Comments (8)
rhancockn
commented on June 28, 2024
I’ve seen something similar happen when the input T1 has been preprocessed with intensity normalization. Is this the case in your data, eg does the white matter have an intensity of 110?
… On Feb 22, 2022, at 11:05 AM, Soichi Hayashi ***@***.***> wrote:
Hello. We are running HCPpipeline docker://bids/hcppipelines:v4.1.3-1. When we feed t1w and t2w input file, we run into the following error message.
Fri Feb 18 18:17:36 EST 2022:T2wToT1wReg.sh: START: T2w2T1Reg
Running FAST segmentation
Exception: Not enough classes detected to init KMeans
Image Exception : #63 :: No image files match: /output/sub-NDARINV0LEM88KP/T2w/T2wToT1wReg/T2w2T1w_fast_pve_2
terminate called after throwing an instance of 'std::runtime_error'
what(): No image files match: /output/sub-NDARINV0LEM88KP/T2w/T2wToT1wReg/T2w2T1w_fast_pve_2
/usr/local/fsl/bin/epi_reg: line 320: 13055 Aborted $FSLDIR/bin/fslmaths ${vout}_fast_pve_2 -thr 0.5 -bin ${vout}_fast_wmseg
Image Exception : #63 :: No image files match: /output/sub-NDARINV0LEM88KP/T2w/T2wToT1wReg/T2w2T1w_fast_wmseg
terminate called after throwing an instance of 'std::runtime_error'
what(): No image files match: /output/sub-NDARINV0LEM88KP/T2w/T2wToT1wReg/T2w2T1w_fast_wmseg
/usr/local/fsl/bin/epi_reg: line 329: 13086 Aborted $FSLDIR/bin/fslmaths ${vout}_fast_wmseg -edge -bin -mas ${vout}_fast_wmseg ${vout}_fast_wmedge
I think this means that FAST segmentation is failing to generate the output file T2w2T1w_fast_pve_2 because something is not right with the input files. Is that correct? If so, do you have any suggestion on what we should do to troubleshoot this problem?
We are running the container with the following options
https://github.com/brainlife/app-hcp-pipeline/blob/v4.1.3/main
singularity exec -e \
-B `pwd`/bids:/bids \
-B `pwd`/output:/output \
docker://bids/hcppipelines:v4.1.3-1 \
./run.py /bids /output participant \
--n_cpus 8 \
--stages $stage \
--license_key "$FREESURFER_LICENSE" \
--participant_label $sub \
--processing_mode $processing_mode \
$skipbidsvalidation
We are running a slightly modified version of run.py for our jobs and here is the current content > https://github.com/brainlife/app-hcp-pipeline/blob/v4.1.3/run.py
—
Reply to this email directly, view it on GitHub, or unsubscribe.
Triage notifications on the go with GitHub Mobile for iOS or Android.
You are receiving this because you are subscribed to this thread.
from hcppipelines.
soichih
commented on June 28, 2024
We are seeing this error on ABCD subject NDARINV0LEM88KP. I believe the T1W is not preprocessed. What do you mean by having an intensity of 110? As far as I can tell, different voxel has different intensities.
from hcppipelines.
rhancockn
commented on June 28, 2024
Indeed that doesn't look like a preprocessed image. The data does not look
very good though—I would expect to see some grey matter near your cursor.
Could be a quality issue with this participant. Are you
consistently getting this error on other ABCD subjects? You should have a
brain extracted T1 in /output/sub-NDARINV0LEM88KP/T2w/T2wToT1wReg/. Does
that look okay?
Roeland Hancock
…On Tue, Feb 22, 2022 at 11:20 AM Soichi Hayashi ***@***.***> wrote:
We are seeing this error on ABCD subject NDARINV0LEM88KP. I believe the
T1W is not preprocessed. What do you mean by having an intensity of 110? As
far as I can tell, different voxel has different intensities.
[image: image]
<https://user-images.githubusercontent.com/923896/155173994-715b2796-18fd-48f0-9b2c-00ae807b7e91.png>
—
Reply to this email directly, view it on GitHub
<#76 (comment)>,
or unsubscribe
<https://github.com/notifications/unsubscribe-auth/AARMKW5H6IHUSEHDJOJHRILU4OZWTANCNFSM5PB2LRFA>
.
Triage notifications on the go with GitHub Mobile for iOS
<https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675>
or Android
<https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.
You are receiving this because you commented.Message ID:
***@***.***>
from hcppipelines.
soichih
commented on June 28, 2024
No the T2wToT1wReg/T1w_acpc_brain.nii.gz is all blank.
