I know what was wrong . My run folders are not zero-padded strings! Thank you for the hint!
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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
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