Description:
When trying to run the dwi_legacy_gpu command, it complained of missing scanner manufacturer despite the relevant parameter being included in the command call. Please advise, thank you.
Call:
cn2107:~ moana004$ item="FM0001"; qunex_container dwi_legacy_gpu -sessionsfolder="${study_sharedfolder}/sessions" --sessions="${item}" --scanner="siemens" --usefieldmap="yes" --echospacing="0.73" --PEdir="2" --unwarpdir="y" --diffdatasuffix="DWI_dir42_AP" --TE="2.46" --overwrite="yes" --test --bind="${study_sharedfolder}:/${study_sharedfolder}" --container="${HOME}/qunex/qunex_suite-0.94.4.sif"
--> QuNex will run the command over 1 sessions. It will utilize:
Maximum sessions run in parallel for a job: 1.
Maximum elements run in parallel for a session: 1.
Up to 1 processes will be utilized for a job.
Job #1 will run sessions: FM0001
cn2107:~ moana004$ --> unsetting the following environment variables: PATH MATLABPATH PYTHONPATH QUNEXVer TOOLS QUNEXREPO QUNEXPATH QUNEXLIBRARY QUNEXLIBRARYETC TemplateFolder FSL_FIXDIR FREESURFERDIR FREESURFER_HOME FREESURFER_SCHEDULER FreeSurferSchedulerDIR WORKBENCHDIR DCMNIIDIR DICMNIIDIR MATLABDIR MATLABBINDIR OCTAVEDIR OCTAVEPKGDIR OCTAVEBINDIR RDIR HCPWBDIR AFNIDIR ANTSDIR PYLIBDIR FSLDIR FSLGPUDIR PALMDIR QUNEXMCOMMAND HCPPIPEDIR CARET7DIR GRADUNWARPDIR HCPPIPEDIR_Templates HCPPIPEDIR_Bin HCPPIPEDIR_Config HCPPIPEDIR_PreFS HCPPIPEDIR_FS HCPPIPEDIR_PostFS HCPPIPEDIR_fMRISurf HCPPIPEDIR_fMRIVol HCPPIPEDIR_tfMRI HCPPIPEDIR_dMRI HCPPIPEDIR_dMRITract HCPPIPEDIR_Global HCPPIPEDIR_tfMRIAnalysis HCPCIFTIRWDIR MSMBin HCPPIPEDIR_dMRITractFull HCPPIPEDIR_dMRILegacy AutoPtxFolder FSL_GPU_SCRIPTS FSLGPUBinary EDDYCUDADIR USEOCTAVE QUNEXENV CONDADIR MSMBINDIR MSMCONFIGDIR R_LIBS FSL_FIX_CIFTIRW FSFAST_HOME SUBJECTS_DIR MINC_BIN_DIR MNI_DIR MINC_LIB_DIR MNI_DATAPATH FSF_OUTPUT_FORMAT
Generated by QuNex
------------------------------------------------------------------------
Version: 0.94.4
User: moana004
System: cn2107
OS: RedHat Linux #1 SMP Tue Jun 28 15:37:28 UTC 2022
------------------------------------------------------------------------
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DEVELOPED & MAINTAINED BY:
Anticevic Lab, Yale University
Mind & Brain Lab, University of Ljubljana
Murray Lab, Yale University
COPYRIGHT & LICENSE NOTICE:
Use of this software is subject to the terms and conditions defined in
'LICENSES' which is a part of the QuNex Suite source code package:
https://gitlab.qunex.yale.edu/qunex/qunex/-/tree/master/LICENSES
---> Setting up Octave
........................ Running QuNex v0.94.4 ........................
ERROR: Scanner manufacturer missing
** For an example of how to report an issue, please refer to this post.
The problem is that you have inconsistently provided parameters, for the first one you use a single dash and then for others you use a double dash. You need to be consistent.
Also, I believe that you should be able to run hcp_diffusion given your data. The dwi_legacy_gpu is really old and later versions of hcp_diffusion should be able to run on your data. If you have any issues with setting it up let me know.
