Dear Tim, I got it. Thank you for detailed explanation.
Best, Mahmoud On Fri, Dec 18, 2015 at 11:29 AM, Timothy B. Brown <tbbr...@wustl.edu> wrote: > 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 > HCP-Users@humanconnectome.org > 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 HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
