Dear Doug, Finally, I was able to solve the 3dvolreg.afni error problem. I installed the recent AFNI version for Linux and replaced the 3dvolreg file in Freesurfer/bin by the AFNI 3dvolreg.afni of the AFNI software package. After adding the Suffix .afni (the AFNI-3dvolreg file doesn't end with .afni) the mc-sess runs well.
Best wishes, Christopher -----Ursprüngliche Nachricht----- Von: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Douglas N Greve Gesendet: Freitag, 22. August 2014 18:42 An: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] 3dvolreg.afni error during mc-sess Hmm, that means that 3dvolreg.afni that comes with FS does not run properly on your system. Do you already have a full version of AFNI installed on your system? doug On 08/22/2014 05:00 AM, Milde, Christopher wrote: > Dear Freesurfer Experts, > > I'm struggling with running only motion correction. > After running mktemplate-sess which ran well, the mc-sess terminates > with the following error. > > The terminal otput is attached: > > "3dvolreg.afni: symbol lookup error: 3dvolreg.afni: undefined symbol: > afni_ncerr > ERROR: 3dvolreg.afni" > > Some important comments: > 1.) 3dvolreg.afni is within the bin-folder of Freesurfer > 2.) I use partial-field-of-view EPI > 3.) I run mc-sess und dcm2nii formated DICOM-files (is it a > prerequisite to use unpacksdcmdir)? > > Thank you, for your support!!! > > Greets Christopher > > *TERMINAL OUTPUT:* > > mc-sess -s PM_00031 -d $FSF_DIR -per-run -fstem -outfmt nii.gz > > [christopher@fu20a S1]$ mc-sess -s PM_00923 -d $FSF_DIR -per-run > -fstem 20 -outfmt nii.gz > fmt: Undefinierte Variable. > [christopher@fu20a S1]$ mc-sess -s PM_00923 -d $FSF_DIR -per-run > -fstem 20 Logfile is > /home/christopher/Desktop/freesurfer/subjects/S1/log/mc-PM_00923-bold. > log > ------------------------------------------- > /home/christopher/Desktop/freesurfer/subjects/S1/PM_00923 > RunList: 001 002 004 > ------- ************************** ----------- > ------- Motion Correcting Run 001 ----------- > ------- ************************** ----------- sess = PM_00923 Fr > 22. Aug 09:35:07 CEST 2014 > mc-afni2 --i 001/20.nii.gz --t 001/template.nii.gz --o > 001/fmcpr.nii.gz --mcdat 001/fmcpr.mcdat > /home/christopher/Desktop/freesurfer/subjects/S1/PM_00923/bold > mri_info --nframes --o /tmp/mriinfo.19767 001/template.nii.gz log file > is 001/fmcpr.nii.gz.mclog mcdat file is 001/fmcpr.mcdat tmp dir is > 001/tmp.mc-afni2.19767 #@# -------------------------------- > /home/christopher/Desktop/freesurfer/subjects/S1/PM_00923/bold > mri_convert 001/template.nii.gz 001/tmp.mc-afni2.19767/tempvol.nii.gz > --nskip 0 --ndrop 0 -odt float > mri_convert 001/template.nii.gz 001/tmp.mc-afni2.19767/tempvol.nii.gz > --nskip 0 --ndrop 0 -odt float > nskip = 0 > ndrop = 0 > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > reading from 001/template.nii.gz... > TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras > = (0, -0.218143, 0.975917) k_ras = (0, -0.975917, -0.218143) writing > to 001/tmp.mc-afni2.19767/tempvol.nii.gz... > #@# -------------------------------- > /home/christopher/Desktop/freesurfer/subjects/S1/PM_00923/bold > mri_convert 001/20.nii.gz 001/tmp.mc-afni2.19767/invol.nii.gz -odt > float mri_convert 001/20.nii.gz 001/tmp.mc-afni2.19767/invol.nii.gz > -odt float > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > reading from 001/20.nii.gz... > TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras > = (0, -0.218143, 0.975917) k_ras = (0, -0.975917, -0.218143) writing > to 001/tmp.mc-afni2.19767/invol.nii.gz... > #@# -------------------------------- > /home/christopher/Desktop/freesurfer/subjects/S1/PM_00923/bold > 3dvolreg.afni -verbose -dfile 001/fmcpr.mcdat -1Dmatrix_save > 001/fmcpr.mat -base 001/tmp.mc-afni2.19767/tempvol.nii.gz -prefix > 001/tmp.mc-afni2.19767/outvol.nii.gz > 001/tmp.mc-afni2.19767/invol.nii.gz > 3dvolreg.afni: symbol lookup error: 3dvolreg.afni: undefined symbol: > afni_ncerr > ERROR: 3dvolreg.afni > Ungültiger leerer Befehl. > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. 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