Dear PANDA-experts, 

i'm having some trouble running PANDA on Ubuntu 12.04 (Matlab R2012b)

It says:

***************************************************************************

JobName: BedpostX_postproc_00044
Status: failed
***************************************************************************
******************************
Log of the (matlab) job : BedpostX_postproc_00044
Started on 09-Jul-2014 15:59:40
User: isabella
host : Niklas
system : unix
******************************
********************
The job starts now !
********************
Usage: fslmerge <-x/y/z/t/a/tr> [tr value in seconds]
-t : concatenate images in time
-x : concatenate images in the x direction
-y : concatenate images in the y direction
-z : concatenate images in the z direction
-a : auto-choose: single slices -> volume, volumes -> 4D (time series)
-tr : concatenate images in time and set the output image tr to the final option value
Usage: fslmerge <-x/y/z/t/a/tr> [tr value in seconds]
-t : concatenate images in time
-x : concatenate images in the x direction
-y : concatenate images in the y direction
-z : concatenate images in the z direction
-a : auto-choose: single slices -> volume, volumes -> 4D (time series)
-tr : concatenate images in time and set the output image tr to the final option value
Usage: fslmerge <-x/y/z/t/a/tr> [tr value in seconds]
-t : concatenate images in time
-x : concatenate images in the x direction
-y : concatenate images in the y direction
-z : concatenate images in the z direction
-a : auto-choose: single slices -> volume, volumes -> 4D (time series)
-tr : concatenate images in time and set the output image tr to the final option value
Cannot open volume /home/isabella/Documents/UNI/Projects/Diplomarbeit/data/PANDA_RESULTS//00044/native_space.bedpostX/merged_th1samples for reading!
Cannot open volume /home/isabella/Documents/UNI/Projects/Diplomarbeit/data/PANDA_RESULTS//00044/native_space.bedpostX/merged_ph1samples for reading!
Cannot open volume /home/isabella/Documents/UNI/Projects/Diplomarbeit/data/PANDA_RESULTS//00044/native_space.bedpostX/merged_f1samples for reading!
Image Exception : #22 :: ERROR: Could not open image /home/isabella/Documents/UNI/Projects/Diplomarbeit/data/PANDA_RESULTS//00044/native_space.bedpostX/merged_th1samples
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted (core dumped)
make_dyadic_vectors /home/isabella/Documents/UNI/Projects/Diplomarbeit/data/PANDA_RESULTS//00044/native_space.bedpostX/merged_th1samples /home/isabella/Documents/UNI/Projects/Diplomarbeit/data/PANDA_RESULTS//00044/native_space.bedpostX/merged_ph1samples /home/isabella/Documents/UNI/Projects/Diplomarbeit/data/PANDA_RESULTS//00044/native_space.bedpostX/nodif_brain_mask /home/isabella/Documents/UNI/Projects/Diplomarbeit/data/PANDA_RESULTS//00044/native_space.bedpostX/dyads1 && touch /home/isabella/Documents/UNI/Projects/Diplomarbeit/data/PANDA_RESULTS//00044/native_space.bedpostX/diff_slices/dyads.done: Aborted
Usage: fslmerge <-x/y/z/t/a/tr> [tr value in seconds]
-t : concatenate images in time
-x : concatenate images in the x direction
-y : concatenate images in the y direction
-z : concatenate images in the z direction
-a : auto-choose: single slices -> volume, volumes -> 4D (time series)
-tr : concatenate images in time and set the output image tr to the final option value
Usage: fslmerge <-x/y/z/t/a/tr> [tr value in seconds]
-t : concatenate images in time
-x : concatenate images in the x direction
-y : concatenate images in the y direction
-z : concatenate images in the z direction
-a : auto-choose: single slices -> volume, volumes -> 4D (time series)
-tr : concatenate images in time and set the output image tr to the final option value
Usage: fslmerge <-x/y/z/t/a/tr> [tr value in seconds]
-t : concatenate images in time
-x : concatenate images in the x direction
-y : concatenate images in the y direction
-z : concatenate images in the z direction
-a : auto-choose: single slices -> volume, volumes -> 4D (time series)
-tr : concatenate images in time and set the output image tr to the final option value
Cannot open volume /home/isabella/Documents/UNI/Projects/Diplomarbeit/data/PANDA_RESULTS//00044/native_space.bedpostX/merged_th2samples for reading!
Cannot open volume /home/isabella/Documents/UNI/Projects/Diplomarbeit/data/PANDA_RESULTS//00044/native_space.bedpostX/merged_ph2samples for reading!
Cannot open volume /home/isabella/Documents/UNI/Projects/Diplomarbeit/data/PANDA_RESULTS//00044/native_space.bedpostX/merged_f2samples for reading!
Image Exception : #22 :: ERROR: Could not open image /home/isabella/Documents/UNI/Projects/Diplomarbeit/data/PANDA_RESULTS//00044/native_space.bedpostX/merged_th2samples
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted (core dumped)
make_dyadic_vectors /home/isabella/Documents/UNI/Projects/Diplomarbeit/data/PANDA_RESULTS//00044/native_space.bedpostX/merged_th2samples /home/isabella/Documents/UNI/Projects/Diplomarbeit/data/PANDA_RESULTS//00044/native_space.bedpostX/merged_ph2samples /home/isabella/Documents/UNI/Projects/Diplomarbeit/data/PANDA_RESULTS//00044/native_space.bedpostX/nodif_brain_mask /home/isabella/Documents/UNI/Projects/Diplomarbeit/data/PANDA_RESULTS//00044/native_space.bedpostX/dyads2 && touch /home/isabella/Documents/UNI/Projects/Diplomarbeit/data/PANDA_RESULTS//00044/native_space.bedpostX/diff_slices/dyads.done: Aborted
****************
Checking outputs
****************
The output file or directory /home/isabella/Documents/UNI/Projects/Diplomarbeit/data/PANDA_RESULTS/00044/native_space.bedpostX/BedpostX.done has not been generated!
**********************************************
09-Jul-2014 15:59:47 : The job has FAILED
Total time used to process the job : 6.29 sec.
**********************************************
ans =
1


