Dear HCP experts Hi, I am Qunjun, A PhD student in China.
I got an error when I ran PreFreeSurfer.sh. It came out when the program proceeded to AtlasRegistionToMNI152_FLIRTandFNIRT.sh. ----------------------------------- START: AtlasRegistration to MNI152 Unrecognised option / --------------------------------------- I realized that it maybe due to an needless ‘/’ in script. But after searching the script, I still have no idea about this problem. Anyway, I found a log text in /MNINonLinear/ and I think it would be helpful to fix the problem so I placed it in attachment. Looking forward to your reply Best wishes Qunjun 发送自 Windows 10 版邮件<https://go.microsoft.com/fwlink/?LinkId=550986>应用 _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
/mnt/d/HCPpipelines/HCPpipelines/PreFreeSurfer/scripts/AtlasRegistrationToMNI152_FLIRTandFNIRT.sh --workingdir=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear --t1=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T1w_acpc_dc --t1rest=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T1w_acpc_dc_restore --t1restbrain=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T1w_acpc_dc_restore_brain --t2=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T2w_acpc_dc --t2rest=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T2w_acpc_dc_restore --t2restbrain=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T2w_acpc_dc_restore_brain --ref= --refbrain= --refmask= --ref2mm= --ref2mmmask= --owarp=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/xfms/acpc_dc2standard.nii.gz --oinvwarp=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/xfms/standard2acpc_dc.nii.gz --ot1=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/T1w --ot1rest=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/T1w_restore --ot1restbrain=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/T1w_restore_brain --ot2=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/T2w --ot2rest=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/T2w_restore --ot2restbrain=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/T2w_restore_brain --fnirtconfig= PWD = /mnt/d/HCPpipelines/HCPpipelines/PreFreeSurfer date: Tue Sep 18 23:35:03 DST 2018 /mnt/d/HCPpipelines/HCPpipelines/PreFreeSurfer/scripts/AtlasRegistrationToMNI152_FLIRTandFNIRT.sh --workingdir=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear --t1=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T1w_acpc_dc --t1rest=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T1w_acpc_dc_restore --t1restbrain=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T1w_acpc_dc_restore_brain --t2=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T2w_acpc_dc --t2rest=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T2w_acpc_dc_restore --t2restbrain=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T2w_acpc_dc_restore_brain --ref= --refbrain= --refmask= --ref2mm= --ref2mmmask= --owarp=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/xfms/acpc_dc2standard.nii.gz --oinvwarp=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/xfms/standard2acpc_dc.nii.gz --ot1=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/T1w --ot1rest=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/T1w_restore --ot1restbrain=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/T1w_restore_brain --ot2=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/T2w --ot2rest=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/T2w_restore --ot2restbrain=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/T2w_restore_brain --fnirtconfig= PWD = /mnt/d/HCPpipelines/HCPpipelines date: Wed Sep 19 10:37:36 DST 2018 /mnt/d/HCPpipelines/HCPpipelines/PreFreeSurfer/scripts/AtlasRegistrationToMNI152_FLIRTandFNIRT.sh --workingdir=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear --t1=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T1w_acpc_dc --t1rest=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T1w_acpc_dc_restore --t1restbrain=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T1w_acpc_dc_restore_brain --t2=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T2w_acpc_dc --t2rest=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T2w_acpc_dc_restore --t2restbrain=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T2w_acpc_dc_restore_brain --ref= --refbrain= --refmask= --ref2mm= --ref2mmmask= --owarp=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/xfms/acpc_dc2standard.nii.gz --oinvwarp=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/xfms/standard2acpc_dc.nii.gz --ot1=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/T1w --ot1rest=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/T1w_restore --ot1restbrain=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/T1w_restore_brain --ot2=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/T2w --ot2rest=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/T2w_restore --ot2restbrain=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/T2w_restore_brain PWD = /mnt/d/HCPpipelines/HCPpipelines date: Wed Sep 19 10:40:27 DST 2018 /mnt/d/HCPpipelines/HCPpipelines/PreFreeSurfer/scripts/AtlasRegistrationToMNI152_FLIRTandFNIRT.sh --workingdir=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear --t1=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T1w_acpc_dc --t1rest=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T1w_acpc_dc_restore --t1restbrain=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T1w_acpc_dc_restore_brain --t2=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T2w_acpc_dc --t2rest=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T2w_acpc_dc_restore --t2restbrain=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T2w_acpc_dc_restore_brain --ref= --refbrain= --refmask= --ref2mm= --ref2mmmask= --owarp=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/xfms/acpc_dc2standard.nii.gz --oinvwarp=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/xfms/standard2acpc_dc.nii.gz --ot1=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/T1w --ot1rest=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/T1w_restore --ot1restbrain=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/T1w_restore_brain --ot2=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/T2w --ot2rest=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/T2w_restore --ot2restbrain=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/T2w_restore_brain --fnirtconfig= PWD = /mnt/d/HCPpipelines/HCPpipelines date: Wed Sep 19 10:40:40 DST 2018 /mnt/d/HCPpipelines/HCPpipelines/PreFreeSurfer/scripts/AtlasRegistrationToMNI152_FLIRTandFNIRT.sh --workingdir=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear --t1=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T1w_acpc_dc --t1rest=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T1w_acpc_dc_restore --t1restbrain=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T1w_acpc_dc_restore_brain --t2=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T2w_acpc_dc --t2rest=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T2w_acpc_dc_restore --t2restbrain=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T2w_acpc_dc_restore_brain --ref= --refbrain= --refmask= --ref2mm= --ref2mmmask= --owarp=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/xfms/acpc_dc2standard.nii.gz --oinvwarp=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/xfms/standard2acpc_dc.nii.gz --ot1=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/T1w --ot1rest=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/T1w_restore --ot1restbrain=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/T1w_restore_brain --ot2=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/T2w --ot2rest=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/T2w_restore --ot2restbrain=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/T2w_restore_brain PWD = /mnt/d/HCPpipelines/HCPpipelines date: Wed Sep 19 11:26:31 DST 2018 /mnt/d/HCPpipelines/HCPpipelines/PreFreeSurfer/scripts/AtlasRegistrationToMNI152_FLIRTandFNIRT.sh --workingdir=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear --t1=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T1w_acpc_dc --t1rest=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T1w_acpc_dc_restore --t1restbrain=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T1w_acpc_dc_restore_brain --t2=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T2w_acpc_dc --t2rest=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T2w_acpc_dc_restore --t2restbrain=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T2w_acpc_dc_restore_brain --ref= --refbrain= --refmask= --ref2mm= --ref2mmmask= --owarp=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/xfms/acpc_dc2standard.nii.gz --oinvwarp=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/xfms/standard2acpc_dc.nii.gz --ot1=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/T1w --ot1rest=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/T1w_restore --ot1restbrain=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/T1w_restore_brain --ot2=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/T2w PWD = /mnt/d/HCPpipelines/HCPpipelines date: Wed Sep 19 11:26:49 DST 2018 /mnt/d/HCPpipelines/HCPpipelines/PreFreeSurfer/scripts/AtlasRegistrationToMNI152_FLIRTandFNIRT.sh --workingdir=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear --t1=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T1w_acpc_dc --t1rest=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T1w_acpc_dc_restore --t1restbrain=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T1w_acpc_dc_restore_brain --t2=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T2w_acpc_dc --t2rest=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T2w_acpc_dc_restore --t2restbrain=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T2w_acpc_dc_restore_brain --ref= --refbrain= --refmask= --ref2mm= --ref2mmmask= --owarp=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/xfms/acpc_dc2standard.nii.gz --oinvwarp=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/xfms/standard2acpc_dc.nii.gz --ot1=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/T1w --ot1rest=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/T1w_restore --ot1restbrain=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/T1w_restore_brain PWD = /mnt/d/HCPpipelines/HCPpipelines date: Wed Sep 19 11:27:13 DST 2018 /mnt/d/HCPpipelines/HCPpipelines/PreFreeSurfer/scripts/AtlasRegistrationToMNI152_FLIRTandFNIRT.sh --workingdir=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear --t1=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T1w_acpc_dc --t1rest=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T1w_acpc_dc_restore --t1restbrain=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T1w_acpc_dc_restore_brain --t2=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T2w_acpc_dc --t2rest=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T2w_acpc_dc_restore --t2restbrain=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T2w_acpc_dc_restore_brain --ref= --refbrain= --refmask= --ref2mm= --ref2mmmask= --owarp=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/xfms/acpc_dc2standard.nii.gz --oinvwarp=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/xfms/standard2acpc_dc.nii.gz --ot1=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/T1w --ot1rest=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/T1w_restore --ot1restbrain=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/T1w_restore_brain --ot2=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/T2w PWD = /mnt/d/HCPpipelines/HCPpipelines date: Wed Sep 19 11:27:40 DST 2018 /mnt/d/HCPpipelines/HCPpipelines/PreFreeSurfer/scripts/AtlasRegistrationToMNI152_FLIRTandFNIRT.sh --workingdir=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear --t1=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T1w_acpc_dc --t1rest=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T1w_acpc_dc_restore --t1restbrain=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T1w_acpc_dc_restore_brain --t2=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T2w_acpc_dc --t2rest=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T2w_acpc_dc_restore --t2restbrain=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T2w_acpc_dc_restore_brain --ref= --refbrain= --refmask= --ref2mm= --ref2mmmask= --owarp=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/xfms/acpc_dc2standard.nii.gz --oinvwarp=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/xfms/standard2acpc_dc.nii.gz --ot1=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/T1w --ot1rest=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/T1w_restore --ot1restbrain=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/T1w_restore_brain PWD = /mnt/d/HCPpipelines/HCPpipelines date: Wed Sep 19 11:28:03 DST 2018 /mnt/d/HCPpipelines/HCPpipelines/PreFreeSurfer/scripts/AtlasRegistrationToMNI152_FLIRTandFNIRT.sh --workingdir=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear --t1=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T1w_acpc_dc --t1rest=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T1w_acpc_dc_restore --t1restbrain=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T1w_acpc_dc_restore_brain --t2=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T2w_acpc_dc --t2rest=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T2w_acpc_dc_restore --t2restbrain=/mnt/d/HCPpipelines/lqj_HCP/sub1/T1w/T2w_acpc_dc_restore_brain --ref= --refbrain= --refmask= --ref2mm= --ref2mmmask= --owarp=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/xfms/acpc_dc2standard.nii.gz --oinvwarp=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/xfms/standard2acpc_dc.nii.gz --ot1=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/T1w --ot1rest=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/T1w_restore --ot1restbrain=/mnt/d/HCPpipelines/lqj_HCP/sub1/MNINonLinear/T1w_restore_brain PWD = /mnt/d/HCPpipelines/HCPpipelines date: Wed Sep 19 11:30:34 DST 2018
