Hi!
I’m having some trouble with running BOLD Atlas QC for my functional data, as, after running preprocessing steps up to fmri_surface, I’m missing the following files in my subj/hcp/subj/MNNonLinear/Results/# directory:
#_Atlas_GS.dtseries.nii
#_Atlas_GS.sdseries.nii.txt
#_Atlas_TSNR.dscalar.nii
In addition, the BOLD QC logs say that my #_Atlas.dtseries.nii file is truncated.
In which step of preprocessing should these files have been generated? I’ve been running fmri_volume and fmri_surface after the pre_freesurfer/freesurfer/post_freesurfer steps.
Hi,
Welcome to QuNex forums!
Can you please post the QC command you are trying to run? Also, can you provide us with the contents (just the list of files) in one of the BOLD directories, e.g. MNINonLinear/Results/1?
Thanks, Jure
Yes!
QC Command:
qunex_container run_qc
–sessionsfolder=“$study_folder/sessions”
–sessions=“$sub8”
–batchfile=“$batch_file”
–modality=‘BOLD’
–boldsuffix=‘Atlas’
–overwrite=“yes”
–logfolder=“$study_folder/processing/logs/noah/”
–container=“$qunex_container”
The first image is a directory that’s failing, the second image is of another subject that I had done before that was successful and seems to have the full contents.
Thank you!
The files you re looking for are generated by the run_qc command itself. So maybe one of the initial steps fails.
Can you try running this:
STUDY_FOLDER="!!! SET THIS"
QUNEX_CONTAINER="!!! SET THIS"
qunex_container run_qc \
--sessionsfolder="${STUDY_FOLDER}/sessions" \
--sessions="HCPA001" \
--batchfile="${STUDY_FOLDER}/processing/batch.txt" \
--modality="BOLD" \
--boldsuffix="Atlas" \
--overwrite="yes" \
--container="${QUNEX_CONTAINER}"
And then upoad the relevant run_qc log found in ${STUDY_FOLDER}/processing/logs/comlogs here.
Thanks!
yep! here you go:
error_run_qc_pb13481_2024-05-20_09.11.16.025095.log (66.6 KB)
It’s the same as all previous error logs when running this before.
Hi, this is the actual error:
While running:
/opt/workbench/workbench-1.5.0/bin_rh_linux64/../exe_rh_linux64/wb_command -cifti-reduce /gpfs/gibbs/pi/n3/Studies/Adolescent.WM.Reward/sessions/pb13481/hcp/pb13481/MNINonLinear/Results/1/1_Atlas.dtseries.nii TSNR /gpfs/gibbs/pi/n3/Studies/Adolescent.WM.Reward/sessions/pb13481/hcp/pb13481/MNINonLinear/Results/1/1_Atlas_TSNR.dscalar.nii -exclude-outliers 4 4
ERROR: nifti file is truncated: /gpfs/gibbs/pi/n3/Studies/Adolescent.WM.Reward/sessions/pb13481/hcp/pb13481/MNINonLinear/Results/1/1_Atlas.dtseries.nii
Looks like an issue with input data X_Atlas.dtseries.nii. Which is why QuNex is unable to calculate TSNR. This error pops up for bolds 1 through 6, while the data for BOLD 7 is simply not there:
e[31m ---> ERROR: BOLD data specified for BOLD 7 not found: e[0m
e[31m --> /gpfs/gibbs/pi/n3/Studies/Adolescent.WM.Reward/sessions/pb13481/hcp/pb13481/MNINonLinear/Results/7/7_Atlas.dtseries.nii e[0m
Can you upload done logs for hcp_fmri_volume and hcp_fmri_surface this looks like an issue in one of those steps.
Best, Jure
I have never seen this error and it seems like some kind of an issue with input data. Because of this there is only as much I can do, everything looks good so far from the QuNex perspective. Did you try inspecting the BOLD image (unprocessed, and processed) with some kind of a visualization tool, e.g. wb_command?
Also, please upload the batch.txt from <study>/processing so I can take a look if there is something weird in there.
noah_batch_hcp_reruns.txt (30.9 KB)
With a few particular subjects, there are things like a missing single-band ref image or a surplus, but I’ve manually edited the labeling in the batch file from the beginning.
I’ll try to visualize the files later today (need to figure out permissions of wb_view), but from the looks of file sizes and output directories it seems that both unprocessed and processed BOLD scans are fine.
I skimmed over the batch file and nothing sticks out. The command that is failing is:
wb_command -cifti-reduce \
/gpfs/gibbs/pi/n3/Studies/Adolescent.WM.Reward/sessions/pb13481/hcp/pb13481/MNINonLinear/Results/1/1_Atlas.dtseries.nii \
TSNR \
/gpfs/gibbs/pi/n3/Studies/Adolescent.WM.Reward/sessions/pb13481/hcp/pb13481/MNINonLinear/Results/1/1_Atlas_TSNR.dscalar.nii \
-exclude-outliers 4 4
You can try running it manually (not through run_qc) to test faster. I see you have multiple sessions in the batchfile is the result the same for all of them?
Did you try running some denoising pipelines (hcp_icafix, hcp_msmall …)? I am wondering if those will work or it they will also crash.
Best, Jure