Hi Juergen,
we haven't used 7T for surface recons, just for hires partial brain studies. The dielectric effects are pretty severe, which may be causing your problem. Can you get whole brain 1mm data as well as the hires data? You can use the "conform to min" option (I can't remember what it is - check the help), but you're probably better off acquiring a lower res scan near 1mm isotropic. In any case, surface recons at 7T are something that we haven't really tried. We are waiting for a good solution to the transmit inhomogeneities.
cheers, Bruce On Fri, 25 Jan 2008, Juergen Haenggi wrote:
Dear FS experts
I tried to preprocess two T1-w. scans from a 7T scanner (dimensions 448x448x180; resolution 0.5x0.5x0.8mm) but the Talairch quality check failed.
Fri Jan 25 08:47:06 CET 2008 talairach_avi done \n cp transforms/talairach.auto.xfm transforms/talairach.xfm \n #-------------------------------------------- #@# Talairach Failure Detection Fri Jan 25 08:47:07 CET 2008 /Applications/freesurfer/subjects/RO_reorient/mri \n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.3873, pval=0.0643 >= threshold=0.0050) \n awk -f /Applications/freesurfer/bin/extract_talairach_avi_QA.awk /Applications/freesurfer/subjects/RO_reorient/mri/transforms/talairach_avi.l og \n TalAviQA: 0.92008 z-score: -12 ERROR: Talairach QA check failed! z-score = -12 < -5 = threshold Darwin Macintosh-3.local 9.1.0 Darwin Kernel Version 9.1.0: Wed Oct 31 17:46:22 PDT 2007; root:xnu-1228.0.2~1/RELEASE_I386 i386
recon-all exited with ERRORS at Fri Jan 25 08:47:07 CET 2008
[Macintosh-3:/Applications/freesurfer/subjects] juergenhaenggi%
Do you have any idea why that problem occurred? Does anyone have experience with scans acquired at 7T and FS? Another question is whether we can run FS with a resolution smaller that 1x1x1mm (larger matrix that 288x288x288)?
Thanks in advance Best regards Juergen Haenggi
Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi@psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website)
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