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HALFpipe / HALFpipe

ENIGMA HALFpipe is a user-friendly software that facilitates reproducible analysis of fMRI data
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Inputs do not occupy the same physical space #713

Closed hjameei closed 7 months ago

hjameei commented 7 months ago

What happened? I am running HALFpipe in a HPC on a set of subjects. I am providing T1 and resting state data. The preprocessing I am using contains generating atlas-based connectivity matrices, which runs for most of the subjects. However, on a number of subjects, I encounter an error when N4BiasFieldCorrection is run. Below is an example of the error for one subject (I have attached the err.txt file as well).

Is there an error message?

Cmdline:
│       N4BiasFieldCorrection --bspline-fitting [ 200 ] -d 3 --input-image /ext/data/gpfs/projects/punim0963/snuh/nipype/fmriprep_wf/single_subject_C044_wf/func_preproc_task_rsfMRI_wf/initial_boldref_wf/gen_ref/ref_bold.nii.gz --mask-image /ext/data/gpfs/projects/punim0963/snuh/nipype/fmriprep_wf/single_subject_C044_wf/func_preproc_task_rsfMRI_wf/initial_boldref_wf/enhance_and_skullstrip_bold_wf/check_hdr/tpl-MNI152NLin2009cAsym_res-01_label-brain_probseg_trans_mask_dil_hdr.nii.gz --output ref_bold_corrected.nii.gz -r
│     Stdout:
Stderr:
    terminate called after throwing an instance of 'itk::ExceptionObject'
      what():  /src/ants/build/staging/include/ITK-5.1/itkImageSink.hxx:242:
    itk::ERROR: LabelStatisticsImageFilter(0x26b0550): Inputs do not occupy the same physical space!
    InputImage Direction: 9.9999406e-01 3.4033828e-03 -5.4513358e-04
    3.4033827e-03 -9.4996626e-01 3.1233401e-01
    -5.4513357e-04 3.1233400e-01 9.4997219e-01
    , InputImagePrimary Direction: 9.9999379e-01 3.5189875e-03 1.7661476e-04
    3.2877769e-03 -9.4996626e-01 3.1233521e-01
    -1.2668819e-03 3.1233270e-01 9.4997194e-01

        Tolerance: 1.0000000e-06

    Aborted (core dumped)

What is the exact command that you used to run Halfpipe? I have attached Here is the script that I submitted on HPC:

#!/bin/bash

#SBATCH --job-name=halfpipe
#SBATCH --output=halfpipe.log.txt

#SBATCH --time=1-0
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=2
#SBATCH --mem=15706M

#SBATCH --array=1-118

if ! [ -x "$(command -v singularity)" ]; then
module load foss/2022a Apptainer/1.1.8
fi

singularity run \
--contain --cleanenv \
--bind /:/ext \
/data/gpfs/projects/punim0934/yuanzhe_run/halfpipe-halfpipe-latest.sif \
--workdir /ext/data/gpfs/projects/punim0963/snuh \
--only-run \
--uuid eed5b6a9 \
--subject-list /ext/data/gpfs/projects/punim0963/snuh/subject-list.txt \
--subject-chunks \
--only-chunk-index ${SLURM_ARRAY_TASK_ID} \
--nipype-n-procs 2 \
--keep some

Which settings did you use? Here is the spec.json file that I used for the preprocessing:

