fieldmap

[bidhanlamichhane]

Hello, I have received following error while running fmriprep-docker: as : "fmriprep-docker --fs-license-file $FREESURFER_HOM /Users/.../Desktop/BIDS/Test_data/sub-001 /Users/.../Desktop/BIDS/Test_data002/" and my subject's data folder consists of : anat/fmap/func data collected using CMRR and multi-band factor: 4

Running fMRIPREP version 1.0.15:

• BIDS dataset path: /data.
• Participant list: ['sub-002'].
• Run identifier: 20180527-184833_a0043697-6e85-443e-939d-7794bbf24eab.

180527-18:48:34,638 workflow IMPORTANT: Creating bold processing workflow for "/data/sub-001/ses-01/func/sub-001_ses-01task-reward......._run-01_bold.nii.gz" (0.26 GB / 368 TRs). Memory resampled/largemem=1.06/2.03 GB. 180527-18:48:35,776 workflow IMPORTANT: Slice-timing correction will be included. Process Process-2: Traceback (most recent call last): File "/usr/local/miniconda/lib/python3.6/multiprocessing/process.py", line 258, in _bootstrap self.run() File "/usr/local/miniconda/lib/python3.6/multiprocessing/process.py", line 93, in run self._target(*self._args, **self._kwargs) File "/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/cli/run.py", line 510, in build_workflow ignore_aroma_err=opts.ignore_aroma_denoising_errors, File "/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/workflows/base.py", line 202, in init_fmriprep_wf ignore_aroma_err=ignore_aroma_err) File "/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/workflows/base.py", line 458, in init_single_subject_wf ignore_aroma_err=ignore_aroma_err) File "/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/workflows/bold/base.py", line 401, in init_func_preproc_wf debug=debug, fmap_demean=fmap_demean, fmap_bspline=fmap_bspline) File "/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/workflows/fieldmap/base.py", line 178, in init_sdc_wf name='pepolar_unwarp_wf') File "/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/workflows/fieldmap/pepolar.py", line 97, in init_pepolar_unwarp_wf raise Exception("None of the discovered fieldmaps has the right " Exception: None of the discovered fieldmaps has the right phase encoding direction. Possibly a problem with metadata. If not, rerun with '--ignore fieldmaps' to skip distortion correction step.

[chrisgorgo]

Could you share the metadata (content of the JSON files) from func and fmap folders? Does this dataset pass the validator ( https://github.com/INCF/bids-validator) without warnings?

BTW - this is unrelated, but you should increase the amount of memory (RAM) accessible to Docker. 2gb is not enough. You can change this in Docker settings.

On Sun, May 27, 2018 at 12:32 PM bidhanlamichhane notifications@github.com wrote:

Hello, I have received following error while running fmriprep-docker: as : "fmriprep-docker --fs-license-file $FREESURFER_HOM /Users/.../Desktop/BIDS/Test_data/sub-001 /Users/.../Desktop/BIDS/Test_data002/" and my subject's data folder consists of : anat/fmap/func data collected using CMRR and multi-band factor: 4

Running fMRIPREP version 1.0.15:

• BIDS dataset path: /data.
• Participant list: ['sub-002'].
• Run identifier: 20180527-184833_a0043697-6e85-443e-939d-7794bbf24eab.

180527-18:48:34,638 workflow IMPORTANT: Creating bold processing workflow for "/data/sub-001/ses-01/func/sub-001_ses-01task-reward......._run-01_bold.nii.gz" (0.26 GB / 368 TRs). Memory resampled/largemem=1.06/2.03 GB. 180527-18:48:35,776 workflow IMPORTANT: Slice-timing correction will be included. Process Process-2: Traceback (most recent call last): File "/usr/local/miniconda/lib/python3.6/multiprocessing/process.py", line 258, in _bootstrap self.run() File "/usr/local/miniconda/lib/python3.6/multiprocessing/process.py", line 93, in run self._target(*self._args, **self._kwargs) File "/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/cli/run.py", line 510, in build_workflow ignore_aroma_err=opts.ignore_aroma_denoising_errors, File "/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/workflows/base.py", line 202, in init_fmriprep_wf ignore_aroma_err=ignore_aroma_err) File "/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/workflows/base.py", line 458, in init_single_subject_wf ignore_aroma_err=ignore_aroma_err) File "/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/workflows/bold/base.py", line 401, in init_func_preproc_wf debug=debug, fmap_demean=fmap_demean, fmap_bspline=fmap_bspline) File "/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/workflows/fieldmap/base.py", line 178, in init_sdc_wf name='pepolar_unwarp_wf') File "/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/workflows/fieldmap/pepolar.py", line 97, in init_pepolar_unwarp_wf raise Exception("None of the discovered fieldmaps has the right " Exception: None of the discovered fieldmaps has the right phase encoding direction. Possibly a problem with metadata. If not, rerun with '--ignore fieldmaps' to skip distortion correction step.

