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Jun 2, 2015  04:06 AM | joana pereira - KI
Network construction
Dear all,

I have ran the full pipeline of PANDA on Siemens DTI gated data with 64 directions on Mac OS X Yosemite 10.10.2.

I used the full pipeline and no errors came out.

However, when I loaded the white matter tracts built using FACT on trackvis, I saw they were not being reconstructed correctly, probably due to the issues related to how the bvecs are saved in siemens scanners.

Since my main interest in using PANDA is to make network constructions I thought of using the Test Bvecs and Tracking & Network options instead of the full pipeline.

The tracts were reconstructed correctly after using the previous options.

However, the network construction did not finish due to problems with the T1 image.
After I launch the Tracking & Network option, the T1 image disapears from the folder were I kept it and the error below comes out. I tried it several times and the T1 image always disappears.

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

JobName: CopyT1_00010
Status: failed
***************************************************************************
******************************
Log of the (matlab) job : CopyT1_00010
Started on 02-Jun-2015 11:45:07
User: joaper
host : NVNGC02NXAHTG3QD.hs.sll.se
system : unix
******************************
********************
The job starts now !
********************
cp: /Users/joaper/Desktop/FINAL/T1/subj01.nii.gz: No such file or directory
****************
Checking outputs
****************
The output file or directory /Users/joaper/Desktop/FINAL/T1/subj01.nii.gz has not been generated!
**********************************************
02-Jun-2015 11:45:07 : The job has FAILED
Total time used to process the job : 0.01 sec.
**********************************************
ans =
1

Does anyone know how to solve this?

Many thanks!
Jun 8, 2015  07:06 AM | cui zaixu
RE: Network construction
Dear,

Please attach your .PANDA configuration file here.
This file should be in the resultant folder.

Best

Zaixu
Jun 9, 2015  05:06 AM | joana pereira - KI
RE: Network construction
Dear Zaixu,

Thank you for replying!

I'm attaching the 2015_06_09_13_50.PANDA_Tracking file that was in Tracking_logs/

Is this the one you were referring to?

Best wishes,

Joana
Jun 12, 2015  11:06 PM | Zaixu Cui
RE: Network construction
Dear pereira,

I don't think this configuration file is related to the error you posted in the Jun 2, 2015, as this file in generated in the Jun 9.
Moreover, the parameter is not match.

So, with this new configuration, have you solved the problem, or if there is still some problems.
If it does, please post the logs of failed job just as you did in Jun 2.

Best wishes

Zaixu
Jun 14, 2015  06:06 AM | joana pereira - KI
RE: Network construction
Dear Zaixu,

No, that was not the same configuration file. Before I replied to your last email, I ran the pipeline again to make sure the same error was still there.

The error is still there. I just run the pipeline again and I'm attaching the new configuration file.

Here is the error:

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

JobName: CopyT1_00010
Status: failed
***************************************************************************
******************************
Log of the (matlab) job : CopyT1_00010
Started on 14-Jun-2015 06:17:51
User: joaper
host : NVNGC02NXAHTG3QD.local
system : unix
******************************
********************
The job starts now !
********************
cp: /Users/joaper/Desktop/new/T1/20101123_095122MPRAGEGRAPPAs008a1001.nii.gz: No such file or directory
****************
Checking outputs
****************
The output file or directory /Users/joaper/Desktop/new/T1/20101123_095122MPRAGEGRAPPAs008a1001.nii.gz has not been generated!
**********************************************
14-Jun-2015 06:17:51 : The job has FAILED
Total time used to process the job : 0.01 sec.
**********************************************
ans =
1
May 28, 2019  02:05 AM | romane legrand
RE: Network construction
Hello,
I've the exact same problem excepting I'm working on Ubuntu 
Using "Tracking & Network" or "Brain parcellation", both leads to the same error status "Copy T1" ---> failed.

"No such file or directory"

And.... puf, the file disappear from the folder I entered the path for T1 images.

Anyone has any idea on this question ?

Many thanks.
Romane