{
    "halfpipe_version": "0.0.post1.dev1+g6781c9b",
    "schema_version": "3.0",
    "timestamp": "2024-03-06_18-28",
    "global_settings": {
        "dummy_scans": 4,
        "slice_timing": true,
        "use_bbr": null,
        "skull_strip_algorithm": "ants",
        "run_mriqc": false,
        "run_fmriprep": true,
        "run_halfpipe": true,
        "fd_thres": 0.5,
        "anat_only": false,
        "write_graph": false,
        "hires": false,
        "run_reconall": false,
        "t2s_coreg": false,
        "medial_surface_nan": false,
        "bold2t1w_dof": 9,
        "fmap_bspline": true,
        "force_syn": false,
        "longitudinal": false,
        "regressors_all_comps": false,
        "regressors_dvars_th": 1.5,
        "regressors_fd_th": 0.5,
        "skull_strip_fixed_seed": false,
        "skull_strip_template": "OASIS30ANTs",
        "aroma_err_on_warn": false,
        "aroma_melodic_dim": -200,
        "sloppy": false
    },
    "files": [
        {
            "path": "/ext/data/gpfs/projects/punim0963/snuh/snuh_data/{sub}_T1.nii.gz",
            "datatype": "anat",
            "suffix": "T1w",
            "extension": ".nii.gz",
            "tags": {}
        },
        {
            "path": "/ext/data/gpfs/projects/punim0963/snuh/snuh_data/{sub}_RS.nii.gz",
            "datatype": "func",
            "suffix": "bold",
            "extension": ".nii.gz",
            "tags": {
                "task": "rsfMRI"
            },
            "metadata": {
                "slice_encoding_direction": "si"
            }
        },
        {
            "path": "/ext/data/scratch/projects/punim0564/ENIGMA_rs_halfpipe/{desc}_seed_2009.nii.gz",
            "datatype": "ref",
            "suffix": "seed",
            "extension": ".nii.gz",
            "tags": {},
            "metadata": {}
        },
        {
            "path": "/ext/data/scratch/projects/punim0564/ENIGMA_rs_halfpipe/{desc}_maps_2009.nii.gz",
            "datatype": "ref",
            "suffix": "map",
            "extension": ".nii.gz",
            "tags": {},
            "metadata": {}
        },
        {
            "path": "/ext/data/scratch/projects/punim0564/ENIGMA_rs_halfpipe/tpl-MNI152NLin2009cAsym_atlas-{desc}.nii.gz",
            "datatype": "ref",
            "suffix": "atlas",
            "extension": ".nii.gz",
            "tags": {},
            "metadata": {}
        }
    ],
    "settings": [
        {
            "ica_aroma": true,
            "smoothing": {
                "fwhm": 6.0
            },
            "grand_mean_scaling": {
                "mean": 10000.0
            },
            "bandpass_filter": {
                "type": "gaussian",
                "hp_width": 125.0,
                "lp_width": null
            },
            "name": "seedCorrSetting",
            "output_image": false
        },
        {
            "ica_aroma": false,
            "smoothing": {
                "fwhm": 6.0
            },
            "grand_mean_scaling": {
                "mean": 10000.0
            },
            "bandpass_filter": {
                "type": "gaussian",
                "hp_width": 125.0,
                "lp_width": null
            },
            "confounds_removal": [
                "a_comp_cor_0[0-4]"
            ],
            "name": "seedCorr1Setting",
            "output_image": false
        },
        {
            "ica_aroma": true,
            "smoothing": {
                "fwhm": 6.0
            },
            "grand_mean_scaling": {
                "mean": 10000.0
            },
            "bandpass_filter": {
                "type": "gaussian",
                "hp_width": 125.0,
                "lp_width": null
            },
            "confounds_removal": [
                "a_comp_cor_0[0-4]"
            ],
            "name": "seedCorr2Setting",
            "output_image": false
        },
        {
            "ica_aroma": true,
            "smoothing": {
                "fwhm": 6.0
            },
            "grand_mean_scaling": {
                "mean": 10000.0
            },
            "bandpass_filter": {
                "type": "gaussian",
                "hp_width": 125.0,
                "lp_width": null
            },
            "name": "dualRegSetting",
            "output_image": false
        },
        {
            "ica_aroma": false,
            "smoothing": {
                "fwhm": 6.0
            },
            "grand_mean_scaling": {
                "mean": 10000.0
            },
            "bandpass_filter": {
                "type": "gaussian",
                "hp_width": 125.0,
                "lp_width": null
            },
            "confounds_removal": [
                "a_comp_cor_0[0-4]"
            ],
            "name": "dualReg1Setting",
            "output_image": false
        },
        {
            "ica_aroma": true,
            "smoothing": {
                "fwhm": 6.0
            },
            "grand_mean_scaling": {
                "mean": 10000.0
            },
            "bandpass_filter": {
                "type": "gaussian",
                "hp_width": 125.0,
                "lp_width": null
            },
            "confounds_removal": [
                "a_comp_cor_0[0-4]"
            ],
            "name": "dualReg2Setting",
            "output_image": false
        },
        {
            "ica_aroma": true,
            "grand_mean_scaling": {
                "mean": 10000.0
            },
            "bandpass_filter": {
                "type": "gaussian",
                "hp_width": 125.0,
                "lp_width": null
            },
            "name": "corrMatrixSetting",
            "output_image": false
        },
        {
            "ica_aroma": false,
            "grand_mean_scaling": {
                "mean": 10000.0
            },
            "bandpass_filter": {
                "type": "gaussian",
                "hp_width": 125.0,
                "lp_width": null
            },
            "confounds_removal": [
                "a_comp_cor_0[0-4]"
            ],
            "name": "corrMatrix1Setting",
            "output_image": false
