Re: [HCP-Users] FreesurferPipelineBatch

[Glasser, Matthew]

I’d use the latest version. Peace, Matt. From: Peka Savayan <savay...@umn.edu> Date: Saturday, April 4, 2015 at 7:54 AM To: Matt Glasser <glass...@wusm.wustl.edu> Subject: Re: [HCP-Users] FreesurferPipelineBatch Hi, Thank you for your answer. What is the difference between pipeline 3.4.1, pipeline 3.5.0 and pipeline 3.6.0-GEFM? Which one to use? Best, Peka On Sat, Apr 4, 2015 at 7:51 AM, Peka Savayan <savay...@umn.edu> wrote: Thank you. Best, Peka On Fri, Apr 3, 2015 at 11:34 PM, Glasser, Matthew <glass...@wusm.wustl.edu> wrote: I would delete your attempted preprocessing and start over from the raw data.  Then, confirm that FreeSurfer ran successfully and don’t try to run it multiple times on the same data. Peace, Matt. From: Peka Savayan <savay...@umn.edu> Date: Friday, April 3, 2015 at 11:25 PM To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: [HCP-Users] FreesurferPipelineBatch 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 HCP-Users@humanconnectome.org 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.   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 HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users