Vasudev, Yes, that is very likely to be the problem. In general, if a part of the pipeline fails, it is **very likely** that it will not generate the necessary files for the next step. If you have not been able to successfully run all of the Pre-FreeSurfer pipeline, I would not expect the necessary files to be available in order to run the next major step which is the FreeSurfer pipeline. Tim
On Thu, Mar 17, 2016, at 12:47, Dev vasu wrote: > Dear Sir, > > > After running Prefreesuferpipeline.sh my script does not generate > "acpc_dc2standard" and "acpc_dc_restore" is it because my > PreFreesurferpipeline.sh got terminated in middle, since i could not > do gradient unwarping ?. > > > Thanks > Vasudev > > > On 17 March 2016 at 18:41, Timothy B. Brown <[email protected]> wrote: >> Vasudev, >> >> > I would like to know if the "acpc_dc2standard" and >> > "standard2acpc_dc" atlas was provided by HCP, or whether they are >> > output generated from Freesurfer.sh script, >> >> The file acpc_dc2standard.nii.gz is generated in the >> AtlasRegistrationToMNI152_FLIRTandFNIRT.sh script which is invoked by >> the PreFreeSurferPipeline.sh script. >> It is subsequently used in the PostFreeSurferPipeline.sh script and >> in the GenericfMRIVolumeProcessingPipeline.sh script. >> >> If you search in your pipelines directory for acpc_dc2standard in all files, >> you should see something like: >> >> [HCPpipeline@login01 Pipelines-3.6.0]$ find . -exec grep --with- >> filename "acpc_dc2standard" {} \; >> ./PreFreeSurfer/PreFreeSurferPipeline.sh: -- owarp=${AtlasSpaceFolder}/xfms/acpc_dc2standard.nii.gz \ >> ./PostFreeSurfer/PostFreeSurferPipeline.sh:AtlasTransform="acpc_dc- 2standard" >> ./fMRIVolume/GenericfMRIVolumeProcessingPipeline.sh:AtlasTransform="acp- c_dc2standard" >> [HCPpipeline@login01 Pipelines-3.6.0]$ >> >> The file standard2acpc_dc.nii.gz file is similarly generated in the >> AtlasRegistrationToMNI152_FLIRTandFNIRT.sh script and subsequently >> used in the PostFreeSurferPipeline.sh script. >> >> > also could you please let >> > me know if the "acpc_dc_restore" files which is used as naming >> > convention in Postfreesurfer script are outputs generated by >> > freesurfer.sh ?. >> >> The files named *acpc_dc_restore* are generated and used by the >> PreFreeSurferPipeline.sh script. They are also used as inputs to >> several subsequent pipelines including FreeSurferPipeline.sh, >> PostFreeSurferPipeline.sh, and >> GenericfMRIVolumeProcessingPipeline.sh. >> >> Regards, >> >> Tim >> >> -- >> Timothy B. Brown >> Business & Technology Application Analyst III >> Pipeline Developer (Human Connectome Project) >> tbbrown(at)wustl.edu >> ________________________________________ >> The material in this message is private and may contain Protected >> Healthcare Information (PHI). >> 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. -- Timothy B. Brown Business & Technology Application Analyst III Pipeline Developer (Human Connectome Project) tbbrown(at)wustl.edu ________________________________________ The material in this message is private and may contain Protected Healthcare Information (PHI). 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