        },
        {
            "ica_aroma": true,
            "grand_mean_scaling": {
                "mean": 10000.0
            },
            "bandpass_filter": {
                "type": "gaussian",
                "hp_width": 125.0,
                "lp_width": null
            },
            "confounds_removal": [
                "a_comp_cor_0[0-4]"
            ],
            "name": "corrMatrix2Setting",
            "output_image": false
        },
        {
            "ica_aroma": true,
            "grand_mean_scaling": {
                "mean": 10000.0
            },
            "bandpass_filter": {
                "type": "frequency_based",
                "low": 0.01,
                "high": 0.1
            },
            "name": "reHoSetting",
            "output_image": false
        },
        {
            "ica_aroma": false,
            "grand_mean_scaling": {
                "mean": 10000.0
            },
            "bandpass_filter": {
                "type": "frequency_based",
                "low": 0.01,
                "high": 0.1
            },
            "confounds_removal": [
                "a_comp_cor_0[0-4]"
            ],
            "name": "reHo1Setting",
            "output_image": false
        },
        {
            "ica_aroma": true,
            "grand_mean_scaling": {
                "mean": 10000.0
            },
            "bandpass_filter": {
                "type": "frequency_based",
                "low": 0.01,
                "high": 0.1
            },
            "confounds_removal": [
                "a_comp_cor_0[0-4]"
            ],
            "name": "reHo2Setting",
            "output_image": false
        },
        {
            "ica_aroma": true,
            "grand_mean_scaling": {
                "mean": 10000.0
            },
            "bandpass_filter": {
                "type": "frequency_based",
                "low": 0.01,
                "high": 0.1
            },
            "name": "fAlffSetting",
            "output_image": false
        },
        {
            "ica_aroma": true,
            "grand_mean_scaling": {
                "mean": 10000.0
            },
            "name": "fALFFUnfilteredSetting",
            "output_image": false
        },
        {
            "ica_aroma": false,
            "grand_mean_scaling": {
                "mean": 10000.0
            },
            "bandpass_filter": {
                "type": "frequency_based",
                "low": 0.01,
                "high": 0.1
            },
            "confounds_removal": [
                "a_comp_cor_0[0-4]"
            ],
            "name": "fAlff1Setting",
            "output_image": false
        },
        {
            "ica_aroma": false,
            "grand_mean_scaling": {
                "mean": 10000.0
            },
            "confounds_removal": [
                "a_comp_cor_0[0-4]"
            ],
            "name": "fALFF1UnfilteredSetting",
            "output_image": false
        },
        {
            "ica_aroma": true,
            "grand_mean_scaling": {
                "mean": 10000.0
            },
            "bandpass_filter": {
                "type": "frequency_based",
                "low": 0.01,
                "high": 0.1
            },
            "confounds_removal": [
                "a_comp_cor_0[0-4]"
            ],
            "name": "fAlff2Setting",
            "output_image": false
        },
        {
            "ica_aroma": true,
            "grand_mean_scaling": {
                "mean": 10000.0
            },
            "confounds_removal": [
                "a_comp_cor_0[0-4]"
            ],
            "name": "fALFF2UnfilteredSetting",
            "output_image": false
        }
    ],
    "features": [
        {
            "name": "seedCorr",
            "setting": "seedCorrSetting",
            "type": "seed_based_connectivity",
            "seeds": [
                "R_dorsalnexus",
                "R_postInsula",
                "Middle_PAG",
                "L_SPL",
                "L_lOFC",
                "L_ventralstriatum",
                "R_subcallosal",
                "R_rACC",
                "R_mOFC",
                "R_vmPFC",
                "L_vlPFC_pt",
                "Middle_Precuneus",
                "R_dACC",
                "L_thalamus",
                "L_antInsula",
                "R_thalamus",
                "L_STG_post",
                "L_subcallosal",
                "R_putamen",
                "L_postInsula",
                "Middle_subgenual",
                "L_putamen",
                "L_dlPFC",
                "L_vlPFC_po",
                "R_IPL",
                "L_amygdala",
                "L_mOFC",
                "R_caudate",
                "R_fusiform",
                "R_SPL",
                "L_rACC",
                "L_dACC",
                "L_hippocampus",
                "L_vmPFC",
                "R_MTG",
                "R_lOFC",
                "L_supramarginal",
                "R_dlPFC",
                "R_amygdala",
                "R_STG_post",
                "L_IPL",
                "L_ITG_tempocc",
                "Middle_PCC",
                "Middle_dmPFC",
                "R_ITG_tempocc",
                "R_vlPFC_po",
                "R_hippocampus",
                "R_vlPFC_pt",
                "R_supramarginal",
                "R_ventralstriatum",
                "L_fusiform",
                "L_caudate",
                "L_MTG_post",
                "L_dorsalnexus",
                "R_antInsula"
            ],
            "min_seed_coverage": 0.8
        },
        {
            "name": "seedCorr1",
            "setting": "seedCorr1Setting",
            "type": "seed_based_connectivity",
            "seeds": [
                "R_dorsalnexus",
                "R_postInsula",
                "Middle_PAG",
                "L_SPL",
                "L_lOFC",
                "L_ventralstriatum",
                "R_subcallosal",
                "R_rACC",
                "R_mOFC",
                "R_vmPFC",
                "L_vlPFC_pt",
                "Middle_Precuneus",
