Hi there! I am running into an issue during prefreesurfer, and I think it is because I am doing something wrong with my Siemens fieldmaps. Structural processing runs totally OK when I set hcp_avgrdcmethod=‘NONE’ otherwise it fails. The scans were collected on siemens magnetom 7T.
The code finds the fieldmap OK, but it breaks during “fsl_prepare_fieldmap” I think (see below). I’ve tried using BET to skull-strip the magnitute image, but that didn’t fix the issue. Both fieldmaps look OK when I look at the nii images. I’d appreciate any help in figuring out this error. Thank you a lot! See below for my command, hcp mapping, and the full error message from comlogs.
Here is my command:
qunex_container hcp_pre_freesurfer \
--container="gitlab.qunex.yale.edu:5002/qunex/qunexcontainer:0.96.2a" \
--batchfile="/Users/kolobarica/Desktop/pals/processing/batch.txt" \
--sessionsfolder="/Users/kolobarica/Desktop/pals/sessions" \
--sessions="PALS_011" \
--overwrite=yes \
--parsessions=2 \
--hcp_avgrdcmethod='SiemensFieldMap'
Here is the session_hcp file:
id: PALS_011
subject: PALS
dicom: /Users/kolobarica/Desktop/pals/sessions/PALS_011/dicom
raw_data: /Users/kolobarica/Desktop/pals/sessions/PALS_011/nii
data: /Users/kolobarica/Desktop/pals/sessions/PALS_011/4dfp
hcp: /Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp
hcpready: true
11: : localizer [1/3] cR14_i00002
12: : localizer [2/3] cR16_i00001
13: : localizer [3/3] cR20_i00003
21: : localizer [1/3] i00001
22: : localizer [2/3] i00002
23: : localizer [3/3] i00003
31: T1w : T1 MPRAGE : fm(99)
41: T1w : T1 MPRAGE : fm(99)
51: : sagT1 [1/4]
52: : sagT1 [2/4] ROI1
53: : sagT1 [3/4]
54: : sagT1 [4/4] ROI1
61: : corT1 [1/4]
62: : corT1 [2/4] ROI1
63: : corT1 [3/4]
64: : corT1 [4/4] ROI1
71: T2w : T2 TSE Coronal_ND : fm(99)
81: T2w : T2 TSE Coronal : fm(99)
91: T2w : T2 TSE Coronal : fm(99)
181: : TOF 7slabs
191: : TOF 7slabs_MIP_SAG
201: : TOF 7slabs_MIP_COR
211: : TOF 7slabs_MIP_TRA
221: : TOF 7slabs
231: FM-Magnitude : Mag_Images [1/2] e1 : fm(99)
232: FM-Magnitude : Mag_Images [2/2] e2 : fm(99)
241: FM-Phase : Pha_Images [1/2] e1_ph : fm(99)
242: FM-Phase : Pha_Images [2/2] e2_ph : fm(99)
251: : mIP_Images(SW) [1/2] e1
252: : mIP_Images(SW) [2/2] e2
261: : SWI_Images [1/2] e1
262: : SWI_Images [2/2] e2
Here is the error I get:
# Generated by QuNex 0.96.2 on 2023-01-23_16.05.10.469966
#
------------------------------------------------------------
Running external command via QuNex:
/opt/HCP/HCPpipelines/PreFreeSurfer/PreFreeSurferPipeline.sh --path="/Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp" --subject="PALS_011" --t1="/Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/unprocessed/T1w/PALS_011_T1w_MPR1.nii.gz@/Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/unprocessed/T1w/PALS_011_T1w_MPR2.nii.gz" --t2="/Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/unprocessed/T2w/PALS_011_T2w_SPC1.nii.gz@/Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/unprocessed/T2w/PALS_011_T2w_SPC2.nii.gz@/Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/unprocessed/T2w/PALS_011_T2