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[bidhanlamichhane]

Hello, Thanks you so much for your quick response: Please find JSON files ( bold and fmap) for one of my task run attached.

Thanks Bidhan Lamichhane

On May 27, 2018, at 2:51 PM, Chris Filo Gorgolewski notifications@github.com<mailto:notifications@github.com> wrote:

Could you share the metadata (content of the JSON files) from func and fmap folders? Does this dataset pass the validator ( https://github.com/INCF/bids-validator) without warnings?

BTW - this is unrelated, but you should increase the amount of memory (RAM) accessible to Docker. 2gb is not enough. You can change this in Docker settings.

On Sun, May 27, 2018 at 12:32 PM bidhanlamichhane notifications@github.com<mailto:notifications@github.com> wrote:

Hello, I have received following error while running fmriprep-docker: as : "fmriprep-docker --fs-license-file $FREESURFER_HOM /Users/.../Desktop/BIDS/Test_data/sub-001 /Users/.../Desktop/BIDS/Test_data002/" and my subject's data folder consists of : anat/fmap/func data collected using CMRR and multi-band factor: 4

Running fMRIPREP version 1.0.15:

• BIDS dataset path: /data.
• Participant list: ['sub-002'].
• Run identifier: 20180527-184833_a0043697-6e85-443e-939d-7794bbf24eab.

180527-18:48:34,638 workflow IMPORTANT: Creating bold processing workflow for "/data/sub-001/ses-01/func/sub-001_ses-01task-reward......._run-01_bold.nii.gz" (0.26 GB / 368 TRs). Memory resampled/largemem=1.06/2.03 GB. 180527-18:48:35,776 workflow IMPORTANT: Slice-timing correction will be included. Process Process-2: Traceback (most recent call last): File "/usr/local/miniconda/lib/python3.6/multiprocessing/process.py", line 258, in _bootstrap self.run() File "/usr/local/miniconda/lib/python3.6/multiprocessing/process.py", line 93, in run self._target(*self._args, **self._kwargs) File "/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/cli/run.py", line 510, in build_workflow ignore_aroma_err=opts.ignore_aroma_denoising_errors, File "/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/workflows/base.py", line 202, in init_fmriprep_wf ignore_aroma_err=ignore_aroma_err) File "/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/workflows/base.py", line 458, in init_single_subject_wf ignore_aroma_err=ignore_aroma_err) File "/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/workflows/bold/base.py", line 401, in init_func_preproc_wf debug=debug, fmap_demean=fmap_demean, fmap_bspline=fmap_bspline) File "/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/workflows/fieldmap/base.py", line 178, in init_sdc_wf name='pepolar_unwarp_wf') File "/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/workflows/fieldmap/pepolar.py", line 97, in init_pepolar_unwarp_wf raise Exception("None of the discovered fieldmaps has the right " Exception: None of the discovered fieldmaps has the right phase encoding direction. Possibly a problem with metadata. If not, rerun with '--ignore fieldmaps' to skip distortion correction step.

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[chrisgorgo]

Attachments don't work over email when sent to ggithub. Please include the content of your JSON files in the body of the message.

