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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 >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> ------------------------------ >>>>> >>>>> To unsubscribe from the FSL list, click the following link: >>>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 >>>>> >>>> >>>> >>>> ------------------------------ >>>> >>>> To unsubscribe from the FSL list, click the following link: >>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 >>>> >>> >>> ------------------------------ >>> >>> To unsubscribe from the FSL list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 >>> >> >> >> ------------------------------ >> >> To unsubscribe from the FSL list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 >> > > ------------------------------ > > To unsubscribe from the FSL list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 > > > > ------------------------------ > > To unsubscribe from the FSL list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 > ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1