w_SPC3.nii.gz" --t1template="/opt/HCP/HCPpipelines/global/templates/MNI152_T1_0.7mm.nii.gz" --t1templatebrain="/opt/HCP/HCPpipelines/global/templates/MNI152_T1_0.7mm_brain.nii.gz" --t1template2mm="/opt/HCP/HCPpipelines/global/templates/MNI152_T1_2mm.nii.gz" --t2template="/opt/HCP/HCPpipelines/global/templates/MNI152_T2_0.7mm.nii.gz" --t2templatebrain="/opt/HCP/HCPpipelines/global/templates/MNI152_T2_0.7mm_brain.nii.gz" --t2template2mm="/opt/HCP/HCPpipelines/global/templates/MNI152_T2_2mm.nii.gz" --templatemask="/opt/HCP/HCPpipelines/global/templates/MNI152_T1_0.7mm_brain_mask.nii.gz" --template2mmmask="/opt/HCP/HCPpipelines/global/templates/MNI152_T1_2mm_brain_mask_dil.nii.gz" --brainsize="150" --fnirtconfig="/opt/HCP/HCPpipelines/global/config/T1_2_MNI152_2mm.cnf" --fmapmag="/Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/unprocessed/FieldMap99/PALS_011_FieldMap_Magnitude.nii.gz" --fmapphase="/Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/unprocessed/FieldMap99/PALS_011_FieldMap_Phase.nii.gz" --gdcoeffs="NONE" --avgrdcmethod="SiemensFieldMap" --processing-mode="HCPStyleData"
Test file:
/Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/MNINonLinear/T1w_restore_brain.nii.gz
------------------------------------------------------------
========================================
DIRECTORY: /opt/HCP/HCPpipelines
PRODUCT: HCP Pipeline Scripts
VERSION: v4.7.0
COMMIT: f8cac6892f88bdf889d644711ff038198eb81533
MODIFIED: no
========================================
Mon Jan 23 16:05:11 EST 2023:PreFreeSurferPipeline.sh: HCPPIPEDIR: /opt/HCP/HCPpipelines
Mon Jan 23 16:05:11 EST 2023:PreFreeSurferPipeline.sh: FSLDIR: /opt/fsl/fsl
Mon Jan 23 16:05:11 EST 2023:PreFreeSurferPipeline.sh: HCPPIPEDIR_Global: /opt/HCP/HCPpipelines/global/scripts
Mon Jan 23 16:05:11 EST 2023:PreFreeSurferPipeline.sh: Platform Information Follows:
Linux 7ce105f07731 5.15.49-linuxkit #1 SMP Tue Sep 13 07:51:46 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux
Mon Jan 23 16:05:11 EST 2023:PreFreeSurferPipeline.sh: Parsing Command Line Options
Mon Jan 23 16:05:12 EST 2023:PreFreeSurferPipeline.sh: Finished Parsing Command Line Options
Mon Jan 23 16:05:12 EST 2023:PreFreeSurferPipeline.sh: StudyFolder: /Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp
Mon Jan 23 16:05:12 EST 2023:PreFreeSurferPipeline.sh: Subject: PALS_011
Mon Jan 23 16:05:12 EST 2023:PreFreeSurferPipeline.sh: T1wInputImages: /Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/unprocessed/T1w/PALS_011_T1w_MPR1.nii.gz@/Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/unprocessed/T1w/PALS_011_T1w_MPR2.nii.gz
Mon Jan 23 16:05:12 EST 2023:PreFreeSurferPipeline.sh: T2wInputImages: /Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/unprocessed/T2w/PALS_011_T2w_SPC1.nii.gz@/Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/unprocessed/T2w/PALS_011_T2w_SPC2.nii.gz@/Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/unprocessed/T2w/PALS_011_T2w_SPC3.nii.gz
Mon Jan 23 16:05:12 EST 2023:PreFreeSurferPipeline.sh: T1wTemplate: /opt/HCP/HCPpipelines/global/templates/MNI152_T1_0.7mm.nii.gz
