Re: [Freesurfer] registration problems

[Chris Baker]

Hi Doug, We're running on a Red Hat Enterprise 4 (kernel 2.6.9-22) using Freesurfer 3 (downloaded on 3/406) We can give you all the path for the files, but since this is not an MGH server I'm not sure this will be useful to you. Here is the command and the output. tkmedit-sess -sf sessid -df sessdir -analysis localizer_sm5 -contrast avb -map sig -mgz [tashmoo:analysis] (freesurfer-stable) tkmedit-sess -sf sessid -df sessdir -analysis localizer_sm5 -contrast avb -map sig -mgz -------------------------------------------------------------- tkmedit-sess logfile is /space/dilks/filling-in/analysis/log/tkmedit-sess.log -------------------------------------------------------------- setenv SUBJECTS_DIR /space/sharedProjects/subjectsDir INFO: Found session in: /space/dilks/filling-in/data//filling-in001 grep: /space/dilks/filling-in/data//filling-in001/session.info: No such file or directory INFO: Found session in: /space/dilks/filling-in/data//filling-in001 grep: /space/dilks/filling-in/data//filling-in001/session.info: No such file or directory INFO: subject is filling-in001 INFO: subject is filling-in001 INFO: Anatomical directory set to /space/sharedProjects/subjectsDir/filling-in001/mri/orig ------------------------ SUBJECTS_DIR /space/sharedProjects/subjectsDir /space/dilks/filling-in/analysis tkmedit filling-in001 orig.mgz -overlay /space/dilks/filling-in/data/filling-in001/bold/localizer_sm5/avb/sig_000.bfloat -overlay-reg /space/dilks/filling-in/data/filling-in001/bold/register.dat -fthresh 2 -fmid 5 -fslope 1 -aux brain.mgz ------------------------ ----------------------------------------------------------------- Could not find the direction cosine information. Will use the CORONAL orientation. If not suitable, please provide the information in /space/dilks/filling-in/data/filling-in001/bold/localizer_sm5/avb/sig.bhdr file ----------------------------------------------------------------- Reading /space/analysis_tools/freesurfer/freesurfer-2006-03-05/lib/tcl/tkm_common.tcl Reading /space/analysis_tools/freesurfer/freesurfer-2006-03-05/lib/tcl/tkm_wrappers.tcl   Talairach transform /nfs_data2/data/subjects/filling-in001/mri/transforms/talairach.xfm does not exist ... Loading tal xfm file /space/sharedProjects/subjectsDir/filling-in001/mri/transforms/talairach.xfm   Talairach transform /nfs_data2/data/subjects/filling-in001/mri/transforms/talairach.xfm does not exist ... Loading tal xfm file /space/sharedProjects/subjectsDir/filling-in001/mri/transforms/talairach.xfm INFO: bvolumeRead: min = -41.5851, max = 17.3363 Cheers, Chris. On May 3, 2006, at 1:36 PM, Doug Greve wrote: hi chris, We're going to need more info. Please consult surfer.nmr.mgh.harvard.edu/fswiki/BugReporting doug Chris Baker wrote: Hi, I'm trying to register a set of functionals with anatomical data and  am finding that even though the registration looks good when viewed  in tkregister (see snapshot below), when I look at the data in  tkmedit or tksurfer, the alignment is completely off (see second  snapshot). It looks almost as if the size of the functional slab is  being read incorrectly with respect to the anatomicals, although all  the information in register.dat looks OK (see below). Any ideas how to fix this or what the problem is? Could this be a  problem with paint-sess or surf-sess. I'm using versions $Id: paint-sess,v 1.9 2006/01/09 23:44:42 greve Exp $ $Id: surf-sess,v 1.12 2005/08/30 16:56:04 greve Exp $ Thanks for any help, Chris. filling-in001 3.000000 3.300000 0.100000 9.998358e-01 -8.742601e-04 7.647049e-04 8.429348e-01 -6.269891e-04 6.565273e-01 7.541288e-01 4.779076e+01 9.408451e-04 7.537801e-01 -6.573987e-01 2.930424e+01 5.640810e-12 8.807770e-12 -1.513114e-12 1.000000e+00 round _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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