Cameron, If a bad talairach alignment prevents the creation of the surfaces (the files in the subjects surf directory), then just exclude the '--surf orig' flag from the tkregister2 cmd line. Use the 'Compare' button to switch between the template (the blurry image) and your subject. It is a lot more work to do the alignment this way, versus having the subject surface overlap the template, but you can still get the job done.
Nick On Mon, 2007-01-08 at 16:33 -0500, Cameron Ellis wrote: > Hi, > Hopefully this is something simple. When I try to check the talairach > transform for my subjects I type: > > tkregister2 --mgz --s SM1C2_autoreconall --fstal --surf orig > > and then I get this error: > > subject = SM1C2_autoreconall > Reading lh surface orig > MRISread(/space/troy/3/users/retrievalnewest/SM1C2_autoreconall/surf/lh.orig): > could not open file > No such file or directory > /usr/local/freesurfer/stable/bin/tkregister2.bin: could not read surface orig > No such file or directory > > orig.mgz is in the mri folder. why is it looking for lh.orig? Without the > surf tag, tkregister loads the transform fine but I do not get the green > surface outlines to assist with the registration. A more detailed > transcription of the error is pasted below if needed. > Thanks, > Cameron > > [troy:SM1C2_autoreconall] (nmr-std-env) cd .. > [troy:retrievalnewest] (nmr-std-env) pwd > /autofs/space/troy_003/users/retrievalnewest > [troy:retrievalnewest] (nmr-std-env) tkregister2 --mgz --s > SM1C2_autoreconall --fstal --surf orig > > surfname set to orig > INFO: no target volume specified, assuming FreeSurfer orig volume. > target volume orig > movable volume (null) > reg file (null) > LoadVol 1 > $Id: tkregister2.c,v 1.49.2.4 2006/03/27 21:48:16 greve Exp $ > Diagnostic Level -1 > > %Mon Jan 8 14:55:02 2007>>> /usr/local/freesurfer/dev/mni/bin/minctracc > -clobber -debug /tmp/mritotal_2618/src_8_dxyz.mnc > /usr/local/freesurfer/dev/mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc > transforms/talairach.auto.xfm -transformation > /tmp/mritotal_2618/src_8tmp2c.xfm -lsq9 -xcorr -model_mask > /usr/local/freesurfer/dev/mni/bin/../share/mni_autoreg/average_305_8_mask.mnc > -center -2.114464 54.148323 -58.055290 -step 4 4 4 -tol 0.004 -simplex 2 > > talairach.xfm --------------------- > 0.790 -0.163 0.022 8.207; > 0.189 0.845 -0.535 -58.555; > 0.093 0.573 0.939 13.334; > 0.000 0.000 0.000 1.000; > INFO: loading target > /space/troy/3/users/retrievalnewest/SM1C2_autoreconall/mri/orig.mgz > INFO: changing target type to float > Ttarg: -------------------- > -1.000 -0.000 0.000 125.117; > 0.000 -0.000 1.000 -84.596; > -0.000 -1.000 0.000 84.914; > 0.000 0.000 0.000 1.000; > INFO: loading movable /usr/local/freesurfer/stable/average/mni305.cor.mgz > INFO: changing move type to float > Tmov: -------------------- > -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; > mkheaderreg = 0, float2int = 0 > ---- Input registration matrix -------- > 0.790 -0.163 0.022 8.207; > 0.189 0.845 -0.535 -58.555; > 0.093 0.573 0.939 13.334; > 0.000 0.000 0.000 1.000; > subject = SM1C2_autoreconall > Reading lh surface orig > MRISread(/space/troy/3/users/retrievalnewest/SM1C2_autoreconall/surf/lh.orig): > could not open file > No such file or directory > /usr/local/freesurfer/stable/bin/tkregister2.bin: could not read surface orig > No such file or directory > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