Here is the entire log. I don't see anything ominous.. but maybe something went wrong with bet?
jan/15/2021
--> Modality: anat
--> Number of inputs for anat found: 1
creating directory bids/sub-NDARINV0LEM88KP/ses-baselineYear1Arm1/anat
hard-linking (existing) ../620fea73ff10f482da8be573/60cbab4acdfdb54b1bfee5ea/t1.nii.gz to (new link) bids/sub-NDARINV0LEM88KP/ses-baselineYear1Arm1/anat/sub-NDARINV0LEM88KP_ses-baselineYear1Arm1_T1w.nii.gz
--> Modality: anat
--> Number of inputs for anat found: 1
creating directory bids/sub-NDARINV0LEM88KP/ses-baselineYear1Arm1/anat
hard-linking (existing) ../620fea73ff10f482da8be573/60cbab51cdfdb55de3fee5ed/t2.nii.gz to (new link) bids/sub-NDARINV0LEM88KP/ses-baselineYear1Arm1/anat/sub-NDARINV0LEM88KP_ses-baselineYear1Arm1_T2w.nii.gz
writing dataset_description.json {'Name': 'brainlife', 'BIDSVersion': '1.4.0', 'Authors': ['Brainlife <[email protected]>']}
Running stages: PreFreeSurfer FreeSurfer PostFreeSurfer
Running local run.py
bids-validator /bids
[email protected]
1: [WARN] The recommended file /README is missing. See Section 03 (Modality agnostic files) of the BIDS specification. (code: 101 - README_FILE_MISSING)
Please visit https://neurostars.org/search?q=README_FILE_MISSING for existing conversations about this issue.
2: [WARN] The Authors field of dataset_description.json should contain an array of fields - with one author per field. This was triggered based on the presence of only one author field. Please ignore if all contributors are already properly listed. (code: 102 - TOO_FEW_AUTHORS)
Please visit https://neurostars.org/search?q=TOO_FEW_AUTHORS for existing conversations about this issue.
Summary: Available Tasks: Available Modalities:
5 Files, 23.41MB T1w
1 - Subject T2w
1 - Session
If you have any questions, please post on https://neurostars.org/tags/bids.
PreFreeSurfer in HCPStyleData mode
/opt/HCP-Pipelines/PreFreeSurfer/PreFreeSurferPipeline.sh --path="/output" --subject="sub-NDARINV0LEM88KP" --t1="/bids/sub-NDARINV0LEM88KP/ses-baselineYear1Arm1/anat/sub-NDARINV0LEM88KP_ses-baselineYear1Arm1_T1w.nii.gz" --t2="/bids/sub-NDARINV0LEM88KP/ses-baselineYear1Arm1/anat/sub-NDARINV0LEM88KP_ses-baselineYear1Arm1_T2w.nii.gz" --t1template="/opt/HCP-Pipelines/global/templates/MNI152_T1_1mm.nii.gz" --t1templatebrain="/opt/HCP-Pipelines/global/templates/MNI152_T1_1mm_brain.nii.gz" --t1template2mm="/opt/HCP-Pipelines/global/templates/MNI152_T1_2mm.nii.gz" --t2template="/opt/HCP-Pipelines/global/templates/MNI152_T2_1mm.nii.gz" --t2templatebrain="/opt/HCP-Pipelines/global/templates/MNI152_T2_1mm_brain.nii.gz" --t2template2mm="/opt/HCP-Pipelines/global/templates/MNI152_T2_2mm.nii.gz" --t2samplespacing="NONE" --templatemask="/opt/HCP-Pipelines/global/templates/MNI152_T1_1mm_brain_mask.nii.gz" --template2mmmask="/opt/HCP-Pipelines/global/templates/MNI152_T1_2mm_brain_mask_dil.nii.gz" --brainsize="150" --fnirtconfig="/opt/HCP-Pipelines/global/config/T1_2_MNI152_2mm.cnf" --fmapmag="NONE" --fmapphase="NONE" --fmapgeneralelectric="NONE" --echodiff="NONE" --SEPhaseNeg="NONE" --SEPhasePos="NONE" --seechospacing="NONE" --seunwarpdir="NONE" --t1samplespacing="NONE" --unwarpdir="NONE" --gdcoeffs=NONE --avgrdcmethod=NONE --topupconfig="/opt/HCP-Pipelines/global/config/b02b0.cnf" --processing-mode="HCPStyleData" --printcom=""