                "R_dACC",
                "L_thalamus",
                "L_antInsula",
                "R_thalamus",
                "L_STG_post",
                "L_subcallosal",
                "R_putamen",
                "L_postInsula",
                "Middle_subgenual",
                "L_putamen",
                "L_dlPFC",
                "L_vlPFC_po",
                "R_IPL",
                "L_amygdala",
                "L_mOFC",
                "R_caudate",
                "R_fusiform",
                "R_SPL",
                "L_rACC",
                "L_dACC",
                "L_hippocampus",
                "L_vmPFC",
                "R_MTG",
                "R_lOFC",
                "L_supramarginal",
                "R_dlPFC",
                "R_amygdala",
                "R_STG_post",
                "L_IPL",
                "L_ITG_tempocc",
                "Middle_PCC",
                "Middle_dmPFC",
                "R_ITG_tempocc",
                "R_vlPFC_po",
                "R_hippocampus",
                "R_vlPFC_pt",
                "R_supramarginal",
                "R_ventralstriatum",
                "L_fusiform",
                "L_caudate",
                "L_MTG_post",
                "L_dorsalnexus",
                "R_antInsula"
            ],
            "min_seed_coverage": 0.8
        },
        {
            "name": "seedCorr2",
            "setting": "seedCorr2Setting",
            "type": "seed_based_connectivity",
            "seeds": [
                "R_dorsalnexus",
                "R_postInsula",
                "Middle_PAG",
                "L_SPL",
                "L_lOFC",
                "L_ventralstriatum",
                "R_subcallosal",
                "R_rACC",
                "R_mOFC",
                "R_vmPFC",
                "L_vlPFC_pt",
                "Middle_Precuneus",
                "R_dACC",
                "L_thalamus",
                "L_antInsula",
                "R_thalamus",
                "L_STG_post",
                "L_subcallosal",
                "R_putamen",
                "L_postInsula",
                "Middle_subgenual",
                "L_putamen",
                "L_dlPFC",
                "L_vlPFC_po",
                "R_IPL",
                "L_amygdala",
                "L_mOFC",
                "R_caudate",
                "R_fusiform",
                "R_SPL",
                "L_rACC",
                "L_dACC",
                "L_hippocampus",
                "L_vmPFC",
                "R_MTG",
                "R_lOFC",
                "L_supramarginal",
                "R_dlPFC",
                "R_amygdala",
                "R_STG_post",
                "L_IPL",
                "L_ITG_tempocc",
                "Middle_PCC",
                "Middle_dmPFC",
                "R_ITG_tempocc",
                "R_vlPFC_po",
                "R_hippocampus",
                "R_vlPFC_pt",
                "R_supramarginal",
                "R_ventralstriatum",
                "L_fusiform",
                "L_caudate",
                "L_MTG_post",
                "L_dorsalnexus",
                "R_antInsula"
            ],
            "min_seed_coverage": 0.8
        },
        {
            "name": "dualReg",
            "setting": "dualRegSetting",
            "type": "dual_regression",
            "maps": [
                "FIND_ica"
            ]
        },
        {
            "name": "dualReg1",
            "setting": "dualReg1Setting",
            "type": "dual_regression",
            "maps": [
                "FIND_ica"
            ]
        },
        {
            "name": "dualReg2",
            "setting": "dualReg2Setting",
            "type": "dual_regression",
            "maps": [
                "FIND_ica"
            ]
        },
        {
            "name": "corrMatrix",
            "setting": "corrMatrixSetting",
            "type": "atlas_based_connectivity",
            "atlases": [
                "power2011_dseg",
                "schaefer2011Combined_dseg",
                "brainnetomeCombined_dseg"
            ],
            "min_region_coverage": 0.8
        },
        {
            "name": "corrMatrix1",
            "setting": "corrMatrix1Setting",
            "type": "atlas_based_connectivity",
            "atlases": [
                "power2011_dseg",
                "schaefer2011Combined_dseg",
                "brainnetomeCombined_dseg"
            ],
            "min_region_coverage": 0.8
        },
        {
            "name": "corrMatrix2",
            "setting": "corrMatrix2Setting",
            "type": "atlas_based_connectivity",
            "atlases": [
                "power2011_dseg",
                "schaefer2011Combined_dseg",
                "brainnetomeCombined_dseg"
            ],
            "min_region_coverage": 0.8
        },
        {
            "name": "reHo",
            "setting": "reHoSetting",
            "type": "reho",
            "smoothing": {
                "fwhm": 6.0
            }
        },
        {
            "name": "reHo1",
            "setting": "reHo1Setting",
            "type": "reho",
            "smoothing": {
                "fwhm": 6.0
            }
        },
        {
            "name": "reHo2",
            "setting": "reHo2Setting",
            "type": "reho",
            "smoothing": {
                "fwhm": 6.0
            }
        },
        {
            "name": "fALFF",
            "setting": "fAlffSetting",
            "type": "falff",
            "smoothing": {
                "fwhm": 6.0
            },
            "unfiltered_setting": "fALFFUnfilteredSetting"
        },
        {
            "name": "fALFF1",
            "setting": "fAlff1Setting",
            "type": "falff",
            "smoothing": {
                "fwhm": 6.0
            },
            "unfiltered_setting": "fALFF1UnfilteredSetting"
        },
        {
            "name": "fALFF2",
            "setting": "fAlff2Setting",
            "type": "falff",
            "smoothing": {
                "fwhm": 6.0
            },
            "unfiltered_setting": "fALFF2UnfilteredSetting"
        }
    ],
    "models": []
}

