Issue with pyconnectome

[ErinKoch2]

Hello,

I am trying to get Pypreclin up and running in our lab. I am trying just to run the example code on one of my functional and anatomical scans, as a first step (before adding fieldmap distortion correction). The pipeline is getting stuck after getting through most of step 5 (normalization) and throwing an error that traces back to pyconnectome. See the attached screen shot of the error messages. I do have the proper versions of python and all of the other dependencies installed. Do you have any insight? Thanks,

Erin

[DimitriPapadopoulos]

Out of curiosity, I see two mount points here:
/mnt/data2

cwd = /mnt/data2/data/erink/cooked/2020/200109Jamie/bold/007/output/Jamie/5-Nomalization

/mnt/data1/helios

ValueError: '/mnt/data1/helios/data/erink/cooked/2020/200109Jamie/bold/007/output/Jamie/5-Nomalization/wdomprage.nii' is not a valid input file.

Are both of these paths valid at the same time?

[ErinKoch2]

Thanks for the reply. Both are valid. '/mnt/data1/helios/data/erink' is a link to /mnt/data2/data/erink . Just to be sure this wasn't the issue, I reran everything making sure to use the same directory when defining paths to the relevant scans. I get the same error (see attached). I tried to trace back this issue. Indeed I do not have a file in the Normalization folder called "wanat.nii" . In my Normalization folder there are 3 files 1) align.com, 2) danat.nii, 3) distortions.nii . Is wanat.nii the output of the "applymask" function? Or, should this be output when JIP outputs the align.com file. Do you have any insight?
Thanks again.
Erin

[AGrigis]

Dear Erin,

Something is going wrong in the 'jip_align' function of the 'pypreclin.preproc.register' module, and more precisely when calling the command defined line 304: cmd = ["jip", aplly_nonlin_batch, source_file, register_file].
The 'register_file' is the one missing (that was not generated).
This command applies the computed deformation field (align.com, distortions.nii) to the anatomical image (danat.nii) using the batch 'apply_nonlin.com' available in 'pypreclin.resources'.
As you can see in the code we execute the command using 'subprocess.call' that will not stop if an error occurs. Can you please replace this command by 'subprocess.check_call'. I hope the error will be a bit more explicit like that.
You can also directly execute the command in a terminal.

Hope it will help.