========================================
DIRECTORY: /opt/HCP-Pipelines
PRODUCT: HCP Pipeline Scripts
VERSION: v4.1.3
========================================
Fri Feb 18 17:14:26 EST 2022:PreFreeSurferPipeline.sh: HCPPIPEDIR: /opt/HCP-Pipelines
Fri Feb 18 17:14:26 EST 2022:PreFreeSurferPipeline.sh: FSLDIR: /usr/local/fsl
Fri Feb 18 17:14:26 EST 2022:PreFreeSurferPipeline.sh: HCPPIPEDIR_Global: /opt/HCP-Pipelines/global/scripts
Fri Feb 18 17:14:26 EST 2022:PreFreeSurferPipeline.sh: Platform Information Follows:
Linux c14 3.10.0-1160.49.1.el7.x86_64 #1 SMP Tue Nov 9 16:09:48 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
Fri Feb 18 17:14:26 EST 2022:PreFreeSurferPipeline.sh: Parsing Command Line Options
Fri Feb 18 17:14:28 EST 2022:PreFreeSurferPipeline.sh: Finished Parsing Command Line Options
Fri Feb 18 17:14:28 EST 2022:PreFreeSurferPipeline.sh: StudyFolder: /output
Fri Feb 18 17:14:28 EST 2022:PreFreeSurferPipeline.sh: Subject: sub-NDARINV0LEM88KP
Fri Feb 18 17:14:28 EST 2022:PreFreeSurferPipeline.sh: T1wInputImages: /bids/sub-NDARINV0LEM88KP/ses-baselineYear1Arm1/anat/sub-NDARINV0LEM88KP_ses-baselineYear1Arm1_T1w.nii.gz
Fri Feb 18 17:14:28 EST 2022:PreFreeSurferPipeline.sh: T2wInputImages: /bids/sub-NDARINV0LEM88KP/ses-baselineYear1Arm1/anat/sub-NDARINV0LEM88KP_ses-baselineYear1Arm1_T2w.nii.gz
Fri Feb 18 17:14:28 EST 2022:PreFreeSurferPipeline.sh: T1wTemplate: /opt/HCP-Pipelines/global/templates/MNI152_T1_1mm.nii.gz
Fri Feb 18 17:14:28 EST 2022:PreFreeSurferPipeline.sh: T1wTemplateBrain: /opt/HCP-Pipelines/global/templates/MNI152_T1_1mm_brain.nii.gz
Fri Feb 18 17:14:28 EST 2022:PreFreeSurferPipeline.sh: T1wTemplate2mm: /opt/HCP-Pipelines/global/templates/MNI152_T1_2mm.nii.gz
Fri Feb 18 17:14:28 EST 2022:PreFreeSurferPipeline.sh: T2wTemplate: /opt/HCP-Pipelines/global/templates/MNI152_T2_1mm.nii.gz
Fri Feb 18 17:14:28 EST 2022:PreFreeSurferPipeline.sh: T2wTemplateBrain: /opt/HCP-Pipelines/global/templates/MNI152_T2_1mm_brain.nii.gz
Fri Feb 18 17:14:28 EST 2022:PreFreeSurferPipeline.sh: T2wTemplate2mm: /opt/HCP-Pipelines/global/templates/MNI152_T2_2mm.nii.gz
Fri Feb 18 17:14:28 EST 2022:PreFreeSurferPipeline.sh: TemplateMask: /opt/HCP-Pipelines/global/templates/MNI152_T1_1mm_brain_mask.nii.gz
Fri Feb 18 17:14:28 EST 2022:PreFreeSurferPipeline.sh: Template2mmMask: /opt/HCP-Pipelines/global/templates/MNI152_T1_2mm_brain_mask_dil.nii.gz
Fri Feb 18 17:14:28 EST 2022:PreFreeSurferPipeline.sh: BrainSize: 150
Fri Feb 18 17:14:28 EST 2022:PreFreeSurferPipeline.sh: FNIRTConfig: /opt/HCP-Pipelines/global/config/T1_2_MNI152_2mm.cnf
Fri Feb 18 17:14:28 EST 2022:PreFreeSurferPipeline.sh: MagnitudeInputName: NONE
Fri Feb 18 17:14:28 EST 2022:PreFreeSurferPipeline.sh: PhaseInputName: NONE
Fri Feb 18 17:14:28 EST 2022:PreFreeSurferPipeline.sh: GEB0InputName: NONE