For me it seems like there is a wrong filename because there are two // after PANDA_RESULTS in the path, so it's clear that PANDA cannot open this volume

Cannot open volume /home/isabella/Documents/UNI/Projects/Diplomarbeit/data/PANDA_RESULTS//00044/native_space.bedpostX/merged_th1samples for reading!

You know any help??
Thanks in advance

Isabella

Hi, 
i found the double // but still it isn't working

***************************************************************************

JobName: BedpostX_postproc_00044
Status: failed
***************************************************************************
******************************
Log of the (matlab) job : BedpostX_postproc_00044
Started on 09-Jul-2014 20:27:42
User: isabella
host : Niklas
system : unix
******************************
********************
The job starts now !
********************
Usage: fslmerge <-x/y/z/t/a/tr> [tr value in seconds]
-t : concatenate images in time
-x : concatenate images in the x direction
-y : concatenate images in the y direction
-z : concatenate images in the z direction
-a : auto-choose: single slices -> volume, volumes -> 4D (time series)
-tr : concatenate images in time and set the output image tr to the final option value
Usage: fslmerge <-x/y/z/t/a/tr> [tr value in seconds]
-t : concatenate images in time
-x : concatenate images in the x direction
-y : concatenate images in the y direction
-z : concatenate images in the z direction
-a : auto-choose: single slices -> volume, volumes -> 4D (time series)
-tr : concatenate images in time and set the output image tr to the final option value
Usage: fslmerge <-x/y/z/t/a/tr> [tr value in seconds]
-t : concatenate images in time
-x : concatenate images in the x direction
-y : concatenate images in the y direction
-z : concatenate images in the z direction
-a : auto-choose: single slices -> volume, volumes -> 4D (time series)
-tr : concatenate images in time and set the output image tr to the final option value
Cannot open volume /home/isabella/Documents/UNI/Projects/Diplomarbeit/data/PANDA_RESULTS/00044/native_space.bedpostX/merged_th1samples for reading!
Cannot open volume /home/isabella/Documents/UNI/Projects/Diplomarbeit/data/PANDA_RESULTS/00044/native_space.bedpostX/merged_ph1samples for reading!
Cannot open volume /home/isabella/Documents/UNI/Projects/Diplomarbeit/data/PANDA_RESULTS/00044/native_space.bedpostX/merged_f1samples for reading!
Image Exception : #22 :: ERROR: Could not open image /home/isabella/Documents/UNI/Projects/Diplomarbeit/data/PANDA_RESULTS/00044/native_space.bedpostX/merged_th1samples
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted (core dumped)
make_dyadic_vectors /home/isabella/Documents/UNI/Projects/Diplomarbeit/data/PANDA_RESULTS/00044/native_space.bedpostX/merged_th1samples /home/isabella/Documents/UNI/Projects/Diplomarbeit/data/PANDA_RESULTS/00044/native_space.bedpostX/merged_ph1samples /home/isabella/Documents/UNI/Projects/Diplomarbeit/data/PANDA_RESULTS/00044/native_space.bedpostX/nodif_brain_mask /home/isabella/Documents/UNI/Projects/Diplomarbeit/data/PANDA_RESULTS/00044/native_space.bedpostX/dyads1 && touch /home/isabella/Documents/UNI/Projects/Diplomarbeit/data/PANDA_RESULTS/00044/native_space.bedpostX/diff_slices/dyads.done: Aborted
Usage: fslmerge <-x/y/z/t/a/tr> [tr value in seconds]
-t : concatenate images in time
-x : concatenate images in the x direction
-y : concatenate images in the y direction
-z : concatenate images in the z direction
-a : auto-choose: single slices -> volume, volumes -> 4D (time series)
-tr : concatenate images in time and set the output image tr to the final option value