Mon Jan 23 16:05:12 EST 2023:PreFreeSurferPipeline.sh: T1wTemplateBrain: /opt/HCP/HCPpipelines/global/templates/MNI152_T1_0.7mm_brain.nii.gz
Mon Jan 23 16:05:12 EST 2023:PreFreeSurferPipeline.sh: T1wTemplate2mm: /opt/HCP/HCPpipelines/global/templates/MNI152_T1_2mm.nii.gz
Mon Jan 23 16:05:12 EST 2023:PreFreeSurferPipeline.sh: T2wTemplate: /opt/HCP/HCPpipelines/global/templates/MNI152_T2_0.7mm.nii.gz
Mon Jan 23 16:05:12 EST 2023:PreFreeSurferPipeline.sh: T2wTemplateBrain: /opt/HCP/HCPpipelines/global/templates/MNI152_T2_0.7mm_brain.nii.gz
Mon Jan 23 16:05:12 EST 2023:PreFreeSurferPipeline.sh: T2wTemplate2mm: /opt/HCP/HCPpipelines/global/templates/MNI152_T2_2mm.nii.gz
Mon Jan 23 16:05:12 EST 2023:PreFreeSurferPipeline.sh: TemplateMask: /opt/HCP/HCPpipelines/global/templates/MNI152_T1_0.7mm_brain_mask.nii.gz
Mon Jan 23 16:05:12 EST 2023:PreFreeSurferPipeline.sh: Template2mmMask: /opt/HCP/HCPpipelines/global/templates/MNI152_T1_2mm_brain_mask_dil.nii.gz
Mon Jan 23 16:05:12 EST 2023:PreFreeSurferPipeline.sh: BrainSize: 150
Mon Jan 23 16:05:12 EST 2023:PreFreeSurferPipeline.sh: FNIRTConfig: /opt/HCP/HCPpipelines/global/config/T1_2_MNI152_2mm.cnf
Mon Jan 23 16:05:12 EST 2023:PreFreeSurferPipeline.sh: MagnitudeInputName: /Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/unprocessed/FieldMap99/PALS_011_FieldMap_Magnitude.nii.gz
Mon Jan 23 16:05:12 EST 2023:PreFreeSurferPipeline.sh: PhaseInputName: /Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/unprocessed/FieldMap99/PALS_011_FieldMap_Phase.nii.gz
Mon Jan 23 16:05:12 EST 2023:PreFreeSurferPipeline.sh: GEB0InputName:
Mon Jan 23 16:05:12 EST 2023:PreFreeSurferPipeline.sh: TE:
Mon Jan 23 16:05:12 EST 2023:PreFreeSurferPipeline.sh: SpinEchoPhaseEncodeNegative:
Mon Jan 23 16:05:12 EST 2023:PreFreeSurferPipeline.sh: SpinEchoPhaseEncodePositive:
Mon Jan 23 16:05:12 EST 2023:PreFreeSurferPipeline.sh: SEEchoSpacing:
Mon Jan 23 16:05:12 EST 2023:PreFreeSurferPipeline.sh: SEUnwarpDir:
Mon Jan 23 16:05:12 EST 2023:PreFreeSurferPipeline.sh: T1wSampleSpacing:
Mon Jan 23 16:05:12 EST 2023:PreFreeSurferPipeline.sh: T2wSampleSpacing:
Mon Jan 23 16:05:12 EST 2023:PreFreeSurferPipeline.sh: UnwarpDir:
Mon Jan 23 16:05:12 EST 2023:PreFreeSurferPipeline.sh: GradientDistortionCoeffs: NONE
Mon Jan 23 16:05:12 EST 2023:PreFreeSurferPipeline.sh: AvgrdcSTRING: SiemensFieldMap
Mon Jan 23 16:05:12 EST 2023:PreFreeSurferPipeline.sh: TopupConfig:
Mon Jan 23 16:05:12 EST 2023:PreFreeSurferPipeline.sh: BiasFieldSmoothingSigma:
Mon Jan 23 16:05:12 EST 2023:PreFreeSurferPipeline.sh: UseJacobian: true
Mon Jan 23 16:05:12 EST 2023:PreFreeSurferPipeline.sh: T1wBiasCorrect:
Mon Jan 23 16:05:12 EST 2023:PreFreeSurferPipeline.sh: CustomBrain: NONE
Mon Jan 23 16:05:12 EST 2023:PreFreeSurferPipeline.sh: ProcessingMode: HCPStyleData
Mon Jan 23 16:05:12 EST 2023:PreFreeSurferPipeline.sh: T1wFolder: /Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/T1w
Mon Jan 23 16:05:12 EST 2023:PreFreeSurferPipeline.sh: T2wFolder: /Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/T2w