Thanks for spotting the typo, that should be easy to fix.
To clarify, you’re suggesting that despite processing legacy MRI data I should be able to use “hcp_diffusion” instead? I was following the instructions here: Diffusion weighted imaging (DWI) 'legacy' data preprocessing — QuNex documentation.
This is a DWI cardiac-gated acquisition with 42 directions, and I also have field maps for the DWI data.
- Field map for DTI
12.1. Gradient echo field maps for DWI: one scan as a pair of magnitude and phase image, acquisition time per run =1m20s
12.2. TR = 800 ms; TE1 = 4.92 ms; TE2 = 7.38 ms; TE difference = 2.46 ms; voxel size = 4.0 x 4.0 x 2.0 mm; Slices = 68; FoV read = 256 mm; Filter: None; Flip angle = 60 deg; Measurements = 1; Multi-slice mode: Interleaved; Series: Interleaved; Fat suppr.: None; Phase enc. Dir. = A >> P (Y-axis)
- Diffusion MRI
13.1. 42-directions; Acquisition time per run = 6m56s
13.2. TR = 8000 ms; TE = 83 ms; voxel size = 2.0 mm isotropic; Slices = 68; FoV read = 256 mm; Phase enc. dir. A >> P; Accel. factor PE = 2; Filter: Raw filter, Prescan Normalize; Flip angle = not described; Delay in TR = 0 ms; PAT mode = GRAPPA; Multi-slice mode: Interleaved; Series: Interleaved; Fat suppr.: Fat sat.; Echo spacing = 0.73 ms; b-value 1 = 0 s/mm2; b-value 2 = 1000 s/mm2, b-value 1 and = 1; Diffusion scheme" Monopolar
13.3. Information from pre-2022 documents: Cardiac-gated acquisition; # of volumes = 49 (42 directions, 7 B0)
By using the dwi_legacy_gpu command, it seems that I can take advantage of the field maps. Looking at the “hcp_diffusion” command parameters (hcp_diffusion — QuNex documentation), it seems that I would not be able to use the field maps. What are your thoughts, based on this information? Thank you.
Btw, I asked about using field maps for DWI in the HCP-Users group list and Matt Glasser suggested that the HCP pipelines would need to be patched to accommodate use of field maps for DWI data and that’s why I liked the idea of the dwi_legacy_gpu: https://groups.google.com/a/humanconnectome.org/g/hcp-users/c/LFhoupvzQ_A/m/hIo17d4EBQAJ
Yes, hcp_diffusion does not support field maps. We will discuss this internally and coordinate with HCP folks to see how much work it would take to get this in. My intuition says that this should not be too hard.
Yes, dwi_legacy_gpu supports field maps, you can try that one. What are your plans with DWI, what kind of analyses are you interested in. I can say for sure that hcp_diffusion results can be seamlessly plugged into DWI commands that follow (e.g. bedpostx, tractography, …). It was awhile since we used legacy so we might encounter some issues down the line, but we can work on them once we get there I guess.
Note that for commands that have _gpu in them you need to have a system with an NVIDIA graphic card that supports CUDA and you need to add --nv to the qunex_container call.
I do want to run tractography on these data, so it makes more sense to use the “hcp_diffusion” command. I gave it a shot but there were errors. Please see the command and its output, as well as the batch file I used and the log file.
cn2107:~ moana004$ item="FM0001"; qunex_container hcp_diffusion --batchfile="${study_sharedfolder}/processing/batch_03_struct-fMRI-dwi.txt" --sessionsfolder="${study_sharedfolder}/sessions" --sessions="${item}" --parsessions="1" --bind="${study_sharedfolder}:/${study_sharedfolder}" --container="${HOME}/qunex/qunex_suite-0.94.4.sif"
--> QuNex will run the command over 1 sessions. It will utilize:
Maximum sessions run in parallel for a job: 1.
Maximum elements run in parallel for a session: 1.
Up to 1 processes will be utilized for a job.
