Good afternoon,
We are trying to use Freesurfer to work out NifTi images are on using recon script run into this error message below. . It doesn't seem to move past motion correction in the run. Any input will be greatly appreciated! Adam [mcarlsonspronew:/] m_carlson% recon-all -i $SUBJECTS_DIR/23/Follow-UpIII/MPRAGE/fMPragecorSENSE.nii -subjid 23test22 -all Subject Stamp: freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 Current Stamp: freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/data/test Actual FREESURFER_HOME /Applications/freesurfer Darwin mcarlsonspronew.sph.ad.jhsph.edu 13.2.0 Darwin Kernel Version 13.2.0: Thu Apr 17 23:03:13 PDT 2014; root:xnu-2422.100.13~1/RELEASE_X86_64 x86_64 /Applications/freesurfer/data/test/23test22 \n mri_convert /Applications/freesurfer/data/test/23/Follow-UpIII/MPRAGE/fMPragecorSENSE.nii /Applications/freesurfer/data/test/23test22/mri/orig/001.mgz \n mri_convert /Applications/freesurfer/data/test/23/Follow-UpIII/MPRAGE/fMPragecorSENSE.nii /Applications/freesurfer/data/test/23test22/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /Applications/freesurfer/data/test/23/Follow-UpIII/MPRAGE/fMPragecorSENSE.nii... TR=8.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998364, 0, 0.0571858) j_ras = (0.0555427, -0.237979, 0.969681) k_ras = (-0.0136096, -0.97127, -0.23759) writing to /Applications/freesurfer/data/test/23test22/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Tue Apr 21 15:35:44 EDT 2015 Found 1 runs /Applications/freesurfer/data/test/23test22/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. \n cp /Applications/freesurfer/data/test/23test22/mri/orig/001.mgz /Applications/freesurfer/data/test/23test22/mri/rawavg.mgz \n /Applications/freesurfer/data/test/23test22 \n mri_convert /Applications/freesurfer/data/test/23test22/mri/rawavg.mgz /Applications/freesurfer/data/test/23test22/mri/orig.mgz --conform \n mri_convert /Applications/freesurfer/data/test/23test22/mri/rawavg.mgz /Applications/freesurfer/data/test/23test22/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /Applications/freesurfer/data/test/23test22/mri/rawavg.mgz... TR=8.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998364, 0, 0.0571858) j_ras = (0.0555427, -0.237979, 0.969681) k_ras = (-0.0136096, -0.97127, -0.23759) Original Data has (1, 1, 1) mm size and (256, 256, 200) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /Applications/freesurfer/data/test/23test22/mri/orig.mgz... \n mri_add_xform_to_header -c /Applications/freesurfer/data/test/23test22/mri/transforms/talairach.xfm /Applications/freesurfer/data/test/23test22/mri/orig.mgz /Applications/freesurfer/data/test/23test22/mri/orig.mgz \n INFO: extension is mgz #-------------------------------------------- #@# Talairach Tue Apr 21 15:35:55 EDT 2015 /Applications/freesurfer/data/test/23test22/mri \n mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz \n Darwin mcarlsonspronew.sph.ad.jhsph.edu 13.2.0 Darwin Kernel Version 13.2.0: Thu Apr 17 23:03:13 PDT 2014; root:xnu-2422.100.13~1/RELEASE_X86_64 x86_64 recon-all -s 23test22 exited with ERRORS at Tue Apr 21 15:35:58 EDT 2015 For more details, see the log file /Applications/freesurfer/data/test/23test22/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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