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. <tra...@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-boun...@nmr.mgh.harvard.edu [ > freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Julio Alberto > González Torre [al099...@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! > > _______________________________________________ > 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. > >
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