Job #1 will run sessions: FM0001
cn2107:~ moana004$ --> unsetting the following environment variables: PATH MATLABPATH PYTHONPATH QUNEXVer TOOLS QUNEXREPO QUNEXPATH QUNEXLIBRARY QUNEXLIBRARYETC TemplateFolder FSL_FIXDIR FREESURFERDIR FREESURFER_HOME FREESURFER_SCHEDULER FreeSurferSchedulerDIR WORKBENCHDIR DCMNIIDIR DICMNIIDIR MATLABDIR MATLABBINDIR OCTAVEDIR OCTAVEPKGDIR OCTAVEBINDIR RDIR HCPWBDIR AFNIDIR ANTSDIR PYLIBDIR FSLDIR FSLGPUDIR PALMDIR QUNEXMCOMMAND HCPPIPEDIR CARET7DIR GRADUNWARPDIR HCPPIPEDIR_Templates HCPPIPEDIR_Bin HCPPIPEDIR_Config HCPPIPEDIR_PreFS HCPPIPEDIR_FS HCPPIPEDIR_PostFS HCPPIPEDIR_fMRISurf HCPPIPEDIR_fMRIVol HCPPIPEDIR_tfMRI HCPPIPEDIR_dMRI HCPPIPEDIR_dMRITract HCPPIPEDIR_Global HCPPIPEDIR_tfMRIAnalysis HCPCIFTIRWDIR MSMBin HCPPIPEDIR_dMRITractFull HCPPIPEDIR_dMRILegacy AutoPtxFolder FSL_GPU_SCRIPTS FSLGPUBinary EDDYCUDADIR USEOCTAVE QUNEXENV CONDADIR MSMBINDIR MSMCONFIGDIR R_LIBS FSL_FIX_CIFTIRW FSFAST_HOME SUBJECTS_DIR MINC_BIN_DIR MNI_DIR MINC_LIB_DIR MNI_DATAPATH FSF_OUTPUT_FORMAT
Generated by QuNex
------------------------------------------------------------------------
Version: 0.94.4
User: moana004
System: cn2107
OS: RedHat Linux #1 SMP Tue Jun 28 15:37:28 UTC 2022
------------------------------------------------------------------------
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\██████ / \██████ | ║ ██ | \██ |\███████\██ /\██\
\___███\ \______/ ║ \__| \__| \_______\__/ \__|
\___| ║
DEVELOPED & MAINTAINED BY:
Anticevic Lab, Yale University
Mind & Brain Lab, University of Ljubljana
Murray Lab, Yale University
COPYRIGHT & LICENSE NOTICE:
Use of this software is subject to the terms and conditions defined in
'LICENSES' which is a part of the QuNex Suite source code package:
https://gitlab.qunex.yale.edu/qunex/qunex/-/tree/master/LICENSES
---> Setting up Octave
........................ Running QuNex v0.94.4 ........................
--- Full QuNex call for command: hcp_diffusion
gmri hcp_diffusion --sessionsfolder="/home/moanae/shared/project_FM_Gracely_shared/sessions" --parsessions="1" --batchfile="/home/moanae/shared/project_FM_Gracely_shared/processing/batch_03_struct-fMRI-dwi.txt" --sessions="FM0001"
---------------------------------------------------------
WARNING: Parameter qx_cifti_tail was not specified. Its value was imputed from parameter hcp_cifti_tail and set to '"_Atlas"'!
WARNING: Parameter qx_nifti_tail was not specified. Its value was imputed from parameter hcp_nifti_tail and set to ''!
WARNING: Parameter cifti_tail was not specified. Its value was imputed from parameter qx_cifti_tail and set to '"_Atlas"'!
WARNING: Parameter nifti_tail was not specified. Its value was imputed from parameter qx_nifti_tail and set to ''!
