi]

Hi,
I ran this the command below:
~/dhcp/dhcp-pipeline.sh /home/zeydabadi/data/sourcedata/sub-00008T03 ses-1 50 -T2 anat/sub-00008T03_ses-1_acq-SPC_run-1_T2w.nii.gz

and here is the error log:
cat: /parameters/cortical.csv: No such file or directory
/home/zeydabadi/dhcp/scripts/segmentation/../../parameters/configuration.sh: line 45: /pipelines/neonatal-pipeline.sh: No such file or directory

Any idea how to fix this?

Thank you!
Mahmoud

[amakropoulos]

Hi Mahmoud,

Have you run the pipeline setup?
If yes, can you see a path.sh file inside the parameters directory?

Regards,
Antonis