I think there are instructions somewhere on GitHub, but Tim would know exactly where.
Matt. From: Marc Dubin <[email protected]<mailto:[email protected]>> Date: Wednesday, July 25, 2018 at 9:11 PM To: Matt Glasser <[email protected]<mailto:[email protected]>> Cc: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: [HCP-Users] gradient_unwarp.py error Thanks! Do you know how I would install gradient_unwarp.py ? On 25 Jul 2018, at 21:39, Glasser, Matthew wrote: That error suggests the tool is not installed or not installed correctly so it is available on the path. Peace, Matt. From: <[email protected]<mailto:[email protected]>> on behalf of Marc Dubin <[email protected]<mailto:[email protected]>> Date: Wednesday, July 25, 2018 at 8:37 PM To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: [HCP-Users] gradient_unwarp.py error Hello All, When trying to do the Gradient Distortion Correction in the Pre-Freesurfer stage of the structural preprocessing, I get the following error: /home/mrd9035/projects/Pipelines/global/scripts/GradientDistortionUnwarp.sh: line 89: gradient_unwarp.py: command not found In the code, it says: NB: gradient_unwarp.py must have the filename extensions written out explicitly or it will crash gradient_unwarp.py ${BaseName}_vol1.nii.gz trilinear.nii.gz siemens -g $InputCoeffs -n Which files need to have the filename extensions written? I’m assuming this is the reason the pipeline is crashing at this stage for me. Thanks for any suggestions! Marc _______________________________________________ HCP-Users mailing list [email protected]<mailto:[email protected]> http://lists.humanconnectome.org/mailman/listinfo/hcp-users<https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.humanconnectome.org_mailman_listinfo_hcp-2Dusers&d=DwMFEA&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=C9S_n0bF0p6dJ48M-Lgp1b9KBLxvTD5zOml7nDJ1vZU&m=1_9850qqPCUBU1A_jtOB4R1IeDx8AbVpF1m-Uyqf9rQ&s=-v_5SUEQj97vr1HyUQjPS5oGE7DL9TKROalKYCYdAgs&e=> ________________________________ 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. ________________________________ 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
