Proc_structural [ ERROR ]..... Subject xxx doesn't have T1_nativepro

[nichy-consortium]

Dear Micapipe team,

We are running the structural processing workflow in micapipe and run into some issues after a couple of seconds (see code from log file below). It seems as if the T1 scan cannot be found by the pipeline, whereas the input is BIDS validated. We noticed another issue on this page with a similar error, there it seemed as if the binding of paths within and outside the container was not succesful. We use apptainer on a slurm server and bind our paths like this. This exact command worked well when processing another dataset, but seems to bounce back for this dataset.

Command in job submission script:

apptainer run --bind /scratch/anw/ksvoogd/:/data_ams \
/scratch/anw/evanheese/containers/micapipe-v0.2.2.sif \
-sub ${subj} \
-out /data_ams/output/test_1ppn_14Feb/ \
-bids /data_ams/input/ \
-proc_surf \
-post_structural \
-GD \
-QC_subj \
-freesurfer \
-fs_licence /data_ams/license.txt

Log file output:
`micapipe -sub sub-nt100002ams -out /data_ams/output/test_1ppn_14Feb/ -bids /data_ams/input/ -proc_surf -post_structural -GD -QC_subj -freesurfer -fs_licence /data_ams/license.txt

�[38;5;141m

MICA pipeline - (Version v0.2.2 'Northern flicker') 
	Subject: nt100002ams Session: SINGLE

-------------------------------------------------------------�[0m
Freesurfer licence: �[38;5;122m/data_ams/license.txt�[0m
�[38;5;75m
[ INFO ]..... Subject sub-nt100002ams directory doesn't exist, creating... �[0m
�[38;5;118m
ksvoogd @ luna-02 Wed Feb 14 15:08:25 CET 2024:
COMMAND --> �[38;5;122m mkdir -m 770 -p /data_ams/output/test_1ppn_14Feb/micapipe_v0.2.0/sub-nt100002ams/logs /data_ams/output/test_1ppn_14Feb/micapipe_v0.2.0/sub-nt100002ams/xfm /data_ams/output/test_1ppn_14Feb/micapipe_v0.2.0/sub-nt100002ams/dwi /data_ams/output/test_1ppn_14Feb/micapipe_v0.2.0/sub-nt100002ams/func /data_ams/output/test_1ppn_14Feb/micapipe_v0.2.0/sub-nt100002ams/anat /data_ams/output/test_1ppn_14Feb/micapipe_v0.2.0/sub-nt100002ams/QC /data_ams/output/test_1ppn_14Feb/micapipe_v0.2.0/sub-nt100002ams/parc /data_ams/output/test_1ppn_14Feb/micapipe_v0.2.0/sub-nt100002ams/surf /data_ams/output/test_1ppn_14Feb/micapipe_v0.2.0/sub-nt100002ams/maps �[0m
�[38;5;9m

[ ERROR ]..... Subject nt100002ams doesn't have T1_nativepro
`
Any insights into the issue are appreciated! Thanks.

Best,
Keetje & Eva

[araikes]

@nichy-consortium,

If that's your whole call, you forgot -proc_structural, so it's trying to run -proc_surf without the -proc_structural outputs T1.