Fri Feb 18 17:14:28 EST 2022:PreFreeSurferPipeline.sh: TE: NONE
Fri Feb 18 17:14:28 EST 2022:PreFreeSurferPipeline.sh: SpinEchoPhaseEncodeNegative: NONE
Fri Feb 18 17:14:28 EST 2022:PreFreeSurferPipeline.sh: SpinEchoPhaseEncodePositive: NONE
Fri Feb 18 17:14:28 EST 2022:PreFreeSurferPipeline.sh: SEEchoSpacing: NONE
Fri Feb 18 17:14:28 EST 2022:PreFreeSurferPipeline.sh: SEUnwarpDir: NONE
Fri Feb 18 17:14:28 EST 2022:PreFreeSurferPipeline.sh: T1wSampleSpacing: NONE
Fri Feb 18 17:14:28 EST 2022:PreFreeSurferPipeline.sh: T2wSampleSpacing: NONE
Fri Feb 18 17:14:28 EST 2022:PreFreeSurferPipeline.sh: UnwarpDir: NONE
Fri Feb 18 17:14:28 EST 2022:PreFreeSurferPipeline.sh: GradientDistortionCoeffs: NONE
Fri Feb 18 17:14:28 EST 2022:PreFreeSurferPipeline.sh: AvgrdcSTRING: NONE
Fri Feb 18 17:14:28 EST 2022:PreFreeSurferPipeline.sh: TopupConfig: /opt/HCP-Pipelines/global/config/b02b0.cnf
Fri Feb 18 17:14:28 EST 2022:PreFreeSurferPipeline.sh: BiasFieldSmoothingSigma:
Fri Feb 18 17:14:28 EST 2022:PreFreeSurferPipeline.sh: UseJacobian: true
Fri Feb 18 17:14:28 EST 2022:PreFreeSurferPipeline.sh: T1wBiasCorrect:
Fri Feb 18 17:14:28 EST 2022:PreFreeSurferPipeline.sh: CustomBrain: NONE
Fri Feb 18 17:14:28 EST 2022:PreFreeSurferPipeline.sh: ProcessingMode: HCPStyleData
Fri Feb 18 17:14:28 EST 2022:PreFreeSurferPipeline.sh: T1wFolder: /output/sub-NDARINV0LEM88KP/T1w
Fri Feb 18 17:14:28 EST 2022:PreFreeSurferPipeline.sh: T2wFolder: /output/sub-NDARINV0LEM88KP/T2w
Fri Feb 18 17:14:28 EST 2022:PreFreeSurferPipeline.sh: AtlasSpaceFolder: /output/sub-NDARINV0LEM88KP/MNINonLinear
Fri Feb 18 17:14:28 EST 2022:PreFreeSurferPipeline.sh: mkdir -p /output/sub-NDARINV0LEM88KP/T1w/xfms/
Fri Feb 18 17:14:28 EST 2022:PreFreeSurferPipeline.sh: mkdir -p /output/sub-NDARINV0LEM88KP/T2w/xfms/
Fri Feb 18 17:14:28 EST 2022:PreFreeSurferPipeline.sh: mkdir -p /output/sub-NDARINV0LEM88KP/MNINonLinear/xfms/
Fri Feb 18 17:14:28 EST 2022:PreFreeSurferPipeline.sh: POSIXLY_CORRECT=
Fri Feb 18 17:14:28 EST 2022:PreFreeSurferPipeline.sh: Processing Modality: T1w
Fri Feb 18 17:14:28 EST 2022:PreFreeSurferPipeline.sh: NOT PERFORMING GRADIENT DISTORTION CORRECTION
Fri Feb 18 17:14:34 EST 2022:PreFreeSurferPipeline.sh: Not Averaging T1w Images
Fri Feb 18 17:14:34 EST 2022:PreFreeSurferPipeline.sh: ONLY ONE IMAGE FOUND: COPYING
Fri Feb 18 17:14:34 EST 2022:PreFreeSurferPipeline.sh: Aligning T1w image to /opt/HCP-Pipelines/global/templates/MNI152_T1_1mm.nii.gz to create native volume space
Fri Feb 18 17:14:34 EST 2022:PreFreeSurferPipeline.sh: mkdir -p /output/sub-NDARINV0LEM88KP/T1w/ACPCAlignment
Fri Feb 18 17:14:34 EST 2022:ACPCAlignment.sh: HCPPIPEDIR: /opt/HCP-Pipelines
Fri Feb 18 17:14:34 EST 2022:ACPCAlignment.sh: FSLDIR: /usr/local/fsl
Fri Feb 18 17:14:35 EST 2022:ACPCAlignment.sh: START
Final FOV is:
0.000000 176.000000 0.000000 256.000000 79.000000 150.000000
Fri Feb 18 17:15:25 EST 2022:ACPCAlignment.sh: END
Fri Feb 18 17:15:25 EST 2022:PreFreeSurferPipeline.sh: Performing Brain Extraction using FNIRT-based Masking