Usage: fslmerge <-x/y/z/t/a/tr> [tr value in seconds]
-t : concatenate images in time
-x : concatenate images in the x direction
-y : concatenate images in the y direction
-z : concatenate images in the z direction
-a : auto-choose: single slices -> volume, volumes -> 4D (time series)
-tr : concatenate images in time and set the output image tr to the final option value
Usage: fslmerge <-x/y/z/t/a/tr> [tr value in seconds]
-t : concatenate images in time
-x : concatenate images in the x direction
-y : concatenate images in the y direction
-z : concatenate images in the z direction
-a : auto-choose: single slices -> volume, volumes -> 4D (time series)
-tr : concatenate images in time and set the output image tr to the final option value
Cannot open volume /home/isabella/Documents/UNI/Projects/Diplomarbeit/data/PANDA_RESULTS/00044/native_space.bedpostX/merged_th2samples for reading!
Cannot open volume /home/isabella/Documents/UNI/Projects/Diplomarbeit/data/PANDA_RESULTS/00044/native_space.bedpostX/merged_ph2samples for reading!
Cannot open volume /home/isabella/Documents/UNI/Projects/Diplomarbeit/data/PANDA_RESULTS/00044/native_space.bedpostX/merged_f2samples for reading!
Image Exception : #22 :: ERROR: Could not open image /home/isabella/Documents/UNI/Projects/Diplomarbeit/data/PANDA_RESULTS/00044/native_space.bedpostX/merged_th2samples
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted (core dumped)
make_dyadic_vectors /home/isabella/Documents/UNI/Projects/Diplomarbeit/data/PANDA_RESULTS/00044/native_space.bedpostX/merged_th2samples /home/isabella/Documents/UNI/Projects/Diplomarbeit/data/PANDA_RESULTS/00044/native_space.bedpostX/merged_ph2samples /home/isabella/Documents/UNI/Projects/Diplomarbeit/data/PANDA_RESULTS/00044/native_space.bedpostX/nodif_brain_mask /home/isabella/Documents/UNI/Projects/Diplomarbeit/data/PANDA_RESULTS/00044/native_space.bedpostX/dyads2 && touch /home/isabella/Documents/UNI/Projects/Diplomarbeit/data/PANDA_RESULTS/00044/native_space.bedpostX/diff_slices/dyads.done: Aborted
****************
Checking outputs
****************
The output file or directory /home/isabella/Documents/UNI/Projects/Diplomarbeit/data/PANDA_RESULTS/00044/native_space.bedpostX/BedpostX.done has not been generated!
**********************************************
09-Jul-2014 20:27:47 : The job has FAILED
Total time used to process the job : 5.37 sec.
**********************************************
ans =
1

You know any help?
Thanks, Isabella

PS: I attached the log folder

Hi Radl,

Sorry to reply so late.

What's your version of Linux OS? Ubuntu? Centos?

Best

Zaixu

Hi, 

no problem,
It's Ubuntu 12.04

all the best, Isabella

Hi,

In fact, several people have reported this problem.
Maybe something is wrong in my program.
I will solve it these days, and give you feedback.

If you want to run your data quickly, you can run bedpostx using the independent tool 'Bedpostx' in the utility and then run probabilistic tracking using the 'Tracking' utility.
The data will run smoothly.

Best

Zaixu

Dear experts,

I faced the same problem. Are there solutions available?

best regards

Tuukka Raij

When I use the bedpostx command in fsl to process, an error is still reported, but the following information is prompted in the log file: 
/usr/bin/env: "python": no such file or directory

Therefore, the solution is to use the following command to install python: 
sudo apt-get install python

If there is a "python" file in /usr/bin/, execute the following command instead: 
sudo apt-get --reinstall install python-minimal