Empty TVB Files folder

[dhughe13]

Hi,

I ran the pipeline on the amsterdam sample subject yesterday and after checking the outputs today, I see that while the TVB_inputs zip file was created, it only contains empty folders: when I unzipped the file, I had a functional_inputs directory with rfMRI.ica subdirectory that is empty, a misc_inputs directory that is empty, and a structrual_inputs zip file, that was also empty when unzipped. The QC report was populated. Do you have any idea why this would be, or know which logs or files in the QC report I should be looking in to identify the issue?

Best,
Dominique Hughes

[justinliuyuwang]

Hi Dominique,

This issue may be very early in the pipeline. Could you please go through the log files and paste any logged errors? If there are many, please compress the logs directory and attach it to your message.

[dhughe13]

Hi,

We've been trying to download an older version of afni and we are running into some issues. Following these commands:
cd
curl -O https://afni.nimh.nih.gov/pub/dist/bin/misc/@update.afni.binaries
tcsh @update.afni.binaries -local_package PATH_TO_FILE/linux_ubuntu_16_64.tgz -do_extras

from the afni download page:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/background_install/install_instructs/steps_linux_ubuntu20.html#slow-setup-install-afni-binaries

We ran the command tcsh -x -v @update.afni.binaries -local_package afni_tars/AFNI_20.3.05.tgz -do_extras and get the attached output file, which includes echo command and verbose outputs. I have also requested an account on the AFNI message board and will ask there as well, but thought perhaps that you might have gone through this process as well.

Thanks!
afni_tcsh_output.txt

[shen4brains]

Hi Dominique,

I haven't encountered this before. Were you able to get support from AFNI?

[dhughe13]

Hi again,

After getting into contact with someone from AFNI, we have realized that the issue is actually that the singularity container does not contain any instance of libgsl at all and that is probably the issue that causes the error. Do you have any ideas on why this might be happening or any ideas how to fix it? Would we be able to copy the libgsl.so.19 file from our local machine to the singularity shell with the command in the .sif file? We tried using the command cp but was given the invalid SIF magic error.

Thank you so much again for all your help!

Best,
Dominique Hughes

[dhughe13]

Hi again,

I'm reaching out to follow up on this issue and see if there was any progress on how we can get libgsl.so.19 on the singularity image.

Thanks for you help,
Dominique

[shen4brains]

Hi Dominique,

Thanks for your patience on this. @yilewang has done a lot of work on the container to get it up and running on his HPC system. I copy his response below:

I had exact same problem before and I solved it in my case. I also have a dedicated part for this error in my container def file: https://github.com/yilewang/tvbdemos/blob/master/container/tvb-ukbb-gpu.def#L206
My way to solve it is that, I put the AFNI into the container, and install the libgsl & create symbolic link when I built the container, so 3dROIMAKER can just automatically find all the required libraries inside the container in a proper way. I tried many other approaches but only this way solved my problem.

[yilewang]

Hi @dhughe13 ! I had a similar issue before and just like what Kelly mentioned, I solved it by building my own container. I made my def file publicly accessible in my GitHub repo here. If you want to build your own container, you need to prepare afnibinary and freesurfer in advance, then copy and paste them to your container directory. Feel free to tailor the def file according to your system.

Yile Wang

[yilewang]

I've attached it!

bb_eddy.zip

Hi! I think you need to make sure that the command you use are like this:

singularity run -B /YOUR_WORKSPACE/ /DIR_OF_YOUR_SIF_FILE/tvb-ukbb-gpu.sif THE_CASE_FOLDER /DIR_OF_TVB_UKBB_PIPELINE

first para is the parent folder of you subject
second para is your singularity container path
third para is your case folder
fourth para is your TVB-UKBB pipeline folder.

And you should run the command in your terminal (outside the singularity container, just your regular terminal).

Sorry I have no access to my computer now, but I will check your zip file later~

Best Regards,

Yile

[yilewang]

Hi, actually your bb_eddy looks good.. And it shows that you are in my HSAM_cpu branch... I am wondering what's the singularity command you used to call the container and tvb-ukbb pipeline? That would be the best if you can share it here~

also, I would suggest you trying again using the command I mentioned in my previous reply and see if it works or not... Let us know!

Best Regards,

Yile

[dhughe13]

Hi,

We ran it again using the command structure you recommended above: singularity run -B /home/hughes/tvb-ukbb_cpu/sample_subjects/amsterdam /home/hughes/tvb-ukbb_singularity/tvb-ukbb-cpu.sif sub-0001 /home/hughes/tvb-ukbb_cpu

It did not finish running the QC pipeline after 24 hours and it is still only providing structural TVB inputs, not functional.

I've attached the logs from the latest run. Let me know what other files you'd like to see.

Best,
Dominique Hughes
logs_3_10.zip

[yilewang]

Hi Dominique,

I checked the logs and it looks like your git repo is ok (within my branch) but when the container is executing, it's not using the proper tvb-ukbb branch at all (I said it because when I checked bb_eddy logs, it looks like that it's still running eddy_cuda command instead of eddy). I really have no clue why it happened. Probably you can make sure your data structure looks like this:

|-- tvb-ukbb_cpu
|   |-- tvb-ukbb_cpu.sif
|   |-- tvb-ukbb
|   |-- sample_subjects/amsterdam

One folder is dedicated to tvb-ukbb pipeline, one folder for all your cases, and one singularity container file. Then all three things are in the same folder. However, I don't know if it will work or not because I really don't know what cause the error like that.

The command you can use is this:

singularity run -B /home/hughes/tvb-ukbb_cpu/sample_subjects/amsterdam /home/hughes/tvb-ukbb_cpu/tvb-ukbb-cpu.sif sub-0001 /home/hughes/tvb-ukbb_cpu/tvb-ukbb

[dhughe13]

Hello,

We made the changes to the structure and ran it again, and it worked!! We got all 5 structural inputs and the functional inputs as well. I just tried to input the structural connectivity zip to TVB and it uploaded fine and I ran a basic simulation with it. Thank you so much for your help with this, we could not have done it without you both!! We will be trying the pipeline on our own data soon.

Best,
Dominique Hughes

[yilewang]

Dear Dominique,

Awesome!! I am so glad that it finally works! Thank you for letting us know it!

Enjoy your simulation ;)!

Best Regards,

Yile