[bidhanlamichhane]

No problem, below is the copy-paste of json files . YES this data passed validator. Thanks Bidhan

BOLD JSON: (*002_ses-01_task-reward_acq-multiband2p4flatAP_run-01_bold.json)

Modality "MR" MagneticFieldStrength 3 Manufacturer "Siemens" ManufacturersModelName "Prisma_fit" InstitutionName "Center_for_Clinical_Imaging_Research" InstitutionalDepartmentName "WP-MR30A" InstitutionAddress "South_Kingshighway_510_Saint_Louis_MO_US_63110" DeviceSerialNumber "167047" StationName "CCIRWP-MR30A" BodyPartExamined "BRAIN" PatientPosition "HFS" ProcedureStepDescription "CCIR-00900_CCIR-0987_Braver" SoftwareVersions "syngo_MR_E11" MRAcquisitionType "2D" SeriesDescription "CMRR_fMRI_TASK_AP_2.4mm_368meas" ProtocolName "CMRR_fMRI_TASK_AP_2.4mm_368meas" ScanningSequence "EP" SequenceVariant "SK_SS" ScanOptions "FS_EXT" SequenceName "epfid2d1_96" ImageType 0 "ORIGINAL" 1 "PRIMARY" 2 "M" 3 "MB" 4 "ND" 5 "NORM" 6 "MOSAIC" SeriesNumber 18 AcquisitionTime "15:29:35.875000" AcquisitionNumber 1 ImageComments "Unaliased_MB4_PE3_LB" SliceThickness 2.4 SpacingBetweenSlices 2.4 SAR 0.044071 EchoTime 0.03 RepetitionTime 1.2 FlipAngle 52 PartialFourier 1 BaseResolution 96 ShimSetting 0 4608 1 7714 2 1602 3 416 4 7 5 95 6 -35 7 -18 TxRefAmp 239.132 PhaseResolution 1 ReceiveCoilName "Head_32" ReceiveCoilActiveElements "HEA;HEP" PulseSequenceDetails "%CustomerSeq%_cmrr_mbep2d_bold" ConsistencyInfo "N4_VE11C_LATEST_20160120" MultibandAccelerationFactor 4 PercentPhaseFOV 100 EchoTrainLength 96 PhaseEncodingSteps 96 AcquisitionMatrixPE 96 ReconMatrixPE 96 BandwidthPerPixelPhaseEncode 21.259 EffectiveEchoSpacing 0.000489989 DerivedVendorReportedEchoSpacing 0.000489989 TotalReadoutTime 0.0465489 PixelBandwidth 2605 DwellTime 0.000002 PhaseEncodingDirection "j-" SliceTiming 0 0 1 0.6275 2 0.0775 3 0.7075 4 0.155 5 0.785 6 0.235 7 0.865 8 0.3125 9 0.9425 10 0.3925 11 1.0225 12 0.47 13 1.1 14 0.55 15 0 16 0.6275 17 0.0775 18 0.7075 19 0.155 20 0.785 21 0.235 22 0.865 23 0.3125 24 0.9425 25 0.3925 26 1.0225 27 0.47 28 1.1 29 0.55 30 0 31 0.6275 32 0.0775 33 0.7075 34 0.155 35 0.785 36 0.235 37 0.865 38 0.3125 39 0.9425 40 0.3925 41 1.0225 42 0.47 43 1.1 44 0.55 45 0 46 0.6275 47 0.0775 48 0.7075 49 0.155 50 0.785 51 0.235 52 0.865 53 0.3125 54 0.9425 55 0.3925 56 1.0225 57 0.47 58 1.1 59 0.55 ImageOrientationPatientDICOM 0 0.999268 1 -0.00126896 2 -0.0382435 3 -0.00331375 4 0.992825 5 -0.119529 InPlanePhaseEncodingDirectionDICOM "COL" ConversionSoftware "dcm2niix" TaskName "reward" ConversionSoftwareVersion "v1.0.20180328 (OpenJPEG build) Clang8.1.0"

FMAP JASON: (*002/ses-01/fmap/sub-MOCCAG002_ses-01_acq-multiband2p4flatAP_run-01_epi.json)

