ANTs error - Githubissues

I am running micapipe on my university's cluster, and I am getting a 'cannot stat' error when running proc-structural. This happens during the ANTs step. Running proc_structural therefore results in an error. I am trying to run proc_structural to completion.

I am using MobaXterm v20.3 build 4396 to tunnel into my university cluster from my work computer.

My BIDS format:

dataset/ rawdata/ sub-001/ ses-0/ anat/ sub-001_ses-0_run-1_T1w.nii sub-001_ses-0_run_1_T1w.json dwi/... fmap/... func/... ses-1/... derivatives/ freesurfer/ sub-001_ses-0/ label/ mri/ ... sub-001_ses-1/... micapipe/

Because I am not allowed to run sudo command on the cluster,

I pulled the docker image into a singularity wrapper:

# Create a .singularity directory in Scratch
mkdir $HOME/Scratch/.singularity 

# Create cache subdirectories we will use / export
mkdir $HOME/Scratch/.singularity/tmp
mkdir $HOME/Scratch/.singularity/localcache
mkdir $HOME/Scratch/.singularity/pull

# Set all the Singularity cache dirs to Scratch
export SINGULARITY_CACHEDIR=$HOME/Scratch/.singularity
export SINGULARITY_TMPDIR=$SINGULARITY_CACHEDIR/tmp
export SINGULARITY_LOCALCACHEDIR=$SINGULARITY_CACHEDIR/localcache
export SINGULARITY_PULLFOLDER=$SINGULARITY_CACHEDIR/pull

# Bind the data directory in Scratch so it is accessible from inside the container and the temporary storage jobs are allocated
# add after $USER
export SINGULARITY_BINDPATH=/scratch/scratch/$USER,/tmpdir

# to pull docker image
singularity pull docker://micalab/micapipe:latest

# Prints micapipe version / test commands can be used (this is equivalent to running mica-pipe command)
$SINGULARITY_PULLFOLDER/micapipe_latest.sif -v

below is the error report I get when running proc_structural

[ucjucrs@login12 MICA_BIDS]$ export SINGULARITY_CACHEDIR=$HOME/Scratch/.singularity
[ucjucrs@login12 MICA_BIDS]$ export SINGULARITY_TMPDIR=$SINGULARITY_CACHEDIR/tmp
[ucjucrs@login12 MICA_BIDS]$ export SINGULARITY_LOCALCACHEDIR=$SINGULARITY_CACHEDIR/localcache
[ucjucrs@login12 MICA_BIDS]$ export SINGULARITY_PULLFOLDER=$SINGULARITY_CACHEDIR/pull
[ucjucrs@login12 MICA_BIDS]$ export SINGULARITY_BINDPATH=/scratch/scratch/$USER/Struct_MRI/MICA_BIDS/,/tmpdir
[ucjucrs@login12 MICA_BIDS]$ $SINGULARITY_PULLFOLDER/micapipe_latest.sif -bids /home/ucjucrs/Scratch/Struct_MRI/MICA_BIDS/rawdata -out /home/ucjucrs/Scratch/Struct_MRI/MICA_BIDS/derivatives -sub 001 -ses 0 -proc_structural
WARNING: Bind mount '/home/ucjucrs => /home/ucjucrs' overlaps container CWD /home/ucjucrs/Scratch/Struct_MRI/MICA_BIDS, 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 ]..... sub-001 directory structure:

/scratch/scratch/ucjucrs/Struct_MRI/MICA_BIDS/derivatives/micapipe/sub-001/ses-0
├── anat
│   ├── first
│   ├── surfaces
│   │   └── conte69
│   └── volumetric
├── dwi
├── func
├── logs
├── QC
│   └── png
└── xfm

11 directories

-------------------------------------------------------------
        Structural processing
                micapipe v0.1.1 'Roadrunner', LOCAL
-------------------------------------------------------------