Mon Jan 23 16:05:12 EST 2023:PreFreeSurferPipeline.sh: AtlasSpaceFolder: /Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/MNINonLinear
Mon Jan 23 16:05:12 EST 2023:PreFreeSurferPipeline.sh: POSIXLY_CORRECT=
Mon Jan 23 16:05:12 EST 2023:PreFreeSurferPipeline.sh: Processing Modality: T1w
Mon Jan 23 16:05:12 EST 2023:PreFreeSurferPipeline.sh: NOT PERFORMING GRADIENT DISTORTION CORRECTION
Mon Jan 23 16:05:14 EST 2023:PreFreeSurferPipeline.sh: Averaging T1w Images
Mon Jan 23 16:05:14 EST 2023:PreFreeSurferPipeline.sh: mkdir -p /Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/T1w/AverageT1wImages
Mon Jan 23 16:05:14 EST 2023:PreFreeSurferPipeline.sh: PERFORMING SIMPLE AVERAGING
Mon Jan 23 16:05:14 EST 2023:AnatomicalAverage.sh: HCPPIPEDIR: /opt/HCP/HCPpipelines
Mon Jan 23 16:05:14 EST 2023:AnatomicalAverage.sh: FSLDIR: /opt/fsl/fsl
Mon Jan 23 16:05:14 EST 2023:AnatomicalAverage.sh: Images: /Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/T1w/T1w1_gdc /Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/T1w/T1w2_gdc Output: /Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/T1w/T1w
Final FOV is:
0.000000 230.000000 0.000000 320.000000 36.000000 200.000000
Final FOV is:
0.000000 230.000000 0.000000 320.000000 37.000000 200.000000
1.000956 0.000439 0.000345 -0.155667
-0.000000 1.000775 0.000218 -0.102699
-0.000000 -0.000000 1.000000 -0.374984
0.000000 0.000000 0.000000 1.000000
Mon Jan 23 16:10:17 EST 2023:PreFreeSurferPipeline.sh: Aligning T1w image to /opt/HCP/HCPpipelines/global/templates/MNI152_T1_0.7mm.nii.gz to create native volume space
Mon Jan 23 16:10:17 EST 2023:PreFreeSurferPipeline.sh: mkdir -p /Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/T1w/ACPCAlignment
Mon Jan 23 16:10:17 EST 2023:ACPCAlignment.sh: HCPPIPEDIR: /opt/HCP/HCPpipelines
Mon Jan 23 16:10:17 EST 2023:ACPCAlignment.sh: FSLDIR: /opt/fsl/fsl
Mon Jan 23 16:10:17 EST 2023:ACPCAlignment.sh: START
Final FOV is:
0.000000 230.000000 0.000000 320.000000 36.000000 200.000000
Mon Jan 23 16:11:55 EST 2023:ACPCAlignment.sh: END
Mon Jan 23 16:11:55 EST 2023:PreFreeSurferPipeline.sh: Performing Brain Extraction using FNIRT-based Masking
Mon Jan 23 16:11:55 EST 2023:PreFreeSurferPipeline.sh: mkdir -p /Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/T1w/BrainExtraction_FNIRTbased
Mon Jan 23 16:11:55 EST 2023:BrainExtraction_FNIRTbased.sh: HCPPIPEDIR: /opt/HCP/HCPpipelines
Mon Jan 23 16:11:55 EST 2023:BrainExtraction_FNIRTbased.sh: FSLDIR: /opt/fsl/fsl
Mon Jan 23 16:11:55 EST 2023:BrainExtraction_FNIRTbased.sh: HCPPIPEDIR_Templates: /opt/HCP/HCPpipelines/global/templates
Mon Jan 23 16:11:55 EST 2023:BrainExtraction_FNIRTbased.sh: START: BrainExtraction_FNIRT
Mon Jan 23 16:24:34 EST 2023:BrainExtraction_FNIRTbased.sh: END: BrainExtraction_FNIRT
Mon Jan 23 16:24:34 EST 2023:PreFreeSurferPipeline.sh: Processing Modality: T2w
Mon Jan 23 16:24:34 EST 2023:PreFreeSurferPipeline.sh: NOT PERFORMING GRADIENT DISTORTION CORRECTION
Mon Jan 23 16:24:39 EST 2023:PreFreeSurferPipeline.sh: Averaging T2w Images
Mon Jan 23 16:24:39 EST 2023:PreFreeSurferPipeline.sh: mkdir -p /Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/T2w/AverageT2wImages
