The order of running the pipelines is: PreFreeSurfer —> FreeSurfer —> PostFreeSurfer —> fMRIVolume —> fMRISurface —> ICA+FIX —> MSMAll
PostFreeSurfer —> DiffusionPreprocessing —> BedpostX Peace, Matt. From: <[email protected]<mailto:[email protected]>> on behalf of -- <[email protected]<mailto:[email protected]>> Date: Saturday, April 1, 2017 at 9:24 AM To: hcp-users <[email protected]<mailto:[email protected]>> Subject: [HCP-Users] [fMRIVolumeProcessingPipeline]cannot find eye.dat Dear professors, I tried to run the Pipelines-3.4.0/Examples/Scripts/GenericfMRIVolumeProcessingPipelineBatch.mine.sh (I modified based on HCP course practicals), and I got an error when Pipelines-3.4.0/fMRIVolume/scripts/DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased.sh was running, it said cannot find 100307/T1w/100307/mri/transforms/eye.dat, and actually my data folder has no "100307/T1w/100307" or any file named "eye.dat". The data I used is HCP Course data. Here follows the ERROR info: ############################################################################################## Running FAST segmentation FLIRT pre-alignment Running BBR 0.235096 0.999965 -0.007114 -0.004424 0.000000 0.007161 0.999919 0.010569 0.000000 0.004348 -0.010601 0.999934 0.000000 -1.306487 2.209648 1.469996 1.000000 ERROR: cannot find /home/chenxiayu/Workingdir/Data/HcpData/100307/T1w/100307/mri/transforms/eye.dat set -- --path=/home/chenxiayu/Workingdir/Data/HcpData --subject=100307 --fmriname=tfMRI_EMOTION_LR --fmritcs=/home/chenxiayu/Workingdir/Data/HcpData/100307/unprocessed/3T/tfMRI_EMOTION_LR/100307_3T_tfMRI_EMOTION_LR.nii.gz --fmriscout=/home/chenxiayu/Workingdir/Data/HcpData/100307/unprocessed/3T/tfMRI_EMOTION_LR/100307_3T_tfMRI_EMOTION_LR_SBRef.nii.gz --SEPhaseNeg=/home/chenxiayu/Workingdir/Data/HcpData/100307/unprocessed/3T/tfMRI_EMOTION_LR/100307_3T_SpinEchoFieldMap_LR.nii.gz --SEPhasePos=/home/chenxiayu/Workingdir/Data/HcpData/100307/unprocessed/3T/tfMRI_EMOTION_LR/100307_3T_SpinEchoFieldMap_RL.nii.gz --fmapmag=NONE --fmapphase=NONE --echospacing=0.00058 --echodiff=NONE --unwarpdir=x- --fmrires=2 --dcmethod=TOPUP --gdcoeffs=NONE --topupconfig=/home/chenxiayu/Workingdir/Pipelines-3.4.0/global/config/b02b0.cnf --printcom= ############################################################################################## I wonder why I got this and how to fix it. Thanks in advance, Bai Haohao _______________________________________________ HCP-Users mailing list [email protected]<mailto:[email protected]> http://lists.humanconnectome.org/mailman/listinfo/hcp-users ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