Fri Feb 18 17:15:25 EST 2022:PreFreeSurferPipeline.sh: mkdir -p /output/sub-NDARINV0LEM88KP/T1w/BrainExtraction_FNIRTbased
Fri Feb 18 17:15:25 EST 2022:BrainExtraction_FNIRTbased.sh: HCPPIPEDIR: /opt/HCP-Pipelines
Fri Feb 18 17:15:25 EST 2022:BrainExtraction_FNIRTbased.sh: FSLDIR: /usr/local/fsl
Fri Feb 18 17:15:25 EST 2022:BrainExtraction_FNIRTbased.sh: HCPPIPEDIR_Templates: /opt/HCP-Pipelines/global/templates
Fri Feb 18 17:15:26 EST 2022: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
Fri Feb 18 18:08:41 EST 2022:BrainExtraction_FNIRTbased.sh: END: BrainExtraction_FNIRT
Fri Feb 18 18:08:41 EST 2022:PreFreeSurferPipeline.sh: Processing Modality: T2w
Fri Feb 18 18:08:41 EST 2022:PreFreeSurferPipeline.sh: NOT PERFORMING GRADIENT DISTORTION CORRECTION
Fri Feb 18 18:08:41 EST 2022:PreFreeSurferPipeline.sh: Not Averaging T2w Images
Fri Feb 18 18:08:41 EST 2022:PreFreeSurferPipeline.sh: ONLY ONE IMAGE FOUND: COPYING
Fri Feb 18 18:08:42 EST 2022:PreFreeSurferPipeline.sh: Aligning T2w image to /opt/HCP-Pipelines/global/templates/MNI152_T2_1mm.nii.gz to create native volume space
Fri Feb 18 18:08:42 EST 2022:PreFreeSurferPipeline.sh: mkdir -p /output/sub-NDARINV0LEM88KP/T2w/ACPCAlignment
Fri Feb 18 18:08:42 EST 2022:ACPCAlignment.sh: HCPPIPEDIR: /opt/HCP-Pipelines
Fri Feb 18 18:08:42 EST 2022:ACPCAlignment.sh: FSLDIR: /usr/local/fsl
Fri Feb 18 18:08:42 EST 2022:ACPCAlignment.sh: START
Final FOV is:
0.000000 176.000000 0.000000 256.000000 81.000000 150.000000
Fri Feb 18 18:09:42 EST 2022:ACPCAlignment.sh: END
Fri Feb 18 18:09:42 EST 2022:PreFreeSurferPipeline.sh: Performing Brain Extraction using FNIRT-based Masking
Fri Feb 18 18:09:42 EST 2022:PreFreeSurferPipeline.sh: mkdir -p /output/sub-NDARINV0LEM88KP/T2w/BrainExtraction_FNIRTbased
Fri Feb 18 18:09:42 EST 2022:BrainExtraction_FNIRTbased.sh: HCPPIPEDIR: /opt/HCP-Pipelines
Fri Feb 18 18:09:42 EST 2022:BrainExtraction_FNIRTbased.sh: FSLDIR: /usr/local/fsl
Fri Feb 18 18:09:42 EST 2022:BrainExtraction_FNIRTbased.sh: HCPPIPEDIR_Templates: /opt/HCP-Pipelines/global/templates
Fri Feb 18 18:09:42 EST 2022:BrainExtraction_FNIRTbased.sh: START: BrainExtraction_FNIRT
Fri Feb 18 18:17:36 EST 2022:BrainExtraction_FNIRTbased.sh: END: BrainExtraction_FNIRT
Fri Feb 18 18:17:36 EST 2022:PreFreeSurferPipeline.sh: NOT PERFORMING READOUT DISTORTION CORRECTION
Fri Feb 18 18:17:36 EST 2022:PreFreeSurferPipeline.sh: mkdir -p /output/sub-NDARINV0LEM88KP/T2w/T2wToT1wReg
Fri Feb 18 18:17:36 EST 2022:T2wToT1wReg.sh: HCPPIPEDIR: /opt/HCP-Pipelines
Fri Feb 18 18:17:36 EST 2022:T2wToT1wReg.sh: FSLDIR: /usr/local/fsl
Fri Feb 18 18:17:36 EST 2022:T2wToT1wReg.sh: START: T2w2T1Reg
Running FAST segmentation
Exception: Not enough classes detected to init KMeans
Image Exception : #63 :: No image files match: /output/sub-NDARINV0LEM88KP/T2w/T2wToT1wReg/T2w2T1w_fast_pve_2
terminate called after throwing an instance of 'std::runtime_error'
what(): No image files match: /output/sub-NDARINV0LEM88KP/T2w/T2wToT1wReg/T2w2T1w_fast_pve_2
/usr/local/fsl/bin/epi_reg: line 320: 13055 Aborted $FSLDIR/bin/fslmaths ${vout}_fast_pve_2 -thr 0.5 -bin ${vout}_fast_wmseg
