Hi,

I'm trying to run the parcellation process without following the full pipeline (just as utilities)

I gave as imput the FA file already processed by FSL and the T1 nifti image,  the two file are in different folders iis this a problem?

The process fail and clicking the botton failed jobs I obtain the attached txt.

I have changed the name of the FA file in: dti_FA_CACI.nii.gz can this be a problem? i have other files in the folder in which there is the FA and they are are bvals bvecs and sub.nii.gz, I don't think the presence of those file in the folder is causing the process to fail.

Do you have any idea why I'm having this message?

Thanks for the help.

Dear Mauro,

Yes, its my fault.
Please put file attached in the PANDA folder to replace the origin.
If you still have any problem, please contact me.

PS: Its not a big problem. In fact, the parcellated image in individual space has been already produced.

Best

Zaixu

Dear Zaixu

Thanks, now it works.

owever I run the full pipeline now and the only project which fail is the deterministic tractography, from the log file seems that is due to some error in reading the b0 but  the other processes which used b0 didn't fail.

I'm also  wondering: since the deterministic tractography failed can I trust the result of the probababilistic?

I've attached the log file

Originally posted by Mauro Serra:
Sorry I wrongly cliked on Submit, here is the log files

I'm so sorry to bother you so often in these days, thanks a lot for your availability and all the help!

Dear Mauro,

There is a file named '*.PANDA' in the result path.

Please send it to me.

I want to know the parameters you set.

Best

Zaixu

Dear Zaixu

here is the file .PANDA,

Thanks.

Mauro

Dear Mauro,

I'm sorry, this is the first time I have encountered this problem.

I cannot figure out why now.

Could send the folder 'trackvis' folder under the result path to me ?

Best

Zaixu

And  please send 'Bvecs' and  'Bvals' files in the 'native_space' folder under the result path to me.

Best

Zaixu

Dear Zaixu

The folder 'trackvis' folder under the result path is empty fot both the subject I runned.

There is no need to install diffusion toolkit and trackvis in the computer right? they set up automatically as I add PANDA in matlab is it correct?

Trackvis is not needed.
Diffusion Toolkit is also added in the folder of PANDA.

Please send 'Bvecs' and 'Bvals' files to me.
They are under the 'native_space' folder of result path.

Best

Zaixu

Ok,

I will send 2 mail because I could not upload 2 files in one mail.

here is the bval

and here is the bvec.

Again, thaks to dedicate all this time to my problem

I'm sorry.

I cannot download these two files.

When I download them, it said that 'The attachment is not exist'.

You can have a try.

Best

Zaixu

Ok, maybe it's just easier to copy paste the content of the files:

bvals:

0.000000e+00  0.000000e+00  0.000000e+00  0.000000e+00  0.000000e+00  1.000000e+03  1.000000e+03  1.000000e+03  1.000000e+03  1.000000e+03  1.000000e+03  1.000000e+03  1.000000e+03  1.000000e+03  1.000000e+03  1.000000e+03  1.000000e+03  1.000000e+03  1.000000e+03  1.000000e+03  1.000000e+03  1.000000e+03  1.000000e+03  1.000000e+03  1.000000e+03  1.000000e+03  1.000000e+03  1.000000e+03  1.000000e+03  1.000000e+03  1.000000e+03  1.000000e+03  1.000000e+03  1.000000e+03  1.000000e+03

