I know what was wrong . My run folders are not zero-padded strings! Thank you for the hint!
-----Original Message----- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Tuesday, May 23, 2017 11:46 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FS-FAST (preproc-sess) What was your preproc-sess command and what folder are you running it from? And did you use 3-digit, zero-padded strings as your run folder? On 05/23/2017 09:17 AM, Alshikho, Mohamad J. wrote: > > Hi Doug, > > I want to analyze rsfMRI data using FS-FAST. Kindly, I have question > regarding the command “ preproc-sess / Freesurfer v6” > > In order to begin the analysis, I followed the steps as in FS-FAST > wiki. First, I organized the tree folders for the project as > “study_folder/session_ID/bold/run”. Next, I ran the command > "preproc-sess" as described in wiki. > > Unfortunately, the this command output the following error: “ERORR: no > run directories found” > > I tried to investigate the error by running the command > "getrunlist "study_folder/session_ID/bold" and this failed to see the > runs folders. > > I had to visit the command "getrunlist " to see how it works, and I > found that it depends on the command "find . -maxdepth 1 -name > "[0-9][0-9][0-9]" to build the runs list. I tried to run this command > in the path study_folder/session_ID/bold/ and this command failed to > show any runs folders. I tried "find . -maxdepth 1 " and the output > was ok. I saw the runs folders. Similarly I tried “find . -maxdepth 1 > -type d” and I saw the runs folders as well. > > I am not sure if this is a bug in the command “find”. > > It seems to me that the flags “-name” and “-maxdepth” in command > “find” doesn’t work together, but the flags “-name” and “ -type d” are > ok. > > I am not sure how to handle this or what am doing wrong, so I highly > appreciate any suggestions. > > Best, > > Mohamad > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