Image Exception : #63 :: No image files match: /output/sub-NDARINV0LEM88KP/T2w/T2wToT1wReg/T2w2T1w_fast_wmseg
terminate called after throwing an instance of 'std::runtime_error'
what(): No image files match: /output/sub-NDARINV0LEM88KP/T2w/T2wToT1wReg/T2w2T1w_fast_wmseg
/usr/local/fsl/bin/epi_reg: line 329: 13086 Aborted $FSLDIR/bin/fslmaths ${vout}_fast_wmseg -edge -bin -mas ${vout}_fast_wmseg ${vout}_fast_wmedge
FLIRT pre-alignment
WARNING::in calculating COG, total = 0.0
Running BBR
Image Exception : #63 :: No image files match: /output/sub-NDARINV0LEM88KP/T2w/T2wToT1wReg/T2w2T1w_fast_wmseg
Image Exception : #22 :: Failed to read volume /output/sub-NDARINV0LEM88KP/T2w/T2wToT1wReg/T2w2T1w_fast_wmseg
Error : No image files match: /output/sub-NDARINV0LEM88KP/T2w/T2wToT1wReg/T2w2T1w_fast_wmseg
Failed to read volume /output/sub-NDARINV0LEM88KP/T2w/T2wToT1wReg/T2w2T1w_fast_wmseg
Error : No image files match: /output/sub-NDARINV0LEM88KP/T2w/T2wToT1wReg/T2w2T1w_fast_wmseg
Could not open matrix file /output/sub-NDARINV0LEM88KP/T2w/T2wToT1wReg/T2w2T1w.mat
/usr/local/fsl/bin/epi_reg: line 399: 13999 Segmentation fault $FSLDIR/bin/applywarp -i ${vepi} -r ${vrefhead} -o ${vout} --premat=${vout}.mat --interp=spline
Could not open matrix file /output/sub-NDARINV0LEM88KP/T2w/T2wToT1wReg/T2w2T1w.mat
/opt/HCP-Pipelines/PreFreeSurfer/scripts/T2wToT1wReg.sh: line 78: 14126 Segmentation fault ${FSLDIR}/bin/applywarp --rel --interp=spline --in="$T2wImage" --ref="$T1wImage" --premat="$WD"/T2w2T1w.mat --out="$WD"/T2w2T1w
Fri Feb 18 18:17:55 EST 2022:T2wToT1wReg.sh: While running '/opt/HCP-Pipelines/PreFreeSurfer/scripts/T2wToT1wReg.sh /output/sub-NDARINV0LEM88KP/T2w/T2wToT1wReg /output/sub-NDARINV0LEM88KP/T1w/T1w_acpc /output/sub-NDARINV0LEM88KP/T1w/T1w_acpc_brain /output/sub-NDARINV0LEM88KP/T2w/T2w_acpc /output/sub-NDARINV0LEM88KP/T2w/T2w_acpc_brain /output/sub-NDARINV0LEM88KP/T1w/T1w_acpc_dc /output/sub-NDARINV0LEM88KP/T1w/T1w_acpc_dc_brain /output/sub-NDARINV0LEM88KP/T1w/xfms/T1w_dc /output/sub-NDARINV0LEM88KP/T1w/T2w_acpc_dc /output/sub-NDARINV0LEM88KP/T1w/xfms/T2w_reg_dc':
Fri Feb 18 18:17:55 EST 2022:T2wToT1wReg.sh: ERROR: '/usr/local/fsl/bin/applywarp' command failed with return code: 139
Fri Feb 18 18:17:55 EST 2022:T2wToT1wReg.sh: ERROR: '/usr/local/fsl/bin/applywarp' command failed with return code: 139
===> ERROR: Command returned with nonzero exit code
---------------------------------------------------
script: T2wToT1wReg.sh
stopped at line: 76
call: ${FSLDIR}/bin/applywarp --rel --interp=spline --in="$T2wImage" --ref="$T1wImage" --premat="$WD"/T2w2T1w.mat --out="$WD"/T2w2T1w
expanded call: /usr/local/fsl/bin/applywarp --rel --interp=spline --in=/output/sub-NDARINV0LEM88KP/T2w/T2w_acpc --ref=/output/sub-NDARINV0LEM88KP/T1w/T1w_acpc --premat=/output/sub-NDARINV0LEM88KP/T2w/T2wToT1wReg/T2w2T1w.mat --out=/output/sub-NDARINV0LEM88KP/T2w/T2wToT1wReg/T2w2T1w
exit code: 139
---------------------------------------------------
===> Aborting execution!