Modality "MR" MagneticFieldStrength 3 Manufacturer "Siemens" ManufacturersModelName "Prisma_fit" InstitutionName "Center_for_Clinical_Imaging_Research" InstitutionalDepartmentName "WP-MR30A" InstitutionAddress "South_Kingshighway_510_Saint_Louis_MO_US_63110" DeviceSerialNumber "167047" StationName "CCIRWP-MR30A" BodyPartExamined "BRAIN" PatientPosition "HFS" ProcedureStepDescription "CCIR-00900_CCIR-0987_Braver" SoftwareVersions "syngo_MR_E11" MRAcquisitionType "2D" SeriesDescription "SpinEchoFieldMap_AP_2.4mm" ProtocolName "SpinEchoFieldMap_AP_2.4mm" ScanningSequence "EP" SequenceVariant "SK" ScanOptions "FS" SequenceName "epse2d1_96" ImageType 0 "ORIGINAL" 1 "PRIMARY" 2 "M" 3 "ND" 4 "MOSAIC" SeriesNumber 9 AcquisitionTime "15:07:1.167500" AcquisitionNumber 1 SliceThickness 2.4 SpacingBetweenSlices 2.4 SAR 0.126468 EchoTime 0.066 RepetitionTime 8 FlipAngle 90 PartialFourier 1 BaseResolution 96 ShimSetting 0 4608 1 7714 2 1602 3 416 4 7 5 95 6 -35 7 -18 TxRefAmp 239.132 PhaseResolution 1 ReceiveCoilName "Head_32" ReceiveCoilActiveElements "HEA;HEP" PulseSequenceDetails "%CustomerSeq%_cmrr_mbep2d_se" ConsistencyInfo "N4_VE11C_LATEST_20160120" PercentPhaseFOV 100 EchoTrainLength 96 PhaseEncodingSteps 96 AcquisitionMatrixPE 96 ReconMatrixPE 96 BandwidthPerPixelPhaseEncode 21.259 EffectiveEchoSpacing 0.000489989 DerivedVendorReportedEchoSpacing 0.000489989 TotalReadoutTime 0.0465489 PixelBandwidth 2605 DwellTime 0.000002 PhaseEncodingDirection "j-" SliceTiming 0 3.99 1 0 2 4.1225 3 0.1325 4 4.255 5 0.265 6 4.3875 7 0.3975 8 4.52 9 0.5325 10 4.655 11 0.665 12 4.7875 13 0.7975 14 4.92 15 0.93 16 5.0525 17 1.0625 18 5.185 19 1.1975 20 5.32 21 1.33 22 5.4525 23 1.4625 24 5.585 25 1.595 26 5.7175 27 1.7275 28 5.85 29 1.86 30 5.985 31 1.995 32 6.1175 33 2.1275 34 6.25 35 2.26 36 6.3825 37 2.3925 38 6.515 39 2.525 40 6.65 41 2.66 42 6.7825 43 2.7925 44 6.915 45 2.925 46 7.0475 47 3.0575 48 7.18 49 3.19 50 7.315 51 3.325 52 7.4475 53 3.4575 54 7.58 55 3.59 56 7.7125 57 3.7225 58 7.845 59 3.855 ImageOrientationPatientDICOM 0 0.999268 1 -0.00144229 2 -0.0382226 3 -0.0031393 4 0.992825 5 -0.119535 InPlanePhaseEncodingDirectionDICOM "COL" ConversionSoftware "dcm2niix" IntendedFor "ses-01/func/sub-MOCCAG002_ses-01_task-reward_acq-multiband2p4flatAP_run-01_bold.nii.gz" ConversionSoftwareVersion "v1.0.20180328 (OpenJPEG build) Clang8.1.0”

On May 27, 2018, at 3:01 PM, Chris Filo Gorgolewski notifications@github.com<mailto:notifications@github.com> wrote:

Attachments don't work over email when sent to ggithub. Please include the content of your JSON files in the body of the message.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/poldracklab/fmriprep/issues/1148#issuecomment-392362116, or mute the threadhttps://github.com/notifications/unsubscribe-auth/ARuCRUiaA2v_TDlz-2c-ehMVGmim2aL9ks5t2wYZgaJpZM4UPZyQ.

