-proc_rsfmri states "couldn't find 001 main rsfMRI scan: ls"

[ClaireSmid]

I have been able to run the entire structural leg of the pipeline without issues, -proc_dwi without issues, (-SC not without issues) and I am now trying to run -proc_rsfmri

I am getting the error that the main rsfMRI scan cannot be found, even after manually specifying the scan via -MainScanStr. The file exists, and I have tried using both uncompressed (.nii) and compressed (.nii.gz) files.

I would expect the command to be able to at least find the scan, as it exists, e.g.:

I am running the pipeline through a singularity wrapper, on my university's computing cluster e.g.

$SINGULARITY_PULLFOLDER/micapipe_latest.sif -sub 001 -bids rawdata -out derivatives -ses 0

I am using MobaXterm as a terminal, and running this from a Windows computer.

Could anyone help me figure out what's going wrong here?

[ucjucrs@login12 dataset]$ $SINGULARITY_PULLFOLDER/micapipe_latest.sif -sub 001 -bids rawdata -out derivatives -ses 0 -proc_rsfmri -mainScanStr task-rest_run-1_bold.nii.gz
WARNING: Bind mount '/home/ucjucrs => /home/ucjucrs' overlaps container CWD /home/ucjucrs/Scratch/dataset, may not be available
Some packages in this Docker container are non-free
If you are considering commercial use of this container, please consult the relevant license:
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Licence
-------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /opt/freesurfer-6.0.0
FSFAST_HOME       /opt/freesurfer-6.0.0/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR      /opt/freesurfer-6.0.0/subjects
MNI_DIR           /opt/freesurfer-6.0.0/mni
FSL_DIR           /opt/fsl-6.0.0

-------------------------------------------------------------
        MICA pipeline - (Version v0.1.1 'Roadrunner')
                Subject: 001 Session: ses-0
-------------------------------------------------------------

[ WARNING ]..... fix was not found, ICA-FIX will be skipped

[ INFO ]..... micapipe will use 6 threads for multicore processing

[ INFO ]..... Subject 001 directory exist

[ INFO ]..... Inputs:
                Topup Config     :      DEFAULT
                ICA fix training :      DEFAULT
                Main scan        :      task-rest_run-1_bold.nii.gz
                Phase scan       :      DEFAULT
                Reverse Phase    :      DEFAULT
                Smoothing        :      0
                Perform NSR      :      0
                Perform GSR      :      0
                No FIX           :      0
                Longitudinal ses :      FALSE

[ INFO ]..... Using user provided main scan: /scratch/scratch/ucjucrs/dataset/rawdata/sub-001/ses-0/func/sub-001_ses-0_task-rest_run-1_bold.nii.gz

[ INFO ]..... No run number specified for phase reversals and did not find more than one phase reversal scan - all good!

-------------------------------------------------------------

[ ERROR ]..... Couldn't find 001 main rsfMRI scan :
         ls

-------------------------------------------------------------

Erasing temporal directory: /tmp/*_micapipe*_001
OLD_PATH is unset or empty

-------------------------------------------------------------
        GLOBAL micapipe running time with LOCAL processing: 0.017 minutes
-------------------------------------------------------------

[rcruces]

sorry for the late reply. The pipeline can't find the file because it search the string pattern provided without the extension. your input should be -mainScanStr task-rest_run-1_bold, and that will probably fix it.

For further details check the documentations regarding -proc_rsfmri and also the tutorial Processing databases with micapipe

-mainScanStr         : String to manually identify the main scan for rsfMRI processing (eg. func/sub-001_<mainScanStr>.nii.gz)
                         Default='task-rest_acq-AP_bold'