Fri Feb 18 18:17:55 EST 2022:PreFreeSurferPipeline.sh: While running '/opt/HCP-Pipelines/PreFreeSurfer/PreFreeSurferPipeline.sh --path=/output --subject=sub-NDARINV0LEM88KP --t1=/bids/sub-NDARINV0LEM88KP/ses-baselineYear1Arm1/anat/sub-NDARINV0LEM88KP_ses-baselineYear1Arm1_T1w.nii.gz --t2=/bids/sub-NDARINV0LEM88KP/ses-baselineYear1Arm1/anat/sub-NDARINV0LEM88KP_ses-baselineYear1Arm1_T2w.nii.gz --t1template=/opt/HCP-Pipelines/global/templates/MNI152_T1_1mm.nii.gz --t1templatebrain=/opt/HCP-Pipelines/global/templates/MNI152_T1_1mm_brain.nii.gz --t1template2mm=/opt/HCP-Pipelines/global/templates/MNI152_T1_2mm.nii.gz --t2template=/opt/HCP-Pipelines/global/templates/MNI152_T2_1mm.nii.gz --t2templatebrain=/opt/HCP-Pipelines/global/templates/MNI152_T2_1mm_brain.nii.gz --t2template2mm=/opt/HCP-Pipelines/global/templates/MNI152_T2_2mm.nii.gz --t2samplespacing=NONE --templatemask=/opt/HCP-Pipelines/global/templates/MNI152_T1_1mm_brain_mask.nii.gz --template2mmmask=/opt/HCP-Pipelines/global/templates/MNI152_T1_2mm_brain_mask_dil.nii.gz --brainsize=150 --fnirtconfig=/opt/HCP-Pipelines/global/config/T1_2_MNI152_2mm.cnf --fmapmag=NONE --fmapphase=NONE --fmapgeneralelectric=NONE --echodiff=NONE --SEPhaseNeg=NONE --SEPhasePos=NONE --seechospacing=NONE --seunwarpdir=NONE --t1samplespacing=NONE --unwarpdir=NONE --gdcoeffs=NONE --avgrdcmethod=NONE --topupconfig=/opt/HCP-Pipelines/global/config/b02b0.cnf --processing-mode=HCPStyleData --printcom=':
Fri Feb 18 18:17:55 EST 2022:PreFreeSurferPipeline.sh: ERROR: '/opt/HCP-Pipelines/PreFreeSurfer/scripts/T2wToT1wReg.sh' command failed with return code: 139
Fri Feb 18 18:17:55 EST 2022:PreFreeSurferPipeline.sh: ERROR: '/opt/HCP-Pipelines/PreFreeSurfer/scripts/T2wToT1wReg.sh' command failed with return code: 139
===> ERROR: Command returned with nonzero exit code
---------------------------------------------------
script: PreFreeSurferPipeline.sh
stopped at line: 662
call: ${RUN} ${HCPPIPEDIR_PreFS}/T2wToT1wReg.sh ${wdir} ${T1wFolder}/${T1wImage}_acpc ${T1wFolder}/${T1wImage}_acpc_brain ${T2wFolder_T2wImageWithPath_acpc} ${T2wFolder_T2wImageWithPath_acpc_brain} ${T1wFolder}/${T1wImage}_acpc_dc ${T1wFolder}/${T1wImage}_acpc_dc_brain ${T1wFolder}/xfms/${T1wImage}_dc ${T1wFolder}/${T2wImage}_acpc_dc ${T1wFolder}/xfms/${T2wImage}_reg_dc
expanded call: /opt/HCP-Pipelines/PreFreeSurfer/scripts/T2wToT1wReg.sh /output/sub-NDARINV0LEM88KP/T2w/T2wToT1wReg /output/sub-NDARINV0LEM88KP/T1w/T1w_acpc /output/sub-NDARINV0LEM88KP/T1w/T1w_acpc_brain /output/sub-NDARINV0LEM88KP/T2w/T2w_acpc /output/sub-NDARINV0LEM88KP/T2w/T2w_acpc_brain /output/sub-NDARINV0LEM88KP/T1w/T1w_acpc_dc /output/sub-NDARINV0LEM88KP/T1w/T1w_acpc_dc_brain /output/sub-NDARINV0LEM88KP/T1w/xfms/T1w_dc /output/sub-NDARINV0LEM88KP/T1w/T2w_acpc_dc /output/sub-NDARINV0LEM88KP/T1w/xfms/T2w_reg_dc
exit code: 139
---------------------------------------------------
===> Aborting execution!