# Generated by QuNex 0.94.4 on 2022-08-12_13.54.16.482820
#
=================================================================
gmri hcp_diffusion \
--sessionsfolder="/home/moanae/shared/project_FM_Gracely_shared/sessions" \
--parsessions="1" \
--sessions="/home/moanae/shared/project_FM_Gracely_shared/processing/batch_03_struct-fMRI-dwi.txt" \
--sessionids="FM0001" \
=================================================================
Starting multiprocessing sessions in /home/moanae/shared/project_FM_Gracely_shared/processing/batch_03_struct-fMRI-dwi.txt with a pool of 1 concurrent processes
---- Running local
Starting processing of sessions FM0001 at Friday, 12. August 2022 13:54:16
Running external command: /opt/HCP/HCPpipelines/DiffusionPreprocessing/DiffPreprocPipeline.sh --path="/home/moanae/shared/project_FM_Gracely_shared/sessions/FM0001/hcp" --subject="FM0001" --PEdir=2 --posData="/home/moanae/shared/project_FM_Gracely_shared/sessions/FM0001/hcp/FM0001/unprocessed/Diffusion/FM0001_DWI_42dirs_AP.nii.gz" --negData="EMPTY" --echospacing="0.00073" --gdcoeffs="NONE" --dof="6" --b0maxbval="50" --combine-data-flag="2" --printcom="" --cuda-version=9.1
You can follow command's progress in:
/home/moanae/shared/project_FM_Gracely_shared/processing/logs/comlogs/tmp_hcp_diffusion_FM0001_2022-08-12_13.54.16.488381.log
------------------------------------------------------------
------------------------------------------------------------
Session id: FM0001
[started on Friday, 12. August 2022 13:54:16]
Running HCP DiffusionPreprocessing Pipeline [LegacyStyleData] ...
---> The following pos direction files were found:
FM0001_DWI_42dirs_AP.nii.gz
---> The following neg direction files were found:
EMPTY
---> Using study general EchoSpacing: 0.00073 ms
------------------------------------------------------------
Running HCP Pipelines command via QuNex:
/opt/HCP/HCPpipelines/DiffusionPreprocessing/DiffPreprocPipeline.sh
--path="/home/moanae/shared/project_FM_Gracely_shared/sessions/FM0001/hcp"
--subject="FM0001"
--PEdir=2
--posData="/home/moanae/shared/project_FM_Gracely_shared/sessions/FM0001/hcp/FM0001/unprocessed/Diffusion/FM0001_DWI_42dirs_AP.nii.gz"
--negData="EMPTY"
--echospacing="0.00073"
--gdcoeffs="NONE"
--dof="6"
--b0maxbval="50"
--combine-data-flag="2"
--printcom=""
--cuda-version=9.1
------------------------------------------------------------
Running HCP Diffusion Preprocessing
---> hcp_diffusion test file missing:
/home/moanae/shared/project_FM_Gracely_shared/sessions/FM0001/hcp/FM0001/T1w/Diffusion/data.nii.gz
Try running the command directly for more detailed error information:
/opt/HCP/HCPpipelines/DiffusionPreprocessing/DiffPreprocPipeline.sh --path="/home/moanae/shared/project_FM_Gracely_shared/sessions/FM0001/hcp" --subject="FM0001" --PEdir=2 --posData="/home/moanae/shared/project_FM_Gracely_shared/sessions/FM0001/hcp/FM0001/unprocessed/Diffusion/FM0001_DWI_42dirs_AP.nii.gz" --negData="EMPTY" --echospacing="0.00073" --gdcoeffs="NONE" --dof="6" --b0maxbval="50" --combine-data-flag="2" --printcom="" --cuda-version=9.1
---> logfile: /home/moanae/shared/project_FM_Gracely_shared/processing/logs/comlogs/error_hcp_diffusion_FM0001_2022-08-12_13.54.16.488381.log
HCP Diffusion Preprocessing completed on Friday, 12. August 2022 14:00:10
------------------------------------------------------------
===> Final report for command hcp_diffusion
... FM0001 ---> hcp_diffusion failed
===> Not all tasks completed fully!
batch_03_struct-fMRI-dwi.txt (42.8 KB)
error_hcp_diffusion_FM0001_2022-08-12_13.54.16.488381.log (22.2 KB)
Sorry, I mislead you there. I was not aware that you do not have a Pos/Neg pair of DWI acquisitions which is required by HCP. This means you will have to use dwi_legacy_gpu. I ran some dwi_legacy_gpu just recently and it worked fine, so we should be able to get this going. If any code fixes will be needed to get to tractography we will do them, no worries.
