Hi Talia. Thanks for the quick answer.

But the preprocessing finished correctly without errors as I can check on all the log files generated in the same project folder. "subjectname" and $SUBJECTS_DIR are correctly placed.

The problem is a later step (STEP 5, http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough), when I try to create FC seeds for an individual.

As long as I can read in previously threads, the problem may be the parameter "-per-session", so now I'm trying to do it with "-per-run" parameter to check if the error remains. But I was unable to find a definitive fix for this error.

2016-04-15 14:09 GMT+02:00 Raney, Talia L. <TRANEY@partners.org>:

Hi Julio,
In the past I received this error because the subject was not preprocessed correctly. Make sure you have a link to the subject's structural recon folder in the resting state folder. In order to do this, you have to create a txt file(in this case it would 02_resting/subjectname) and within that txt file you put the name of the recon directory. After doing this, make sure that the $SUBJECTS_DIR is where the subject's recon folder is or else it won't fully run preprocessing.
Hope this helps!
Best,
Talia
________________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Julio Alberto González Torre [al099821@uji.es]
Sent: Thursday, April 14, 2016 6:42 PM
To: Freesurfer support list
Subject: [Freesurfer] fcseed-sess ERROR: could not determine file for .../fmcpr

Hi Freesurfer users.

I am currently performing the steps of Functional Connectivity Walkthrough. And after resolving the problems in the first steps, specially in the preprocessing command (missing AFNI files), I'm now stuck in the 5th step: Creating the FC seeds for each subject.

In the 4th step I've created the parameters for a region of interest. In this case, cheking the FreeSurferColorLUT.txt, I run this command to create the parameters for Left CA1 of Hippocampus (after the reconstruction, I performed the hippocampal subfields):

fcseed-config -segid 552 -fcname L_CA1.dat -fsd rest -mean -cfg mean.L_CA1.config

In the 5th step, when I run the fcseed-sess command, I obtain this error and I'm unable to figure out why:

fcseed-sess -s con_algon -cfg L_CA1.config

ERROR: could not determine file for /Users/acad1215inv/Desktop/ALBERTO/08_Conectividad/CONECTIVIDAD/02_resting/con_algon/rest/009/fmcpr
stem2fname /Users/acad1215inv/Desktop/ALBERTO/08_Conectividad/CONECTIVIDAD/02_resting/con_algon/rest/009/fmcpr

I've checked the "009" folder and there isn't any file with the name "fmcpr".

Does someone have any idea how could I resolve this?

Thanks!

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