[chrisgorgo]

Both _bold and the _epi files have the same phase encoding directions:

PhaseEncodingDirection "j-"

You need to have data with opposing phase encoding directions to be able to perform susceptibility distortion correction.

[bidhanlamichhane]

Thank you Chris, Again, got following error almost at the end of preprocessing...

Thanks Bidhan

**Terminal output ( error portion only).

[Node] Running "apply_mask" ("niworkflows.nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /root/src/fmriprep/work/fmriprep_wf/single_subject_002_wf/func_preproc_ses_01_task_reward_acq_multiband3p0tiltPA_run_08_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize/uni_xform.nii.gz -mas /root/src/fmriprep/work/fmriprep_wf/single_subject_002_wf/func_preproc_ses_01_task_reward_acq_multiband3p0tiltPA_run_08_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_image_corrected_brain_mask_maths.nii.gz /root/src/fmriprep/work/fmriprep_wf/single_subject_002_wf/func_preproc_ses_01_task_reward_acq_multiband3p0tiltPA_run_08_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz 180529-03:27:57,192 workflow INFO: [Node] Finished "fmriprep_wf.single_subject_002_wf.func_preproc_ses_01_task_reward_acq_multiband3p0tiltPA_run_08_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask". 180529-03:28:16,994 workflow INFO: [Node] Finished "fmriprep_wf.single_subject_002_wf.func_preproc_ses_01_task_reward_acq_multiband3p0tiltPA_run_08_wf.bold_confounds_wf.dvars". 180529-03:28:19,139 workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_002_wf.anat_preproc_wf.surface_recon_wf.autorecon1" in "/root/src/fmriprep/work/fmriprep_wf/single_subject_002_wf/anat_preproc_wf/surface_recon_wf/autorecon1". 180529-03:28:19,144 workflow INFO: [Node] Running "autorecon1" ("niworkflows.nipype.interfaces.freesurfer.preprocess.ReconAll"), a CommandLine Interface with command: recon-all -autorecon1 -i /data/sub-002/ses-01/anat/sub-002_ses-01_T1w.nii.gz -T2 /data/sub-002/ses-01/anat/sub-002_ses-01_T2w.nii.gz -noskullstrip -hires -openmp 1 -subjid sub-002 -sd /out/freesurfer -expert /root/src/fmriprep/work/fmriprep_wf/single_subject_002_wf/anat_preproc_wf/surface_recon_wf/autorecon1/expert.opts 180529-03:28:23,323 workflow WARNING: [Node] Error on "fmriprep_wf.single_subject_002_wf.anat_preproc_wf.surface_recon_wf.autorecon1" (/root/src/fmriprep/work/fmriprep_wf/single_subject_002_wf/anat_preproc_wf/surface_recon_wf/autorecon1) Traceback (most recent call last): File "/usr/local/miniconda/bin/fmriprep", line 11, in load_entry_point('fmriprep==1.0.15', 'console_scripts', 'fmriprep')() File "/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/cli/run.py", line 314, in main fmriprep_wf.run(plugin_settings) File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/workflows.py", line 595, in run runner.run(execgraph, updatehash=updatehash, config=self.config) File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/plugins/base.py", line 168, in run self._clean_queue(jobid, graph, result=result)) File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/plugins/base.py", line 227, in _clean_queue raise RuntimeError("".join(result['traceback'])) RuntimeError: Traceback (most recent call last): File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/plugins/multiproc.py", line 68, in run_node result['result'] = node.run(updatehash=updatehash) File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 480, in run result = self._run_interface(execute=True) File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 564, in _run_interface return self._run_command(execute) File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 644, in _run_command result = self._interface.run(cwd=outdir) File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/interfaces/base/core.py", line 520, in run runtime = self._run_interface(runtime) File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/interfaces/base/core.py", line 1020, in _run_interface self.raise_exception(runtime) File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/interfaces/base/core.py", line 957, in raise_exception ).format(runtime.dictcopy())) RuntimeError: Command: recon-all -autorecon1 -i /data/sub-002/ses-01/anat/sub-002_ses-01_T1w.nii.gz -T2 /data/sub-002/ses-01/anat/sub-002_ses-01_T2w.nii.gz -noskullstrip -hires -openmp 1 -subjid sub-002 -sd /out/freesurfer -expert /root/src/fmriprep/work/fmriprep_wf/single_subject_002_wf/anat_preproc_wf/surface_recon_wf/autorecon1/expert.opts Standard output: INFO: hi-res volumes are conformed to the min voxel size Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a INFO: SUBJECTS_DIR is /out/freesurfer Actual FREESURFER_HOME /opt/freesurfer Linux 1b2416ff7830 4.9.87-linuxkit-aufs #1 SMP Wed Mar 14 15:12:16 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux '/opt/freesurfer/bin/recon-all' -> '/out/freesurfer/sub-002/scripts/recon-all.local-copy' /out/freesurfer/sub-002