Mon Jan 23 16:24:39 EST 2023:PreFreeSurferPipeline.sh: PERFORMING SIMPLE AVERAGING
Mon Jan 23 16:24:39 EST 2023:AnatomicalAverage.sh: HCPPIPEDIR: /opt/HCP/HCPpipelines
Mon Jan 23 16:24:39 EST 2023:AnatomicalAverage.sh: FSLDIR: /opt/fsl/fsl
Mon Jan 23 16:24:39 EST 2023:AnatomicalAverage.sh: Images: /Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/T2w/T2w1_gdc /Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/T2w/T2w2_gdc /Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/T2w/T2w3_gdc Output: /Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/T2w/T2w
Final FOV is:
0.000000 456.000000 0.000000 36.000000 102.000000 400.000000
Final FOV is:
0.000000 456.000000 0.000000 36.000000 102.000000 400.000000
Final FOV is:
0.000000 456.000000 0.000000 36.000000 102.000000 400.000000
1.000559 0.000046 0.000001 -0.048667
0.000001 0.999672 0.000021 0.008574
0.000001 -0.000208 0.999747 0.021290
0.000000 0.000000 0.000000 1.000000
Mon Jan 23 16:33:13 EST 2023:PreFreeSurferPipeline.sh: Aligning T2w image to /opt/HCP/HCPpipelines/global/templates/MNI152_T2_0.7mm.nii.gz to create native volume space
Mon Jan 23 16:33:13 EST 2023:PreFreeSurferPipeline.sh: mkdir -p /Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/T2w/ACPCAlignment
Mon Jan 23 16:33:13 EST 2023:ACPCAlignment.sh: HCPPIPEDIR: /opt/HCP/HCPpipelines
Mon Jan 23 16:33:13 EST 2023:ACPCAlignment.sh: FSLDIR: /opt/fsl/fsl
Mon Jan 23 16:33:13 EST 2023:ACPCAlignment.sh: START
Final FOV is:
0.000000 456.000000 0.000000 36.000000 101.000000 400.000000
Mon Jan 23 16:34:04 EST 2023:ACPCAlignment.sh: END
Mon Jan 23 16:34:04 EST 2023:PreFreeSurferPipeline.sh: Performing Brain Extraction using FNIRT-based Masking
Mon Jan 23 16:34:04 EST 2023:PreFreeSurferPipeline.sh: mkdir -p /Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/T2w/BrainExtraction_FNIRTbased
Mon Jan 23 16:34:04 EST 2023:BrainExtraction_FNIRTbased.sh: HCPPIPEDIR: /opt/HCP/HCPpipelines
Mon Jan 23 16:34:04 EST 2023:BrainExtraction_FNIRTbased.sh: FSLDIR: /opt/fsl/fsl
Mon Jan 23 16:34:04 EST 2023:BrainExtraction_FNIRTbased.sh: HCPPIPEDIR_Templates: /opt/HCP/HCPpipelines/global/templates
Mon Jan 23 16:34:04 EST 2023:BrainExtraction_FNIRTbased.sh: START: BrainExtraction_FNIRT
WARNING::in calculating COG, total = 0.0
WARNING::in calculating COG, total = 0.0
WARNING::in calculating COG, total = 0.0
WARNING::in calculating COG, total = 0.0
WARNING::in calculating COG, total = 0.0
WARNING::in calculating COG, total = 0.0
Mon Jan 23 17:32:34 EST 2023:BrainExtraction_FNIRTbased.sh: END: BrainExtraction_FNIRT
Mon Jan 23 17:32:34 EST 2023:PreFreeSurferPipeline.sh: Performing SiemensFieldMap Readout Distortion Correction
Mon Jan 23 17:32:34 EST 2023:PreFreeSurferPipeline.sh: mkdir -p /Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/T2w/T2wToT1wDistortionCorrectAndReg
Mon Jan 23 17:32:34 EST 2023:T2wToT1wDistortionCorrectAndReg.sh: HCPPIPEDIR: /opt/HCP/HCPpipelines
Mon Jan 23 17:32:34 EST 2023:T2wToT1wDistortionCorrectAndReg.sh: FSLDIR: /opt/fsl/fsl
