dear freesurfer team,
i experience trouble to compute the register.dat file when using tkregister2 to import an SPM2 BOLD brain volume f.img together with an 001.mgz structural file. segmentation and flattening worked flawlessly for that 001.mgz file (imported initially from an SPM2 anatomical data). here some examples of my desperate attempts:
tkregister2 --mov ANALYZE/f.img --s fs1 --regheader --noedit --reg register.dat
tkregister2 --mov ANALYZE/f.img --targ ANALYZE/cor.img --s fs1 --regheader --noedit --reg register.dat
tkregister2 --mov ANALYZE/f.img --targ ANALYZE/cfs1/mri/orig/001.mgz --s fs1 --regheader --noedit --reg register.dat
tkregister2 --mov ANALYZE/f.img --targ fs1/mri/orig/001.mgz --s fs1 --regheader --noedit --reg register.dat tkregister2 --mov ANALYZE/f.mat --targ fs1/mri/orig/001.mgz --s fs1 --regheader --noedit --reg register.dat tkregister2 --mov ANALYZE/f.hdr --targ fs1/mri/orig/001.mgz --s fs1 --regheader --noedit --reg register.dat
please, see error messages below. something seems to run wrongly when reading the f.mat file. i use matlab v7.1 with SPM2. the mat file initially was created as compressed mat file (v7 style), but then i converted the f.mat alsoto a v6 style = non-compressed, but no difference. content of the f.mat file is, after doing: 'load f.mat'
mat =
3.7499 -0.0312 0.0122 -128.3677 0.0325 3.6227 -1.2914 -110.0712 -0.0008 0.9686 4.8303 -86.1374 0 0 0 1.0000
==> are there somewhere out there clear instructions how to make SPM2 and freesurfer coexist ?
thanks, bye,
pisti
---------------------------------------------------------------------- error messages:
- 1 ------------------------------------------------------------------ tkregister2 --mov ANALYZE/f.img --s fs1 --regheader --reg register.dat INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume ANALYZE/f.img reg file register.dat LoadVol 1 $Id: tkregister2.c,v 1.49.2.4 2006/03/27 21:48:16 greve Exp $ Diagnostic Level -1 matfile: only read 423 bytes of name (1768711468 specified)
MatlabRead: readHeader returned NULL
WARNING: analyzeRead(): matfile ANALYZE/f.mat exists but could not read ... may not be matlab4 mat file ... proceeding without it. ----------------------------------------------------------------- INFO: could not find ANALYZE/f.mat file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default). INFO: if not valid, please provide the information in ANALYZE/f.mat file ----------------------------------------------------------------- INFO: loading target /data/kodaly/r/pisti/numerals/fMRI_LM_060427/fs1/mri/orig.mgz INFO: changing target type to float Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable ANALYZE/f.img matReadHeader: couldn't allocate 1768711469 bytes for name Cannot allocate memory
- 2 ------------------------------------------------------------------ tkregister2 --mov ANALYZE/f.img --targ fs1/mri/orig/001.mgz --s fs1 --regheader --noedit --reg register.dat target volume fs1/mri/orig/001.mgz movable volume ANALYZE/f.img reg file register.dat LoadVol 0 $Id: tkregister2.c,v 1.49.2.4 2006/03/27 21:48:16 greve Exp $ Diagnostic Level -1 matfile: only read 423 bytes of name (1768711468 specified)
MatlabRead: readHeader returned NULL
WARNING: analyzeRead(): matfile ANALYZE/f.mat exists but could not read ... may not be matlab4 mat file ... proceeding without it. ----------------------------------------------------------------- INFO: could not find ANALYZE/f.mat file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default). INFO: if not valid, please provide the information in ANALYZE/f.mat file ----------------------------------------------------------------- INFO: loading target fs1/mri/orig/001.mgz INFO: target does not conform to COR format, so I'm going to reslice to COR. This will not affect the final registration. Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable ANALYZE/f.img matReadHeader: couldn't allocate 1768711469 bytes for name Cannot allocate memory
- 3 ------------------------------------------------------------------ tkregister2 --mov ANALYZE/f.hdr --targ fs1/mri/orig/001.mgz --s fs1 --regheader --noedit --reg register.dat target volume fs1/mri/orig/001.mgz movable volume ANALYZE/f.hdr reg file register.dat LoadVol 0 $Id: tkregister2.c,v 1.49.2.4 2006/03/27 21:48:16 greve Exp $ Diagnostic Level -1 ERROR: cannot determine type of ANALYZE/f.hdr
- 4 ------------------------------------------------------------------ tkregister2 --mov ANALYZE/f.mat --targ fs1/mri/orig/001.mgz --s fs1 --regheader --noedit --reg register.dat target volume fs1/mri/orig/001.mgz movable volume ANALYZE/f.mat reg file register.dat LoadVol 0 $Id: tkregister2.c,v 1.49.2.4 2006/03/27 21:48:16 greve Exp $ Diagnostic Level -1 matfile: only read 423 bytes of name (1768711468 specified)
MatlabRead: readHeader returned NULL
ImageRead(ANALYZE/f.mat) failed
Segmentation fault
and so on...
----- pisti@bwh.harvard.edu