mri_convert /data/sub-002/ses-01/anat/sub-002_ses-01_T1w.nii.gz /out/freesurfer/sub-002/mri/orig/001.mgz

mri_convert.bin /data/sub-002/ses-01/anat/sub-002_ses-01_T1w.nii.gz /out/freesurfer/sub-002/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /data/sub-002/ses-01/anat/sub-002_ses-01_T1w.nii.gz...

GNU libc version: 2.23 ERROR: Systems running GNU glibc version greater than 2.15 require a newly formatted license file (it's free). Please download a new one from the following page: http://surfer.nmr.mgh.harvard.edu/registration.html

Linux 1b2416ff7830 4.9.87-linuxkit-aufs #1 SMP Wed Mar 14 15:12:16 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub-002 exited with ERRORS at Tue May 29 03:28:22 UTC 2018

For more details, see the log file /out/freesurfer/sub-002/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Standard error:

Return code: 1

Sentry is attempting to send 1 pending error messages Waiting up to 10 seconds Press Ctrl-C to quit fMRIPrep: Please report errors to https://github.com/poldracklab/fmriprep/issues

[chrisgorgo]

Your original post indicated that you used the following command line invocation:

fmriprep-docker --fs-license-file $FREESURFER_HOM /Users/.../Desktop/BIDS/Test_data/sub-001 /Users/.../Desktop/BIDS/Test_data002/

1. Is the FREESURFER_HOM variable set?
2. Does it point to a file (not folder!) with a valid FreeSurfer license?

[bidhanlamichhane]

(1) Yes, FREESURFER_HOME is defined ( as default setting, see terminal output below) as below and I have moved license.txt to/Applications/freesurfer. (2) after pointing the license txt directly (as: $ fmriprep-docker --fs-license-file $FREESURFER_HOM/license.txt ...... I got following error message (which was not the case before)

-------- freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni FSL_DIR /usr/local/fsl Bidhans-MBP:~ bidhan$ ls $FREESURFER_HOME ASegStatsLUT.txt build-stamp.txt AUTHORS data DefectLUT.txt diffusion FreeSurferColorLUT.txt docs FreeSurferEnv.csh fsafd FreeSurferEnv.sh fsfast Freeview.app lib LICENSE license.txt NOTICE matlab README mni SegmentNoLUT.txt sessions SetUpFreeSurfer.csh sources.csh SetUpFreeSurfer.sh sources.sh Simple_surface_labels2009.txt subjects VERSION tkmeditParcColorsCMA WMParcStatsLUT.txt tktools average trctrain Bidhans-MBP:~ bidhan$ fmriprep-docker --fs-license-file $FREESURFER_HOM/license.txt /Users/bidhan/Desktop/BIDS/Test_oppJ_manually_data002/sub-002 /Users/bidhan/Desktop/BIDS/Test_oppJ_manually_data002/ Warning: <8GB of RAM is available within your Docker environment. Some parts of fMRIPrep may fail to complete. Continue anyway? [y/N]y RUNNING: docker run --rm -it -v /license.txt:/opt/freesurfer/license.txt:ro -v /Users/bidhan/Desktop/BIDS/Test_oppJ_manually_data002/sub-002:/data:ro -v /Users/bidhan/Desktop/BIDS/Test_oppJ_manually_data002:/out poldracklab/fmriprep:1.0.15 /data /out participant docker: Error response from daemon: Mounts denied: The path /license.txt is not shared from OS X and is not known to Docker. You can configure shared paths from Docker -> Preferences... -> File Sharing. See https://docs.docker.com/docker-for-mac/osxfs/#namespaces for more info.

