Hi I am trying to analyze a single subject from the HCP 1200 dataset with 'unprocessed' 3T data using the scripts from HCPpipeline 4.0.1. I am trying to analyze the rsfmri data (after having completed the analysis of Structural data successfully).
When starting the script 'GenericfMRIVolumeProcessingPipelineBatch.sh' script, it goes through motion correction with mcflirt which seems to work fine, but then throws an error when going into the Distortion correction and registration functions.
/home/nielsj/HCPpipelines-4.0.1/global/scripts/TopupPreprocessingAll.sh: line 274: 11102 Segmentation fault (core
dumped) ${FSLDIR}/bin/topup --imain=${WD}/BothPhases --datain=$txtfname --config=${TopupConfig} --out=${WD}/Coefficents
--iout=${WD}/Magnitudes --fout=${WD}/TopupField --dfout=${WD}/WarpField --rbmout=${WD}/MotionMatrix --jacout=${WD}/Jac
obian -v
As far as I could see, everything seems to be configured correctly and files are in their locations, so I am not sure why topup throws this error. Anybody can help with this? Or should I just skip on the fieldmap correction?
Thank you very much!
Niels
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Niels Janssen
Brain Imaging Laboratory
Institute of Biomedical Technologies
Institute of Neurosciences
University of La Laguna
Tenerife, Spain