[ INFO ]..... MICA pipe - Software versions
                MRtrix3.....    3.0.1
                                /opt/miniconda-latest/envs/micapipe/bin/mrinfo
                FSL.........    6.0
                                /opt/fsl-6.0.0
                ANFI........     Aug 22 2021 (Version AFNI_21.2.05 'Nerva')
                                /opt/afni-latest/3dresample
                ANTS........     2.3.3.dev168-g29bdf
                                /opt/ants-2.3.4
                WorkBench...    1.3.2
                                /usr/bin/wb_command
                FreeSurfer..    freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
                                /opt/freesurfer-6.0.0
                fix.........
                                /opt/fix
                python......    Python 3.7.10
                                /opt/miniconda-latest/envs/micapipe/bin/python
                R...........    3.6.3
                                /usr/bin/R

[ INFO ]..... mica-pipe inputs:
                id   =  001
                BIDS =  /scratch/scratch/ucjucrs/Struct_MRI/MICA_BIDS/rawdata
                out  =  /scratch/scratch/ucjucrs/Struct_MRI/MICA_BIDS/derivatives/micapipe
                ses  =  ses-0

[ INFO ]..... BIDS naming:
                subject_bids =  /scratch/scratch/ucjucrs/Struct_MRI/MICA_BIDS/rawdata/sub-001/ses-0
                bids_T1ws    =  N-1, e.g. /scratch/scratch/ucjucrs/Struct_MRI/MICA_BIDS/rawdata/sub-001/ses-0/anat/sub-001_ses-0_run-1_T1w.nii
                bids_dwis    =  N-0, e.g.
                subject      =  sub-001
                subject_dir  =  /scratch/scratch/ucjucrs/Struct_MRI/MICA_BIDS/derivatives/micapipe/sub-001/ses-0
                proc_struct  =  /scratch/scratch/ucjucrs/Struct_MRI/MICA_BIDS/derivatives/micapipe/sub-001/ses-0/anat
                dir_warp     =  /scratch/scratch/ucjucrs/Struct_MRI/MICA_BIDS/derivatives/micapipe/sub-001/ses-0/xfm
                logs         =  /scratch/scratch/ucjucrs/Struct_MRI/MICA_BIDS/derivatives/micapipe/sub-001/ses-0/logs

[ INFO ]..... Processing directories:
                subject_dir     =       /scratch/scratch/ucjucrs/Struct_MRI/MICA_BIDS/derivatives/micapipe/sub-001/ses-0
                proc_struct     =       /scratch/scratch/ucjucrs/Struct_MRI/MICA_BIDS/derivatives/micapipe/sub-001/ses-0/anat
                dir_conte69     =       /scratch/scratch/ucjucrs/Struct_MRI/MICA_BIDS/derivatives/micapipe/sub-001/ses-0/anat/surfaces/conte69
                dir_volum       =       /scratch/scratch/ucjucrs/Struct_MRI/MICA_BIDS/derivatives/micapipe/sub-001/ses-0/anat/volumetric
                dir_warp        =       /scratch/scratch/ucjucrs/Struct_MRI/MICA_BIDS/derivatives/micapipe/sub-001/ses-0/xfm
                dir_logs        =       /scratch/scratch/ucjucrs/Struct_MRI/MICA_BIDS/derivatives/micapipe/sub-001/ses-0/logs
                dir_QC          =       /scratch/scratch/ucjucrs/Struct_MRI/MICA_BIDS/derivatives/micapipe/sub-001/ses-0/QC
                dir_freesurfer  =       /scratch/scratch/ucjucrs/Struct_MRI/MICA_BIDS/derivatives/freesurfer/sub-001_ses-0

[ INFO ]..... Utilities directories:
                scriptDir         =     /opt/micapipe/functions
                util_MNIvolumes   =     /opt/micapipe/MNI152Volumes
                util_lut          =     /opt/micapipe/parcellations/lut
                util_parcelations =     /opt/micapipe/parcellations
                util_surface      =     /opt/micapipe/surfaces
                util_mics         =     /opt/micapipe/MICs60_T1-atlas