[oesteban]

You are running fmriprep-docker --fs-license-file $FREESURFER_HOM/license.txt, however $FREESURFER_HOM is not set (please note the typo).

Please make sure you do:

fmriprep-docker --fs-license-file /Applications/freesurfer/license.txt

[bidhanlamichhane]

Thank you so much,
Yes, I did make that change before running again as: fmriprep-docker --fs-license-file /Applications/freesurfer/license.txt ……… but still similar error ( below); Thanks Bidhan Lamichhane

Terminal output: Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni FSL_DIR /usr/local/fsl

Bidhans-MacBook-Pro:~ bidhan$ fmriprep-docker --fs-license-file /Applications/freesurfer/license.txt /Users/bidhan/Desktop/BIDS/Test_oppJ_manually_data002/sub-002 /Users/bidhan/Desktop/BIDS/Test_oppJ_manually_data00 Warning: <8GB of RAM is available within your Docker environment. Some parts of fMRIPrep may fail to complete. Continue anyway? [y/N]y RUNNING: docker run --rm -it -v /Applications/freesurfer/license.txt:/opt/freesurfer/license.txt:ro -v /Users/bidhan/Desktop/BIDS/Test_oppJ_manually_data002/sub-002:/data:ro -v /Users/bidhan/Desktop/BIDS/Test_oppJ_manually_data00:/out poldracklab/fmriprep:1.0.15 /data /out participant docker: Error response from daemon: Mounts denied: The path /Applications/freesurfer/license.txt is not shared from OS X and is not known to Docker. You can configure shared paths from Docker -> Preferences... -> File Sharing. See https://docs.docker.com/docker-for-mac/osxfs/#namespaces for more info. . ERRO[0000] error waiting for container: context canceled fMRIPrep: Please report errors to https://github.com/poldracklab/fmriprep/issuesBidhans-

[oesteban]

The error is similar at the looks of its symptoms, but has nothing to do with the former error.

You first tried to point fmriprep-docker to a path (/license.txt) because of the mistake using an environment variable misspelled.

Now, you are pointing fmriprep-docker to a path that exists indeed in the host (/Applications/freesurfer/license.txt), but docker is complaining:

docker: Error response from daemon: Mounts denied:
The path /Applications/freesurfer/license.txt
is not shared from OS X and is not known to Docker.
You can configure shared paths from Docker -> Preferences... -> File Sharing.
See https://docs.docker.com/docker-for-mac/osxfs/#namespaces for more info.

Luckily this is a pretty explicit message about what is going on. Basically, you'll need to tweak some configurations on you docker installation to allow that path to be used.

Otherwise (and I would advise to take this road, also for security reasons), copy/move the license file to your home directory and point Docker to that license file:

cp /Applications/freesurfer/license.txt $HOME/.freesurfer-license.txt
fmriprep-docker --fs-license-file $HOME/.freesurfer-license.txt

Next time you will encounter that fmriprep breaks because of memory issues. I'm looking at this warning:

Warning: <8GB of RAM is available within your Docker environment.
Some parts of fMRIPrep may fail to complete.
Continue anyway? [y/N]

In order to learn how to increase the RAM available to docker, please read the documentation: https://docs.docker.com/docker-for-mac/#advanced

[bidhanlamichhane]

Thank you so much. But something interesting happening here- I did validate this data online successfully and while running fmriprep-ducker, I did not see any error related to the validity the data before ( even with the typo you pointed, for your references I have pasted terminal output below for this case too). However, now with this modification on license path ( fmriprep-docker --fs-license-file $HOME/.freesurfer-license.txt) I started receiving validation error as follows:

