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.