Hi Mahmoud, Short answer:
Because of directory structure conventions and file naming conventions used in the pipeline scripts, you cannot rename the subject directory and expect that the pipelines will run without (at least) also renaming a number of other files in the subject directory. So renaming the subject directory will break quite a number of things. Long answer: The FreeSurferPipeline in particular and the other pipeline scripts in general depend upon a directory structure for the data that has a root *study* folder in which each subdirectory of that *study* folder is named for the subject id. So if the data you are processing are in a directory named my_study, and you had only two subjects with subject ids xyz and abc, then you would need to have xyz and abc subdirectories in your my_study directory. Seems like you've got that all set up correctly initially. But...the pipeline scripts also depend upon file naming conventions that use the subject id in the file names. For example, if the subject subdirectory is named xyz, then a number of files in that directory tree will be expected to be named starting with xyz. For example, there is an expectation that there will be a file named my_study/xyz/unprocessed/3T/T1_MPR1/xyz_3T_T1w_MPR1.nii.gz. Notice that the two places the subject id is used have to match. Similarly, many of the pipelines will generate output files that are used by subsequent pipelines using a naming convention in which the names of the generated files will start with the subject id. So, I suspect that this is the problem you are encountering. When you run FreeSurferPipeLineBatch and tell it to process subject xyz_1, the FreeSurferPipeline script is expecting to find a number of input files with names that start with xyz_1. But they're not there because your xyz_1 directory is just a copy of the original xyz directory. So many of the files in it start with simply xyz. Hope that helps, Tim On Fri, Dec 18, 2015, at 07:55, Mahmoud wrote: > Dear experts, > > After running the PreFreeSurferPipelineBatch for subjectID = xyz I > changed the ID (i.e. renamed the subject directory name) to xyz_1 and > ran the FreeSurferPipeLineBatch which ended up with this error in the > error log file (I just copied the few last lines): > > measuring cortical thickness... writing cortical thickness estimate to > 'thickness' file. positioning took 5.6 minutes Error: no output > filename specified! > > Is this because of that name change? if so, is there any > solution to it ? > > Thank you! Mahmoud > _______________________________________________ > HCP-Users mailing list > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users -- 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