Bidhans-MacBook-Pro:~ bidhan$ fmriprep-docker --fs-license-file $HOME/.freesurfer-license.txt /Users/bidhan/Desktop/BIDS/Test_fmriPrep_data002/sub-002 /Users/bidhan/Desktop/BIDS/Test_fmriPrep_data002 Warning: <8GB of RAM is available within your Docker environment. Some parts of fMRIPrep may fail to complete. Continue anyway? [y/N]y RUNNING: docker run --rm -it -v /Users/bidhan/.freesurfer-license.txt:/opt/freesurfer/license.txt:ro -v /Users/bidhan/Desktop/BIDS/Test_fmriPrep_data002/sub-002:/data:ro -v /Users/bidhan/Desktop/BIDS/Test_fmriPrep_data002:/out poldracklab/fmriprep:1.0.15 /data /out participant Process Process-2: Traceback (most recent call last): File "/usr/local/miniconda/lib/python3.6/multiprocessing/process.py", line 258, in _bootstrap self.run() File "/usr/local/miniconda/lib/python3.6/multiprocessing/process.py", line 93, in run self._target(*self._args, **self._kwargs) File "/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/cli/run.py", line 383, in build_workflow bids_dir, participant_label=opts.participant_label) File "/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/utils/bids.py", line 89, in collect_participants 'may need to adjust your "File sharing" preferences.', bids_dir) fmriprep.utils.bids.BIDSError: ---------- BIDS root folder: "/data" ---------- Could not find participants. Please make sure the BIDS data structure is present and correct. Datasets can be validated online using the BIDS Validator (http://incf.github.io/bids-validator/). If you are using Docker for Mac or Docker for Windows, you may need to adjust your "File sharing" preferences.

============================================================

Terminal out-put: before— (with the typo- you pointed out) at --fs-license-file

=====================================================

Bidhans-MacBook-Pro:~ bidhan$ fmriprep-docker --fs-license-file $FREESURFER_HOM /Users/bidhan/Desktop/BIDS/Test_fmriPrep_data002/sub-002 /Users/bidhan/Desktop/BIDS/Test_fmriPrep_data002 Warning: <8GB of RAM is available within your Docker environment. Some parts of fMRIPrep may fail to complete. Continue anyway? [y/N]y RUNNING: docker run --rm -it -v /Users/bidhan/Desktop/BIDS/Test_fmriPrep_data002/sub-002:/opt/freesurfer/license.txt:ro -v /Users/bidhan/Desktop/BIDS/Test_fmriPrep_data002:/data:ro -v /Users/bidhan:/out poldracklab/fmriprep:1.0.15 /data /out participant 180529-17:08:57,514 workflow IMPORTANT:

Running fMRIPREP version 1.0.15:
  * BIDS dataset path: /data.
  * Participant list: ['002'].
  * Run identifier: 20180529-170857_ef7ee603-b898-494d-8e6d-e0a515a40fca.

180529-17:08:58,571 workflow IMPORTANT: Creating bold processing workflow for "/data/sub-002/ses-01/func/sub-002_ses-01_task-reward_acq-multiband2p4flatAP_run-01_bold.nii.gz" (0.26 GB / 368 TRs). Memory resampled/largemem=1.06/2.03 GB. 180529-17:09:00,111 workflow IMPORTANT: Slice-timing correction will be included. 180529-17:09:00,323 workflow IMPORTANT: SDC: fieldmap estimation of type "epi" intended for /data/sub-002/ses-01/func/sub-002_ses-01_task-reward_acq-multiband2p4flatAP_run-01_bold.nii.gz found. 180529-17:09:00,867 workflow IMPORTANT: Creating BOLD surface-sampling workflow. 180529-17:09:02,306 workflow IMPORTANT: Creating bold processing workflow for "/data/sub-002/ses-01/func/sub-002_ses-01_task-reward_acq-multiband2p4flatPA_run-02_bold.nii.gz" (0.26 GB / 368 TRs). Memory resampled/largemem=1.05/2.02 GB. 180529-17:09:03,436 workflow IMPORTANT: Slice-timing correction will be included. 180529-17:09:03,614 workflow IMPORTANT:

…………………..........still going on...

[chrisgorgo]

You are pointing to a subject subdirectory instead of root of your dataset:

/Users/bidhan/Desktop/BIDS/Test_fmriPrep_data002/sub-002 

should be

/Users/bidhan/Desktop/BIDS/Test_fmriPrep_data002/

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