Transmit Bias Pipeline with QuNex

[Victoria King]

Hello all!

I am trying to run the TransmitBias command in QuNex (https://qunex.readthedocs.io/en/latest/api/gmri/hcp_transmit_bias_individual.html) on a single subject (I plan to run it on several hundred subjects once I get it to run all the way through). Below, please find the command I ran along with the error attached. I would really appreciate some insight on what might be the issue.

qunex_container hcp_transmit_bias_individual \
    --container=${qunex_container} \
    --batchfile=${batch_file} \
    --sessionsfolder=${sessions_folder} \
    --sessions=BI05874_20230525 \
--hcp_transmit_mode="PseudoTransmit" \
--hcp_gmwm_template=/gpfs/gibbs/pi/n3/Studies/PREDICT/sessions/BI05874_20230525/hcp/BI05874_20230525/MNINonLinear/GMWMTemplate.nii.gz \
--hcp_myelin_template=/gpfs/gibbs/pi/n3/Studies/PREDICT/processing/Partial.MyelinMap_GroupCorr_MSMAll.32k_fs_LR.dscalar.nii \
--hcp_group_uncorrected_myelin=/gpfs/gibbs/pi/n3/Studies/PREDICT/sessions/BI05874_20230525/hcp/BI05874_20230525/MNINonLinear/fsaverage_LR32k/BI05874_20230525.MyelinMap_MSMAll.32k_fs_LR.dscalar.nii \
--hcp_pt_reference_value_file="${pt_file}" \
--hcp_matlab_mode="compiled" \
--scheduler=SLURM,time=00-12:00:00,mem-per-cpu=16000,partition=pi_anticevic,account=anticevic,nodes=1,cpus-per-task=1

Best,

Victoria King

[Elam, Jennifer]

Hi Victoria,

I would also post this on the QuNex forum: https://forum.qunex.yale.edu/

 

Best,

Jenn

 

________________________________________

Jennifer Elam, Ph.D.
Scientific Outreach, Human Connectome Project
Washington University School of Medicine
el...@wustl.edu
www.humanconnectome.org

 

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