That means that there are no voxels in the final ROI in native functional space. You should check your registration and also see how big your original ROI is.
On 04/15/2016 11:32 PM, Julio Alberto González Torre wrote: > I performed the preprocessing again with -per-run parameter. > Everything ok in that step. > > The, when I run the fcseed-sess command, I've got new errors. > > Segmentation fault > > MRIalloc(0, 1, 1): bad parm > > I have attached the log file. > > 2016-04-15 17:56 GMT+02:00 Raney, Talia L. <tra...@partners.org > <mailto:tra...@partners.org>>: > > Hi Julio, > You're right in that the problem is occurring in a later step. > However, the fmcpr file is created during preprocessing. When you > do the preprocessing step, it doesn't show an error occurring in > the logs(this happened to me too because it said that preproc-sess > was completed but fcseed-sess gave me this error that it could not > determine the fmcpr file). > You're right that you have to use the per-run parameter during > preproc-sess. I think this will fix the problem if everything else > is set up correctly. > Best, > Talia > ________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > [freesurfer-boun...@nmr.mgh.harvard.edu > <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of > Julio Alberto González Torre [al099...@uji.es > <mailto:al099...@uji.es>] > Sent: Friday, April 15, 2016 11:42 AM > To: Freesurfer support list > Subject: Re: [Freesurfer] fcseed-sess ERROR: could not determine > file for .../fmcpr > > 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 > <mailto:tra...@partners.org><mailto:tra...@partners.org > <mailto: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 > > <mailto:freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu > <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> > [freesurfer-boun...@nmr.mgh.harvard.edu > > <mailto:freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu > <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>] on behalf of > Julio Alberto González Torre [al099...@uji.es > <mailto:al099...@uji.es><mailto:al099...@uji.es > <mailto: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 > > <mailto:Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto: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. > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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 -- 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