No problems. I ran “dwi_legacy_gpu” without errors. Now I am trying to run “dwi_bedpostx_gpu” and had an error likely due to wrong path to the “T1w/Diffusion” folder. In my case, it is named “/…/sessions/FM0001/hcp/FM0001/T1w/Diffusion_DWI_dir42_AP”. Is there a way to call “dwi_bedpostx_gpu” and set the diffusion folder name as a parameter? This might be enough to prevent this error. Thank you.
cn2107:~ moana004$ sessions2proc="FM0001"; qunex_container dwi_bedpostx_gpu --sessionsfolder="${study_sharedfolder}/sessions" --sessions="${sessions2proc}" --fibers="3" --weight="1" --burnin="1000" --jumps="1250" --sample="25" --model="2" --rician="yes" --nv --bind="${study_sharedfolder}:/${study_sharedfolder}" --container="${HOME}/qunex/qunex_suite-0.94.4.sif"
--> QuNex will run the command over 1 sessions. It will utilize:
Maximum sessions run in parallel for a job: 1.
Maximum elements run in parallel for a session: 1.
Up to 1 processes will be utilized for a job.
Job #1 will run sessions: FM0001
cn2107:~ moana004$ --> unsetting the following environment variables: PATH MATLABPATH PYTHONPATH QUNEXVer TOOLS QUNEXREPO QUNEXPATH QUNEXLIBRARY QUNEXLIBRARYETC TemplateFolder FSL_FIXDIR FREESURFERDIR FREESURFER_HOME FREESURFER_SCHEDULER FreeSurferSchedulerDIR WORKBENCHDIR DCMNIIDIR DICMNIIDIR MATLABDIR MATLABBINDIR OCTAVEDIR OCTAVEPKGDIR OCTAVEBINDIR RDIR HCPWBDIR AFNIDIR ANTSDIR PYLIBDIR FSLDIR FSLGPUDIR PALMDIR QUNEXMCOMMAND HCPPIPEDIR CARET7DIR GRADUNWARPDIR HCPPIPEDIR_Templates HCPPIPEDIR_Bin HCPPIPEDIR_Config HCPPIPEDIR_PreFS HCPPIPEDIR_FS HCPPIPEDIR_PostFS HCPPIPEDIR_fMRISurf HCPPIPEDIR_fMRIVol HCPPIPEDIR_tfMRI HCPPIPEDIR_dMRI HCPPIPEDIR_dMRITract HCPPIPEDIR_Global HCPPIPEDIR_tfMRIAnalysis HCPCIFTIRWDIR MSMBin HCPPIPEDIR_dMRITractFull HCPPIPEDIR_dMRILegacy AutoPtxFolder FSL_GPU_SCRIPTS FSLGPUBinary EDDYCUDADIR USEOCTAVE QUNEXENV CONDADIR MSMBINDIR MSMCONFIGDIR R_LIBS FSL_FIX_CIFTIRW FSFAST_HOME SUBJECTS_DIR MINC_BIN_DIR MNI_DIR MINC_LIB_DIR MNI_DATAPATH FSF_OUTPUT_FORMAT
Generated by QuNex
------------------------------------------------------------------------
Version: 0.94.4
User: moana004
System: cn2107
OS: RedHat Linux #1 SMP Tue Jun 28 15:37:28 UTC 2022
------------------------------------------------------------------------
██████\ ║ ██\ ██\
██ __██\ ║ ███\ ██ |
██ / ██ |██\ ██\ ║ ████\ ██ | ██████\ ██\ ██\
██ | ██ |██ | ██ | ║ ██ ██\██ |██ __██\\██\ ██ |
██ | ██ |██ | ██ | ║ ██ \████ |████████ |\████ /
██ ██\██ |██ | ██ | ║ ██ |\███ |██ ____|██ ██\
\██████ / \██████ | ║ ██ | \██ |\███████\██ /\██\
\___███\ \______/ ║ \__| \__| \_______\__/ \__|
\___| ║
DEVELOPED & MAINTAINED BY:
Anticevic Lab, Yale University
Mind & Brain Lab, University of Ljubljana
Murray Lab, Yale University
COPYRIGHT & LICENSE NOTICE:
Use of this software is subject to the terms and conditions defined in
'LICENSES' which is a part of the QuNex Suite source code package:
https://gitlab.qunex.yale.edu/qunex/qunex/-/tree/master/LICENSES
---> Setting up Octave
........................ Running QuNex v0.94.4 ........................