Mon Jan 23 17:32:34 EST 2023:T2wToT1wDistortionCorrectAndReg.sh: HCPPIPEDIR_Global: /opt/HCP/HCPpipelines/global/scripts
Mon Jan 23 17:32:35 EST 2023:T2wToT1wDistortionCorrectAndReg.sh: START
FieldMapPreprocessingAll.sh: HCPPIPEDIR: /opt/HCP/HCPpipelines
FieldMapPreprocessingAll.sh: FSLDIR: /opt/fsl/fsl
FieldMapPreprocessingAll.sh: HCPPIPEDIR_Global: /opt/HCP/HCPpipelines/global/scripts
Mon Jan 23 17:32:35 EST 2023:FieldMapPreprocessingAll.sh: Field Map Preprocessing and Gradient Unwarping
Mon Jan 23 17:32:35 EST 2023:FieldMapPreprocessingAll.sh: START
Usage: fsl_prepare_fieldmap <scanner> <phase_image> <magnitude_image> <out_image> <deltaTE (in ms)> [--nocheck]
Prepares a fieldmap suitable for FEAT from SIEMENS data - saves output in rad/s format
<scanner> must be SIEMENS
<magnitude image> should be Brain Extracted (with BET or otherwise)
<deltaTE> is the echo time difference of the fieldmap sequence - find this out form the operator (defaults are *usually* 2.46ms on SIEMENS)
--nocheck supresses automatic sanity checking of image size/range/dimensions
e.g. fsl_prepare_fieldmap SIEMENS images_3_gre_field_mapping images_4_gre_field_mapping fmap_rads 2.65
Mon Jan 23 17:33:14 EST 2023:FieldMapPreprocessingAll.sh: While running '/opt/HCP/HCPpipelines/global/scripts/FieldMapPreprocessingAll.sh --workingdir=/Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/T2w/T2wToT1wDistortionCorrectAndReg/FieldMap --method=SiemensFieldMap --fmapmag=/Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/unprocessed/FieldMap99/PALS_011_FieldMap_Magnitude.nii.gz --fmapphase=/Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/unprocessed/FieldMap99/PALS_011_FieldMap_Phase.nii.gz --echodiff= --ofmapmag=/Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/T2w/T2wToT1wDistortionCorrectAndReg/Magnitude --ofmapmagbrain=/Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/T2w/T2wToT1wDistortionCorrectAndReg/Magnitude_brain --ofmap=/Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/T2w/T2wToT1wDistortionCorrectAndReg/FieldMap --gdcoeffs=NONE':
Mon Jan 23 17:33:14 EST 2023:FieldMapPreprocessingAll.sh: ERROR: '/opt/fsl/fsl/bin/fsl_prepare_fieldmap' command failed with return code: 1
Mon Jan 23 17:33:14 EST 2023:FieldMapPreprocessingAll.sh: ERROR: '/opt/fsl/fsl/bin/fsl_prepare_fieldmap' command failed with return code: 1
===> ERROR: Command returned with nonzero exit code
---------------------------------------------------
script: FieldMapPreprocessingAll.sh
stopped at line: 170
call: ${FSLDIR}/bin/fsl_prepare_fieldmap SIEMENS ${WD}/Phase ${WD}/Magnitude_brain ${WD}/FieldMap ${DeltaTE}
expanded call: /opt/fsl/fsl/bin/fsl_prepare_fieldmap SIEMENS /Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/T2w/T2wToT1wDistortionCorrectAndReg/FieldMap/Phase /Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/T2w/T2wToT1wDistortionCorrectAndReg/FieldMap/Magnitude_brain /Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/T2w/T2wToT1wDistortionCorrectAndReg/FieldMap/FieldMap
hostname: 7ce105f07731
exit code: 1
---------------------------------------------------
===> Aborting execution!