I have tried comparing the header of the fMRI file that resulted in an error to the header of the fMRI that was processed successfully using fslhd. However, only the vertex to xyz transformation matrices were different along the two files.

Here is the comparison between the two head files (the second one is the one ending in the error):

< filename  /data/gpfs/projects/punim0963/snuh/nipype/fmriprep_wf/single_subject_C041_wf/func_preproc_task_rsfMRI_wf/initial_boldref_wf/gen_ref/ref_bold.nii.gz
---
> filename  /data/gpfs/projects/punim0963/snuh/nipype/fmriprep_wf/single_subject_C044_wf/func_preproc_task_rsfMRI_wf/initial_boldref_wf/gen_ref/ref_bold.nii.gz
29,30c29,30
< scl_slope 0.025201
< scl_inter 825.784668
---
> scl_slope 0.022466
> scl_inter 736.170654
48,50c48,50
< qto_xyz:1 -1.871556 -0.045740 -0.266174 125.787659
< qto_xyz:2 -0.038281 1.869848 -0.341807 -90.154892
< qto_xyz:3 -0.106946 0.131150 4.780410 -53.380650
---
> qto_xyz:1 -1.874988 -0.006598 -0.000848 119.258224
> qto_xyz:2 -0.006165 1.781187 -1.499209 -76.436783
> qto_xyz:3 -0.002375 0.585624 4.559865 -93.368042
57,59c57,59
< sto_xyz:1 -1.871556 -0.045740 -0.266167 125.787659
< sto_xyz:2 -0.038281 1.869848 -0.341807 -90.154892
< sto_xyz:3 -0.106943 0.131151 4.780411 -53.380650
---
> sto_xyz:1 -1.874989 -0.006545 0.000000 119.258224
> sto_xyz:2 -0.006218 1.781187 -1.499207 -76.436783
> sto_xyz:3 -0.002044 0.585624 4.559865 -93.368042
66c66
< descrip       TE=40;Time=120140.277;phase=1;dwell=0.390
---
> descrip       TE=40;Time=93008.460;phase=1;dwell=0.390

