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>: > 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 [ > freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Julio Alberto > González Torre [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>>: > 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> [ > 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: 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> > 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 > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >
-------- freesurfer-Darwin-lion-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Users/acad1215inv/Desktop/ALBERTO/03_FreeSurfer_EM MNI_DIR /Applications/freesurfer/mni FSL_DIR /usr/local/fsl - Logfile is /Users/acad1215inv/Desktop/ALBERTO/08_Conectividad/CONECTIVIDAD/02_resting/log/fcseed-sess.L_CA1.dat.log.con_algon sábado, 16 de abril de 2016, 05:22:55 CEST Darwin acad1215inv.uji.es 14.5.0 Darwin Kernel Version 14.5.0: Wed Jul 29 02:26:53 PDT 2015; root:xnu-2782.40.9~1/RELEASE_X86_64 x86_64 setenv SUBJECTS_DIR /Users/acad1215inv/Desktop/ALBERTO/03_FreeSurfer_EM cd /Users/acad1215inv/Desktop/ALBERTO/08_Conectividad/CONECTIVIDAD/02_resting /Applications/freesurfer/fsfast/bin/fcseed-sess -s con_algon -cfg mean.L_CA1.config freesurfer-Darwin-lion-stable-pub-v5.3.0 sábado, 16 de abril de 2016, 05:22:55 CEST Darwin acad1215inv.uji.es 14.5.0 Darwin Kernel Version 14.5.0: Wed Jul 29 02:26:53 PDT 2015; root:xnu-2782.40.9~1/RELEASE_X86_64 x86_64 setenv SUBJECTS_DIR /Users/acad1215inv/Desktop/ALBERTO/03_FreeSurfer_EM cd /Users/acad1215inv/Desktop/ALBERTO/08_Conectividad/CONECTIVIDAD/02_resting /Applications/freesurfer/fsfast/bin/fcseed-sess -s con_algon -cfg mean.L_CA1.config freesurfer-Darwin-lion-stable-pub-v5.3.0 mri_label2vol --seg /Users/acad1215inv/Desktop/ALBERTO/03_FreeSurfer_EM/con_algon/mri/aparc+aseg.mgz --reg /Users/acad1215inv/Desktop/ALBERTO/08_Conectividad/CONECTIVIDAD/02_resting/con_algon/rest/009/register.dof6.dat --temp /Users/acad1215inv/Desktop/ALBERTO/08_Conectividad/CONECTIVIDAD/02_resting/con_algon/rest/009/template.nii.gz --fillthresh .5 --o /Users/acad1215inv/Desktop/ALBERTO/08_Conectividad/CONECTIVIDAD/02_resting/con_algon/rest/009/tmp.fcseed-sess.89262/seg.nii.gz --pvf /Users/acad1215inv/Desktop/ALBERTO/08_Conectividad/CONECTIVIDAD/02_resting/con_algon/rest/009/tmp.fcseed-sess.89262/pvf.nii.gz PVF /Users/acad1215inv/Desktop/ALBERTO/08_Conectividad/CONECTIVIDAD/02_resting/con_algon/rest/009/tmp.fcseed-sess.89262/pvf.nii.gz Number of labels: 0 Annot File: (null) Template Volume: /Users/acad1215inv/Desktop/ALBERTO/08_Conectividad/CONECTIVIDAD/02_resting/con_algon/rest/009/template.nii.gz Outut Volume: /Users/acad1215inv/Desktop/ALBERTO/08_Conectividad/CONECTIVIDAD/02_resting/con_algon/rest/009/tmp.fcseed-sess.89262/seg.nii.gz Registration File: /Users/acad1215inv/Desktop/ALBERTO/08_Conectividad/CONECTIVIDAD/02_resting/con_algon/rest/009/register.dof6.dat Fill Threshold: 0.5 Label Vox Vol: 1 ProjType: (null) ProjTypeId: 0 ProjStart: 0 ProjStop: 0 ProjDelta: 0.1 Subject: (null) Hemi: (null) UseNewASeg2Vol: 1 DoLabelStatVol 0 LabelCodeOffset 0 setenv SUBJECTS_DIR /Users/acad1215inv/Desktop/ALBERTO/03_FreeSurfer_EM $Id: mri_label2vol.c,v 1.34.2.5 2012/06/08 17:31:03 greve Exp $ Template RAS-to-Vox: -------- -0.286 0.000 0.000 32.000; -0.000 -0.000 -0.286 32.000; -0.000 0.248 -0.000 15.000; 0.000 0.000 0.000 1.000; Template Voxel Volume: 49.3063 nHits Thresh: 24.6531 Loading registration from /Users/acad1215inv/Desktop/ALBERTO/08_Conectividad/CONECTIVIDAD/02_resting/con_algon/rest/009/register.dof6.dat