[ INFO ]..... Saving temporal dir: FALSE

[ INFO ]..... ANTs will use 6 threads

ucjucrs @ login12.myriad.ucl.ac.uk Thu Sep 30 10:47:17 BST 2021:
COMMAND -->   mkdir -p /tmp/30415_micapipe_proc_struc-vol_001

ucjucrs @ login12.myriad.ucl.ac.uk Thu Sep 30 10:47:17 BST 2021:
COMMAND -->   3dresample -orient LPI -prefix /tmp/30415_micapipe_proc_struc-vol_001/obl-001_ses-0_run-1_T1w.nii -inset /scratch/scratch/ucjucrs/Struct_MRI/MICA_BIDS/rawdata/sub-001/ses-0/anat/sub-001_ses-0_run-1_T1w.nii

ucjucrs @ login12.myriad.ucl.ac.uk Thu Sep 30 10:47:17 BST 2021:
COMMAND -->   fslreorient2std /tmp/30415_micapipe_proc_struc-vol_001/obl-001_ses-0_run-1_T1w.nii /tmp/30415_micapipe_proc_struc-vol_001/reo-001_ses-0_run-1_T1w.nii

ucjucrs @ login12.myriad.ucl.ac.uk Thu Sep 30 10:47:20 BST 2021:
COMMAND -->   cp -v /tmp/30415_micapipe_proc_struc-vol_001/reo-001_ses-0_run-1_T1w.nii /tmp/30415_micapipe_proc_struc-vol_001/sub-001_ses-0_space-nativepro_t1w_n4.nii.gz
cp: cannot stat '/tmp/30415_micapipe_proc_struc-vol_001/reo-001_ses-0_run-1_T1w.nii': No such file or directory

[ INFO ]..... T1w_nativepro biasfield correction and intensity rescaling

ucjucrs @ login12.myriad.ucl.ac.uk Thu Sep 30 10:47:20 BST 2021:
COMMAND -->   N4BiasFieldCorrection -d 3 -i /tmp/30415_micapipe_proc_struc-vol_001/sub-001_ses-0_space-nativepro_t1w_n4.nii.gz -r -o /tmp/30415_micapipe_proc_struc-vol_001/sub-001_ses-0_space-nativepro_t1w_n4.nii.gz -v

Running N4 for 3-dimensional images.

 file /tmp/30415_micapipe_proc_struc-vol_001/sub-001_ses-0_space-nativepro_t1w_n4.nii.gz does not exist .
Mask not read.  Using the entire image as the mask.

/opt/micapipe/functions/utilities.sh: line 584: 95445 Segmentation fault      $l_command

ucjucrs @ login12.myriad.ucl.ac.uk Thu Sep 30 10:47:20 BST 2021:
COMMAND -->   ImageMath 3 /scratch/scratch/ucjucrs/Struct_MRI/MICA_BIDS/derivatives/micapipe/sub-001/ses-0/anat/sub-001_ses-0_space-nativepro_t1w.nii.gz RescaleImage /tmp/30415_micapipe_proc_struc-vol_001/sub-001_ses-0_space-nativepro_t1w_n4.nii.gz 0 100
 file /tmp/30415_micapipe_proc_struc-vol_001/sub-001_ses-0_space-nativepro_t1w_n4.nii.gz does not exist .
terminate called after throwing an instance of 'itk::ExceptionObject'
  what():  /src/ants/build/ITKv5/Modules/Core/Common/src/itkProcessObject.cxx:1340:
itk::ERROR: RescaleIntensityImageFilter(0x43cfa80): Input Primary is required but not set.
/opt/micapipe/functions/utilities.sh: line 584: 95486 Aborted                 $l_command

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

[ ERROR ]..... sub-001_ses-0_space-nativepro_t1w was not generated

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

ucjucrs @ login12.myriad.ucl.ac.uk Thu Sep 30 10:47:20 BST 2021:
COMMAND -->   exit
Erasing temporal directory: /tmp/*_micapipe*_001
OLD_PATH is unset or empty

-------------------------------------------------------------
        GLOBAL micapipe running time with LOCAL processing: 0.083 minutes
-------------------------------------------------------------

MICA-MNI / micapipe

ANTs error #19

My BIDS format:

I pulled the docker image into a singularity wrapper:

below is the error report I get when running proc_structural