Here is the difference between header files of the mask and the fMRI file yeilding error:

< filename  /data/gpfs/projects/punim0963/snuh/nipype/fmriprep_wf/single_subject_C044_wf/func_preproc_task_rsfMRI_wf/initial_boldref_wf/gen_ref/ref_bold.nii.gz
---
> filename  /data/gpfs/projects/punim0963/snuh/nipype/fmriprep_wf/single_subject_C044_wf/func_preproc_task_rsfMRI_wf/initial_boldref_wf/enhance_and_skullstrip_bold_wf/check_hdr/tpl-MNI152NLin2009cAsym_res-01_label-brain_probseg_trans_mask_dil_hdr.nii.gz
4c4
< data_type INT16
---
> data_type FLOAT32
15,17c15,17
< datatype  4
< nbyper        2
< bitpix        16
---
> datatype  16
> nbyper        4
> bitpix        32
22,25c22,25
< pixdim4       1.000000
< pixdim5       1.000000
< pixdim6       1.000000
< pixdim7       1.000000
---
> pixdim4       0.000000
> pixdim5       0.000000
> pixdim6       0.000000
> pixdim7       0.000000
29,30c29,30
< scl_slope 0.022466
< scl_inter 736.170654
---
> scl_slope 1.000000
> scl_inter 0.000000
34,35c34,35
< slice_name    alternating_decreasing
< slice_code    4
---
> slice_name    Unknown
> slice_code    0
48,50c48,50
< qto_xyz:1 -1.874988 -0.006598 -0.000848 119.258224
< qto_xyz:2 -0.006165 1.781187 -1.499209 -76.436783
< qto_xyz:3 -0.002375 0.585624 4.559865 -93.368042
---
> qto_xyz:1 -1.874989 -0.006381 0.002617 119.258224
> qto_xyz:2 -0.006381 1.781187 -1.499203 -76.436783
> qto_xyz:3 -0.001022 0.585626 4.559866 -93.368042
66,67c66,67
< descrip       TE=40;Time=93008.460;phase=1;dwell=0.390
< aux_file  Reference_volume_for_mo
---
> descrip       FSL5.0
> aux_file

This is very strange, considering there is not much difference between header files of the fMRI files that were processed successfully and the files that led to an error. Should I try using N4BiasFieldCorrection with -d 2 on every slice separately?

I appreciate your help in advance. err.txt

HippocampusGirl commented 7 months ago

Hi @hjameei,

we recently fixed an issue related to ANTs (https://github.com/HALFpipe/HALFpipe/pull/692). Could you check if the container you used was downloaded after February 15th this year?

Best, Lea

hjameei commented 7 months ago

Hi @HippocampusGirl

I was using the August 2023 version previously. After trying the new container, the issue is fixed now.

Thanks very much!