from hcppipelines.
giulia-berto
commented on June 28, 2024
Hi, I ran into the same issue. This happens with processing_mode='auto', both with the dockers v4.1.3-1 and v4.3.0-3. My guess is that the script T2wToT1wReg.sh fails at line 76 because it's looking for the file T2w2T1w.mat, but there is only the file T2w2T1w_init.mat in the T2wToT1wReg folder. Is it possible?
from hcppipelines.
rhancockn
commented on June 28, 2024
Has any one tried this https://github.com/DCAN-Labs/abcd-hcp-pipeline? It
looks there's a version of the HCP pipeline for ABCD.
…On Thu, Feb 24, 2022 at 9:58 AM Giulia Bertò ***@***.***> wrote:
Hi, I ran into the same issue. This happens with processing_mode='auto',
both with the dockers v4.1.3-1 and v4.3.0-3. My guess is that the script
T2wToT1wReg.sh fails at line 76 because it's looking for the file
T2w2T1w.mat, but there is only the file T2w2T1w_init.mat in the T2wToT1wReg
folder. Is it possible?
—
Reply to this email directly, view it on GitHub
<#76 (comment)>,
or unsubscribe
<https://github.com/notifications/unsubscribe-auth/AARMKW2K6IKVML4VUVOXTDTU4ZBRRANCNFSM5PB2LRFA>
.
Triage notifications on the go with GitHub Mobile for iOS
<https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675>
or Android
<https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.
You are receiving this because you commented.Message ID:
***@***.***>
from hcppipelines.
ericearl
commented on June 28, 2024
@rhancockn The DCAN-Labs abcd-hcp-pipeline is actually quite flexible to data of most studies. You can read more about the pipeline's behavior here:
https://collection3165.readthedocs.io/en/stable/pipeline/
They're also quite responsive to posting GitHub issues there.
from hcppipelines.
francopestilli
commented on June 28, 2024
Has any one tried this https://github.com/DCAN-Labs/abcd-hcp-pipeline? It looks there's a version of the HCP pipeline for ABCD.
…
On Thu, Feb 24, 2022 at 9:58 AM Giulia Bertò @.> wrote: Hi, I ran into the same issue. This happens with processing_mode='auto', both with the dockers v4.1.3-1 and v4.3.0-3. My guess is that the script T2wToT1wReg.sh fails at line 76 because it's looking for the file T2w2T1w.mat, but there is only the file T2w2T1w_init.mat in the T2wToT1wReg folder. Is it possible? — Reply to this email directly, view it on GitHub <#76 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AARMKW2K6IKVML4VUVOXTDTU4ZBRRANCNFSM5PB2LRFA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub. You are receiving this because you commented.Message ID: @.>
hi @rhancockn
thanks for following up on this. we are looking into the DCAN abcd-hcp app.
regarding this App, it looks like an update to the docker would be necessary to make the App functional.
we were wondering whether it would be helpful for us to help by editing the docker container? would you be interested in that?
Franco
from hcppipelines.
Related Issues (20)
- Implement LegacyStyleData HOT 1
- No T2w files found for sub-{subject_label}. Consider --procesing_mode [legacy | auto ]. HOT 6
- BIDs validation fails inside container on previously validated dataset
- BIDs validation fails on previously validated dataset HOT 3
- Validate stage options
- Check file existence
- Reduce the size of the Docker image
- Python type error HOT 1
- KeyError: 'DwellTime' HOT 7
- BIDs issue- 'BIDS root does not exist' HOT 4
- BIDS App wrapper for HCP Pipelines v4.3.0
- ERROR: crypt() returned null with 4-line file HOT 6
- wb_command not installed in container
- PostFreeSurferPipeline.sh: ERROR: unrecognized option: '--printcom'
- fieldmap for BOLD file not found even though it is present HOT 4
- ICA-FIX implementation for BIDS
- PostFreeSurferPipeline error
- fail to run latest image in CI
- test data failing HOT 2
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from hcppipelines.