Mon Jan 23 17:33:14 EST 2023:T2wToT1wDistortionCorrectAndReg.sh: While running '/opt/HCP/HCPpipelines/PreFreeSurfer/scripts/T2wToT1wDistortionCorrectAndReg.sh --workingdir=/Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/T2w/T2wToT1wDistortionCorrectAndReg --t1=/Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/T1w/T1w_acpc --t1brain=/Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/T1w/T1w_acpc_brain --t2=/Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/T2w/T2w_acpc --t2brain=/Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/T2w/T2w_acpc_brain --fmapmag=/Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/unprocessed/FieldMap99/PALS_011_FieldMap_Magnitude.nii.gz --fmapphase=/Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/unprocessed/FieldMap99/PALS_011_FieldMap_Phase.nii.gz --fmapgeneralelectric= --echodiff= --SEPhaseNeg= --SEPhasePos= --seechospacing= --seunwarpdir= --t1sampspacing= --t2sampspacing= --unwarpdir= --ot1=/Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/T1w/T1w_acpc_dc --ot1brain=/Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/T1w/T1w_acpc_dc_brain --ot1warp=/Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/T1w/xfms/T1w_dc --ot2=/Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/T1w/T2w_acpc_dc --ot2warp=/Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/T1w/xfms/T2w_reg_dc --method=SiemensFieldMap --topupconfig= --gdcoeffs=NONE --usejacobian=true':
Mon Jan 23 17:33:14 EST 2023:T2wToT1wDistortionCorrectAndReg.sh: ERROR: '/opt/HCP/HCPpipelines/global/scripts/FieldMapPreprocessingAll.sh' command failed with return code: 1
Mon Jan 23 17:33:14 EST 2023:T2wToT1wDistortionCorrectAndReg.sh: ERROR: '/opt/HCP/HCPpipelines/global/scripts/FieldMapPreprocessingAll.sh' command failed with return code: 1
===> ERROR: Command returned with nonzero exit code
---------------------------------------------------
script: T2wToT1wDistortionCorrectAndReg.sh
stopped at line: 245
call: ${HCPPIPEDIR_Global}/FieldMapPreprocessingAll.sh --workingdir=${WD}/FieldMap --method="SiemensFieldMap" --fmapmag=${MagnitudeInputName} --fmapphase=${PhaseInputName} --echodiff=${TE} --ofmapmag=${WD}/Magnitude --ofmapmagbrain=${WD}/Magnitude_brain --ofmap=${WD}/FieldMap --gdcoeffs=${GradientDistortionCoeffs}
expanded call: /opt/HCP/HCPpipelines/global/scripts/FieldMapPreprocessingAll.sh --workingdir=/Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/T2w/T2wToT1wDistortionCorrectAndReg/FieldMap --method=SiemensFieldMap --fmapmag=/Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/unprocessed/FieldMap99/PALS_011_FieldMap_Magnitude.nii.gz --fmapphase=/Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/unprocessed/FieldMap99/PALS_011_FieldMap_Phase.nii.gz --echodiff= --ofmapmag=/Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/T2w/T2wToT1wDistortionCorrectAndReg/Magnitude --ofmapmagbrain=/Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/T2w/T2wToT1wDistortionCorrectAndReg/Magnitude_brain --ofmap=/Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/T2w/T2wToT1wDistortionCorrectAndReg/FieldMap --gdcoeffs=NONE
hostname: 7ce105f07731
exit code: 1
---------------------------------------------------
===> Aborting execution!
Mon Jan 23 17:33:14 EST 2023:PreFreeSurferPipeline.sh: While running '/opt/HCP/HCPpipelines/PreFreeSurfer/PreFreeSurferPipeline.sh --path=/Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp --subject=PALS_011 --t1=/Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/unprocessed/T1w/PALS_011_T1w_MPR1.nii.gz@/Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/unprocessed/T1w/PALS_011_T1w_MPR2.nii.gz --t2=/Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/unprocessed/T2w/PALS_011_T2w_SPC1.nii.gz@/Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/unprocessed/T2w/PALS_011_T2w_SPC2.nii.gz@/Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/unprocessed/T2w/PALS_011_T2w_SPC3.nii.gz --t1template=/opt/HCP/HCPpipelines/global/templates/MNI152_T1_0.7mm.nii.gz --t1templatebrain=/opt/HCP/HCPpipelines/global/templates/MNI152_T1_0.7mm_brain.nii.gz --t1template2mm=/opt/HCP/HCPpipelines/global/templates/MNI152_T1_2mm.nii.gz --t2template=/opt/HCP/HCPpipelines/global/templates/MNI152_T2_0.7mm.nii.gz --t2templatebrain=/opt/HCP/HCPpipelines/global/templates/MNI152_T2_0.7mm_brain.nii.gz --t2template2mm=/opt/HCP/HCPpipelines/global/templates/MNI152_T2_2mm.nii.gz --templatemask=/opt/HCP/HCPpipelines/global/templates/MNI152_T1_0.7mm_brain_mask.nii.gz --template2mmmask=/opt/HCP/HCPpipelines/global/templates/MNI152_T1_2mm_brain_mask_dil.nii.gz --brainsize=150 --fnirtconfig=/opt/HCP/HCPpipelines/global/config/T1_2_MNI152_2mm.cnf --fmapmag=/Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/unprocessed/FieldMap99/PALS_011_FieldMap_Magnitude.nii.gz --fmapphase=/Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/unprocessed/FieldMap99/PALS_011_FieldMap_Phase.nii.gz --gdcoeffs=NONE --avgrdcmethod=SiemensFieldMap --processing-mode=HCPStyleData':
Mon Jan 23 17:33:14 EST 2023:PreFreeSurferPipeline.sh: ERROR: '/opt/HCP/HCPpipelines/PreFreeSurfer/scripts/T2wToT1wDistortionCorrectAndReg.sh' command failed with return code: 1
Mon Jan 23 17:33:14 EST 2023:PreFreeSurferPipeline.sh: ERROR: '/opt/HCP/HCPpipelines/PreFreeSurfer/scripts/T2wToT1wDistortionCorrectAndReg.sh' command failed with return code: 1
===> ERROR: Command returned with nonzero exit code
---------------------------------------------------
script: PreFreeSurferPipeline.sh
stopped at line: 629
call: ${RUN} ${HCPPIPEDIR_PreFS}/T2wToT1wDistortionCorrectAndReg.sh --workingdir=${wdir} --t1=${T1wFolder}/${T1wImage}_acpc --t1brain=${T1wFolder}/${T1wImage}_acpc_brain --t2=${T2wFolder_T2wImageWithPath_acpc} --t2brain=${T2wFolder_T2wImageWithPath_acpc_brain} --fmapmag=${MagnitudeInputName} --fmapphase=${PhaseInputName} --fmapgeneralelectric=${GEB0InputName} --echodiff=${TE} --SEPhaseNeg=${SpinEchoPhaseEncodeNegative} --SEPhasePos=${SpinEchoPhaseEncodePositive} --seechospacing=${SEEchoSpacing} --seunwarpdir=${SEUnwarpDir} --t1sampspacing=${T1wSampleSpacing} --t2sampspacing=${T2wSampleSpacing} --unwarpdir=${UnwarpDir} --ot1=${T1wFolder}/${T1wImage}_acpc_dc --ot1brain=${T1wFolder}/${T1wImage}_acpc_dc_brain --ot1warp=${T1wFolder}/xfms/${T1wImage}_dc --ot2=${T1wFolder}/${T2wImage}_acpc_dc --ot2warp=${T1wFolder}/xfms/${T2wImage}_reg_dc --method=${AvgrdcSTRING} --topupconfig=${TopupConfig} --gdcoeffs=${GradientDistortionCoeffs} --usejacobian=${UseJacobian}
expanded call: /opt/HCP/HCPpipelines/PreFreeSurfer/scripts/T2wToT1wDistortionCorrectAndReg.sh --workingdir=/Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/T2w/T2wToT1wDistortionCorrectAndReg --t1=/Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/T1w/T1w_acpc --t1brain=/Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/T1w/T1w_acpc_brain --t2=/Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/T2w/T2w_acpc --t2brain=/Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/T2w/T2w_acpc_brain --fmapmag=/Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/unprocessed/FieldMap99/PALS_011_FieldMap_Magnitude.nii.gz --fmapphase=/Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/unprocessed/FieldMap99/PALS_011_FieldMap_Phase.nii.gz --fmapgeneralelectric= --echodiff= --SEPhaseNeg= --SEPhasePos= --seechospacing= --seunwarpdir= --t1sampspacing= --t2sampspacing= --unwarpdir= --ot1=/Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/T1w/T1w_acpc_dc --ot1brain=/Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/T1w/T1w_acpc_dc_brain --ot1warp=/Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/T1w/xfms/T1w_dc --ot2=/Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/T1w/T2w_acpc_dc --ot2warp=/Users/kolobarica/Desktop/pals/sessions/PALS_011/hcp/PALS_011/T1w/xfms/T2w_reg_dc --method=SiemensFieldMap --topupconfig= --gdcoeffs=NONE --usejacobian=true
hostname: 7ce105f07731
exit code: 1
---------------------------------------------------
===> Aborting execution!