Dear Human Connectome project experts,
I want to run the 3 FreeSurfer shell scripts. I downloaded the second set of Example data to use as input on which gradient distortion correction has already been performed. The PreFreeSurferPipelineBatch. sh finished successfully(see the attached log file). When I run the second script - FreeSurferPipelineBatch.sh I get a message (see the attached log file) to ‘omit all -i flags’ from the - FreeSurferPipeline. sh script. I follow that instruction but this time the error message is that the file T1w_acpc_dc_restore_1mm.nii.gz is unrecognized (see the attached log file). I use : freesurfer-hpc, fsl2.18 in the environment. Both pipelines: 3.5.0 and 3.6.0-GEFM give the same error. Can you please give me advice how to continue with the analysis? Thank you. Best, Peka _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
PreFreeSurferPipeline.sh.o22883
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FreeSurferPipeline.sh.o6767
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FreeSurferPipeline.sh.o7381
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