Dear all,

I'm new with PANDA and I have a doubt with the input. I don't have the different dwi acquisitions in different files, I have a single nifti file. It's possible to configure PANDA to read this kind of files? or is possible to separate the file en the different dwi acquisitions? Thanks in advance

Best regards,

Manuel Blesa

Hi, Blesa,

Of course.
Please look up the manual of PANDA, the input format when nifti data is used.

First, you should create a folder for this subject, for example 'sub1'.
Then, please create a sub-folder in the folder 'sub1', for example 'sub1/ac1'
Then, please put the single 4D nifti file, bvecs file and bvals file in the folder 'sub1/ac1'
Finally, the folder 'sub1' is the input of PANDA

Best

Zaixu

Hi Zaixu,

Thanks, I solved the problem and it works ok until arrive to the eddy
current correction. I think is because I have a problem with the
bvecs, always says index exceeds matrix.

my bvecs is like this

x1 x2......x89
y1 y2......y89
z1 z2......z89

the first 8 values correspond to the b0 values.

It's the mistake here? If not any idea? thanks in advance.

Best regards,

Manuel Blesa

Hi,
You should make sure that your bvals file and bvecs file have the same number of rows , as well as the number of volumes along the 4th dimension in your data.nii.gz file.

Best!
Chenxi
Originally posted by Manuel Blesa:

Hi,

My bvals, bvecs and 4d nifti file have the same dimension, and the error still appears:
***************************************************************************
JobName: EDDYCURRENT_00001
Status: failed
***************************************************************************
******************************
Log of the (matlab) job : EDDYCURRENT_00001
Started on 15-Jul-2014 15:22:48
User: imaging
host : MRI3
system : unix
******************************
********************
The job starts now !
********************
/MRI-D/tentative_maltabtoolbox/results/00001/tmp
00001
1
********************
Something went bad ... the job has FAILED !
The last error message occured was :
Index exceeds matrix dimensions.
File /config/tools/PANDA-1.2.4_64/g_EDDYCURRENT.m at line 204
File /config/tools/PANDA-1.2.4_64/g_EDDYCURRENT.m at line 142
File /config/tools/PANDA-1.2.4_64/psom-0.9/psom_run_job.m at line 203
File /config/tools/PANDA-1.2.4_64/psom-0.9/psom_run_job.m at line 125
****************
Checking outputs
****************
The output file or directory /MRI-D/tentative_maltabtoolbox/results/00001/tmp/00001_DWI_01_0000_crop_eddy.nii.gz was successfully generated!
The output file or directory /MRI-D/tentative_maltabtoolbox/results/00001/native_space/ecclog.mat was successfully generated!
The output file or directory /MRI-D/tentative_maltabtoolbox/results/00001/tmp/OutputDone/EDDYCURRENT_00001.done has not been generated!
The output file or directory /MRI-D/tentative_maltabtoolbox/results/00001/tmp/EDDYCURRENT_output.mat has not been generated!
************************************************
15-Jul-2014 15:25:37 : The job has FAILED
Total time used to process the job : 168.99 sec.
************************************************
ans =
1
I don't know why. Any suggestions? attached is my bvecs file. Thanks in advance.
Best regards,
Manuel Blesa

Hi,

I solved the problem, but now a new one appears:

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

JobName: LDH_00001
Status: failed
***************************************************************************
******************************
Log of the (matlab) job : LDH_00001
Started on 16-Jul-2014 17:17:16
User: imaging
host : MRI3
system : unix
******************************
********************
The job starts now !
********************
Read these 4D ADC images...
********************
Something went bad ... the job has FAILED !
The last error message occured was :
Index exceeds matrix dimensions.
File /config/tools/PANDA-1.2.4_64/g_DWI2LDH.m at line 74
File /config/tools/PANDA-1.2.4_64/psom-0.9/psom_run_job.m at line 203
File /config/tools/PANDA-1.2.4_64/psom-0.9/psom_run_job.m at line 125
****************
Checking outputs
****************
The output file or directory /MRI-D/tentative_maltabtoolbox/results2/00001/native_space/00001_06LDHs.nii.gz has not been generated!
The output file or directory /MRI-D/tentative_maltabtoolbox/results2/00001/native_space/00001_07LDHk.nii.gz has not been generated!
**********************************************
16-Jul-2014 17:17:17 : The job has FAILED
Total time used to process the job : 0.46 sec.
**********************************************
ans =
1

Any suggestions? thanks in advance.

Best regards,

Manuel Blesa

Dear,

I attempt to download the bvecs file, but it warns me that the attachment does not exist. It is strongly suggested that you re-upload it again or just send me an e-mail. nanca386@gmail.com

Best regards!

Chenxi