RegMat: -------- 0.999 -0.051 0.001 0.800; -0.005 -0.073 0.997 -38.876; 0.051 0.996 0.073 4.977; 0.000 0.000 0.000 1.000; Label RAS-to-Vox: -------- -0.285 0.015 -0.000 31.771; -0.015 -0.285 -0.021 30.578; -0.001 -0.018 0.248 5.341; 0.000 0.000 0.000 1.000; ASeg2Vol: Building LUT ASeg2Vol: Sorting ASeg2Vol: Mapping ASeg2Vol: Reverse Map nmisses = 0 (0 filled) ASeg2Vol: done PVF /Users/acad1215inv/Desktop/ALBERTO/08_Conectividad/CONECTIVIDAD/02_resting/con_algon/rest/009/tmp.fcseed-sess.89262/pvf.nii.gz Computing PVF 49.3063 mri_binarize --i /Users/acad1215inv/Desktop/ALBERTO/08_Conectividad/CONECTIVIDAD/02_resting/con_algon/rest/009/tmp.fcseed-sess.89262/seg.nii.gz --o /Users/acad1215inv/Desktop/ALBERTO/08_Conectividad/CONECTIVIDAD/02_resting/con_algon/rest/009/tmp.fcseed-sess.89262/mask.nii.gz --match 552 $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /Users/acad1215inv/Desktop/ALBERTO/08_Conectividad/CONECTIVIDAD/02_resting cmdline mri_binarize --i /Users/acad1215inv/Desktop/ALBERTO/08_Conectividad/CONECTIVIDAD/02_resting/con_algon/rest/009/tmp.fcseed-sess.89262/seg.nii.gz --o /Users/acad1215inv/Desktop/ALBERTO/08_Conectividad/CONECTIVIDAD/02_resting/con_algon/rest/009/tmp.fcseed-sess.89262/mask.nii.gz --match 552 sysname Darwin hostname acad1215inv.uji.es machine x86_64 user acad1215inv input /Users/acad1215inv/Desktop/ALBERTO/08_Conectividad/CONECTIVIDAD/02_resting/con_algon/rest/009/tmp.fcseed-sess.89262/seg.nii.gz frame 0 nErode3d 0 nErode2d 0 output /Users/acad1215inv/Desktop/ALBERTO/08_Conectividad/CONECTIVIDAD/02_resting/con_algon/rest/009/tmp.fcseed-sess.89262/mask.nii.gz Binarizing based on matching values nMatch 1 0 552 binval 1 binvalnot 0 Found 0 values in range Counting number of voxels Found 0 voxels in final mask mri_binarize done mri_segstats --i /Users/acad1215inv/Desktop/ALBERTO/08_Conectividad/CONECTIVIDAD/02_resting/con_algon/rest/009/fmcpr.nii.gz --seg /Users/acad1215inv/Desktop/ALBERTO/08_Conectividad/CONECTIVIDAD/02_resting/con_algon/rest/009/tmp.fcseed-sess.89262/mask.nii.gz --id 1 --sum /Users/acad1215inv/Desktop/ALBERTO/08_Conectividad/CONECTIVIDAD/02_resting/con_algon/rest/009/tmp.fcseed-sess.89262/junk.sum --avgwfvol /Users/acad1215inv/Desktop/ALBERTO/08_Conectividad/CONECTIVIDAD/02_resting/con_algon/rest/009/tmp.fcseed-sess.89262/avgwf.mgh $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --i /Users/acad1215inv/Desktop/ALBERTO/08_Conectividad/CONECTIVIDAD/02_resting/con_algon/rest/009/fmcpr.nii.gz --seg /Users/acad1215inv/Desktop/ALBERTO/08_Conectividad/CONECTIVIDAD/02_resting/con_algon/rest/009/tmp.fcseed-sess.89262/mask.nii.gz --id 1 --sum /Users/acad1215inv/Desktop/ALBERTO/08_Conectividad/CONECTIVIDAD/02_resting/con_algon/rest/009/tmp.fcseed-sess.89262/junk.sum --avgwfvol /Users/acad1215inv/Desktop/ALBERTO/08_Conectividad/CONECTIVIDAD/02_resting/con_algon/rest/009/tmp.fcseed-sess.89262/avgwf.mgh sysname Darwin hostname acad1215inv.uji.es machine x86_64 user acad1215inv UseRobust 0 Loading /Users/acad1215inv/Desktop/ALBERTO/08_Conectividad/CONECTIVIDAD/02_resting/con_algon/rest/009/tmp.fcseed-sess.89262/mask.nii.gz Loading /Users/acad1215inv/Desktop/ALBERTO/08_Conectividad/CONECTIVIDAD/02_resting/con_algon/rest/009/fmcpr.nii.gz Voxel Volume is 49.3063 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 0 0.000 MRIalloc(0, 1, 1): bad parm Reporting on 0 segmentations Computing spatial average of each frame Writing to /Users/acad1215inv/Desktop/ALBERTO/08_Conectividad/CONECTIVIDAD/02_resting/con_algon/rest/009/tmp.fcseed-sess.89262/avgwf.mgh Segmentation fault
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