Dear all,
I've (belatedly) updated FSL from version 4.1.4 to 4.1.5 (on Mac OS
X.5.8), and some of my scripts are now running into problems which
seem to be related to the naming of output files by probtrackx. Did
these change in this patch?
The command I use is below [1]. As far as I remember this form has
worked fine since v4.0.0, with the effect that visitation maps were
created as ".../fdt.track/IMAGE_x_y_z.nii.gz". But now I get the error
shown underneath [2]. It seems that probtrackx now puts the value of
the -o flag after that of the --dir flag to establish its output file,
but if both are given as full paths, as here, then this clearly
doesn't work.
My question is, assuming something did change in FSL 4.1.5, is there a
way around this problem *which is backwards compatible with earlier
versions of FSL*?
Thanks in advance.
All the best,
Jon
--
[1]
/usr/local/fsl/bin/probtrackx --opd
--dir=/Users/jon/Development/Subversion/Working/tractor/tests/data/session-12dir/tractor/fdt.track/IMAGE
--mode=simple -x
/var/folders/i4/i4QIhI5kER4SK2fLTGygV++++TM/-Tmp-/RtmpBSKMVk/file10d63af1
--forcedir -s /Users/jon/Development/Subversion/Working/tractor/tests/data/session-12dir/tractor/fdt.bedpostX/merged
-m /Users/jon/Development/Subversion/Working/tractor/tests/data/session-12dir/tractor/fdt.bedpostX/nodif_brain_mask
-l -c 0.2 -S 2000 --steplength=0.5 -P 5000 -o
/Users/jon/Development/Subversion/Working/tractor/tests/data/session-12dir/tractor/fdt.track/IMAGE
[2]
Log directory is:
/Users/jon/Development/Subversion/Working/tractor/tests/data/session-12dir/tractor/fdt.track/IMAGE
1_1
1_2
1_3
7
48 57 13
Error: failed to open file
/Users/jon/Development/Subversion/Working/tractor/tests/data/session-12dir/tractor/fdt.track/IMAGE//Users/jon/Development/Subversion/Working/tractor/tests/data/session-12dir/tractor/fdt.track/IMAGE_48_57_13.nii.gz
ERROR: Could not open image
/Users/jon/Development/Subversion/Working/tractor/tests/data/session-12dir/tractor/fdt.track/IMAGE//Users/jon/Development/Subversion/Working/tractor/tests/data/session-12dir/tractor/fdt.track/IMAGE_48_57_13
Image Exception : #23 :: Failed to open volume
/Users/jon/Development/Subversion/Working/tractor/tests/data/session-12dir/tractor/fdt.track/IMAGE//Users/jon/Development/Subversion/Working/tractor/tests/data/session-12dir/tractor/fdt.track/IMAGE_48_57_13
for writing
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
|