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Thanks for letting us know, Mark!
On Tue, Jul 17, 2018 at 3:01 PM Mark Jenkinson <[log in to unmask]> wrote:
Hi,

The latest versions of FSL do use python 3 for all of their python scripts - via a virtual environment.
If you use the latest FSL you should not need to set up your own virtual environment.

All the best,
Mark


On 15 Jul 2018, at 20:06, Dmitrii Paniukov <[log in to unmask]> wrote:

Glad to help! I hope FSL updates its code to support python 3. I use a virtual environment with python 2.7 just for FSL.
On Sun, Jul 15, 2018 at 12:48 PM Rabia Mazhar <[log in to unmask]> wrote:
Hi all
Apologies for the late reply as I was traveling. I just wanted to take this opportunity to thank Dmitri. This was the best advice I ever got and I wont have ever been able to figure it out myself. Tons of thanks to the FSL list, saved me a great deal of stress trying to find what the issue was. I had switched to Python 3 lately and had completely forgot that FSL needs to run with python 2.7

Thanks a lot

On Fri, Jun 22, 2018 at 1:44 PM, Dmitrii Paniukov <[log in to unmask]> wrote:
You may wanna run it with python 2.7, not 3.*

On Fri, Jun 22, 2018 at 1:45 AM paul mccarthy <[log in to unmask]> wrote:
Hi Rabia,

The dual regression script creates its own mask image, so it is not looking for the mask in your .ica directory. This is the drB step (and the drA step is the creation of masks for each subject).

Were there any other errors in the scripts+logs directory? Can you send the contents of the dual_regression23_50 directory, and the contents of files23.txt (and verify that all of the input data sets exist, and are in standard space)?

Cheers,

Paul

On 22 June 2018 at 06:49, Rabia Mazhar <[log in to unmask]> wrote:
Dear FSL experts,
I am trying to run dual regression, however it is giving me an error in dr.C files. Here is the error.

cat DualRegression23_50/scripts+logs/drC.e48376.53
Image Exception : #22 :: ERROR: Could not open image DualRegression23_50/mask
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/bin/sh: line 1:  8035 Aborted                 (core dumped) /cm/shared/openmind/fsl/5.0.9/bin/fsl_glm -i mean_hpf128_smooth_PD084_RsfMRIs016a001_FullFile_func2standard -d NTNU23_melodic_50.ica/melodic_IC -o DualRegression23_50/dr_stage1_subject00052.txt --demean -m DualRegression23_50/mask
Image Exception : #22 :: ERROR: Could not open image DualRegression23_50/mask
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/bin/sh: line 1:  8078 Aborted                 (core dumped) /cm/shared/openmind/fsl/5.0.9/bin/fsl_glm -i mean_hpf128_smooth_PD084_RsfMRIs016a001_FullFile_func2standard -d DualRegression23_50/dr_stage1_subject00052.txt -o DualRegression23_50/dr_stage2_subject00052 --out_z=DualRegression23_50/dr_stage2_subject00052_Z --demean -m DualRegression23_50/mask --des_norm
Cannot open volume DualRegression23_50/dr_stage2_subject00052 for reading!


Obviously the error is that, dual regression couldnt find my mask in folder DualRegression23_50/mask
The problem is obviously I have the mask, but dual regression is looking for it in the wrong folder. My mask is in .ica folder, but dual regression for some weird reason is trying to look for it in the DualRegression23_50 folder, which is simply the dual regression output folder. Obviously nothing is in that folder because thats the output folder. I ran the following command
dual_regression NT23_melodic_50.ica/melodic_IC 1 -1 0 DualRegression23_50 `cat /om2/user/qbukhari/project/files23.txt`


Can someone please comment on how to correct this error, and what command should I use ? I have been trying all sorts of things but it still generates the path error because it keeps on looking for the files in the output folder where there is no mask.

Thanks for the help

best
Rabia





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