bvecs

-5.740302e-01  -5.751624e-01  -5.721533e-01  -5.728236e-01  -5.716364e-01  9.999662e-01  1.644269e-01  -1.040065e-01  9.005661e-01  -1.619463e-01  -8.120095e-01  6.611239e-01  5.830750e-01  9.033998e-01  6.953399e-01  3.550852e-01  5.355993e-01  -5.200163e-01  -6.362019e-01  -3.377672e-01  -5.220049e-01  6.026920e-01  2.121724e-01  -8.344338e-03  -5.150832e-01  4.178560e-01  -6.839702e-01  8.856035e-01  2.681560e-01  8.124579e-02  2.969511e-01  8.829391e-01  2.633199e-01  8.259287e-02  8.631831e-01
5.241792e-01  5.237156e-01  5.254488e-01  5.252392e-01  5.262455e-01  1.955039e-03  9.824392e-01  5.943962e-01  -4.062233e-01  -6.705973e-01  -4.223911e-01  3.057329e-01  7.844719e-01  2.252240e-01  -7.107556e-01  -9.066789e-01  -4.217951e-01  -4.621962e-01  6.544571e-01  7.682163e-02  -8.115827e-01  5.682777e-03  -1.436159e-01  -8.669199e-01  6.768992e-01  6.836659e-01  2.031285e-01  -3.288531e-01  3.527024e-01  2.735445e-01  -9.305955e-01  -4.592975e-02  -5.190339e-01  9.080390e-01  5.046622e-01
-6.290669e-01  -6.284189e-01  -6.297176e-01  -6.292827e-01  -6.295220e-01  7.962143e-03  -8.818653e-02  -7.974184e-01  1.548013e-01  -7.239291e-01  -4.027743e-01  -6.851585e-01  -2.112505e-01  -3.648880e-01  -1.064354e-01  2.277018e-01  7.315888e-01  -7.183023e-01  -4.085741e-01  9.380890e-01  -2.623796e-01  7.979535e-01  9.666215e-01  4.983780e-01  5.258288e-01  -5.983280e-01  7.006593e-01  -3.279660e-01  -8.964892e-01  9.584222e-01  -2.140357e-01  4.672364e-01  -8.131830e-01  4.106619e-01  -1.522253e-02

Best

Dear Mauro,

Your data is obviously strange.

From bvals, there are five zero, which indicate there exist 5 b0 with no diffusion weighting.
However, from bvecs file, there is no b0, because the direction of b0 should be [0 0 0].

According to bvals file, your bvecs file should be

0            0            0           0           0         9.999662e-01 1.644269e-01 -1.040065e-01 9.005661e-01 -1.619463e-01 -8.120095e-01 6.611239e-01 5.830750e-01 9.033998e-01 6.953399e-01 3.550852e-01 5.355993e-01 -5.200163e-01 -6.362019e-01 -3.377672e-01 -5.220049e-01 6.026920e-01 2.121724e-01 -8.344338e-03 -5.150832e-01 4.178560e-01 -6.839702e-01 8.856035e-01 2.681560e-01 8.124579e-02 2.969511e-01 8.829391e-01 2.633199e-01 8.259287e-02 8.631831e-01
0            0            0           0           0         1.955039e-03 9.824392e-01 5.943962e-01 -4.062233e-01 -6.705973e-01 -4.223911e-01 3.057329e-01 7.844719e-01 2.252240e-01 -7.107556e-01 -9.066789e-01 -4.217951e-01 -4.621962e-01 6.544571e-01 7.682163e-02 -8.115827e-01 5.682777e-03 -1.436159e-01 -8.669199e-01 6.768992e-01 6.836659e-01 2.031285e-01 -3.288531e-01 3.527024e-01 2.735445e-01 -9.305955e-01 -4.592975e-02 -5.190339e-01 9.080390e-01 5.046622e-01
0            0            0           0           0         7.962143e-03 -8.818653e-02 -7.974184e-01 1.548013e-01 -7.239291e-01 -4.027743e-01 -6.851585e-01 -2.112505e-01 -3.648880e-01 -1.064354e-01 2.277018e-01 7.315888e-01 -7.183023e-01 -4.085741e-01 9.380890e-01 -2.623796e-01 7.979535e-01 9.666215e-01 4.983780e-01 5.258288e-01 -5.983280e-01 7.006593e-01 -3.279660e-01 -8.964892e-01 9.584222e-01 -2.140357e-01 4.672364e-01 -8.131830e-01 4.106619e-01 -1.522253e-02

Hi,

Again me... in our lab, there is a problem in how the bvalue are reported in the dicom header, even thought the first 5 volumes are without gradiet in the bval  file that come from dicom2nii the first 5 entries are "1000" rather then "0"and I have to manually substitute the first five entry with five "0", however I was told that the bvecs were ok, at least for the analysis in FSL.

Now given the problem that I had and given your suggestion, I changed also the bvecs following your indication and I ensured that this would not effect the analysis in FSL by controlling the value of FA (in exactly the same point) obtained after DTIFIT with the bvecs modified and again with the bvecs not modified. Given that the data were exactly the same, I run again the pipeline with PANDA with the Bvecs that you suggest, in order to finally obtain both the probabilistic and the deterministick tractography to do network reconstruction in both ways.

Now I had no error messages, no failed jobs, the pipeline is finished, but the problem is that the ProbabilisticMatrix_OPD_1.txt file is empty.

You think this modification to the bvecs could affect someting in the probabilistick tractography, and Why there are no failed jobs?

Attached is the pipeline history,

Best,

Mauro