--- Full QuNex call for command: dwi_bedpostx_gpu
. /opt/qunex/bash/qx_utilities/dwi_bedpostx_gpu.sh --sessionsfolder='/home/moanae/shared/project_FM_Gracely_TEST_FM0001/sessions' --session='FM0001' --fibers='3' --weight='1' --burnin='1000' --jumps='1250' --sample='25' --model='2' --rician='yes' --gradnonlin='' --overwrite='' --species=''
--------------------------------------------------------------
--------------------------------------------------------------
Running dwi_bedpostx_gpu locally on cn2107
Command log: /home/moanae/shared/project_FM_Gracely_TEST_FM0001/processing/logs/runlogs/Log-dwi_bedpostx_gpu_2022-08-13_16.58.07.464034.log
Command output: /home/moanae/shared/project_FM_Gracely_TEST_FM0001/processing/logs/comlogs/tmp_dwi_bedpostx_gpu_FM0001_2022-08-13_16.58.07.464034.log
--------------------------------------------------------------
------------------------- Start of work --------------------------------
--> Executing qunex.sh dwi_bedpostx_gpu:
Study folder: /home/moanae/shared/project_FM_Gracely_TEST_FM0001
Sessions Folder: /home/moanae/shared/project_FM_Gracely_TEST_FM0001/sessions
Session: FM0001
Number of fibers: 3
ARD weights: 1
Burnin period: 1000
Number of jumps: 1250
Sample every: 25
Model type: 2
Rician flag: yes
Overwrite prior run:
--> Checking if bedpostx was completed on FM0001...
--> Prior bedpostx run not found or incomplete for FM0001. Setting up new run...
--> Generating log folder
--> Not using gradient nonlinearities flag -g
--> Running FSL command:
/opt/qunex/bash/qx_utilities/diffusion_tractography_dense/fsl_gpu/bedpostx_gpu_noscheduler /home/moanae/shared/project_FM_Gracely_TEST_FM0001/sessions/FM0001/hcp/FM0001/T1w/Diffusion/. -n 3 -w 1 -b 1000 -j 1250 -s 25 -model 2 --rician
---------------------------------------------
------------ BedpostX GPU Version -----------
---------------------------------------------
subjectdir is /home/moanae/shared/project_FM_Gracely_TEST_FM0001/sessions/FM0001/hcp/FM0001/T1w/Diffusion/.
subject directory not found
--> Checking outputs...
--> bedpostx run not found or incomplete for FM0001. Something went wrong.
Check output: /home/moanae/shared/project_FM_Gracely_TEST_FM0001/sessions/FM0001/hcp/FM0001/T1w/Diffusion.bedpostX/
ERROR: bedpostx run did not complete successfully
===> ERROR during dwi_bedpostx_gpu. Check final QuNex error log output:
/home/moanae/shared/project_FM_Gracely_TEST_FM0001/processing/logs/comlogs/error_dwi_bedpostx_gpu_FM0001_2022-08-13_16.58.07.464034.log
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Yes, this was expected. I will have to add the ability to define diffdatasuffix for all DWI commands that follow dwi_legacy_gpu. On paper it should not be too much work. I will let you know once it is done and tested here.
Hi, I just have to run some final tests but the functionality to run dwi_legacy_gpu and continue with other DWI calls is almost ready and will be in the next released version.
Great, thanks for the updates.