External Email - Use Caution
It looks like your terminal/character settings are
messed up in the current terminal session. That can happen from trying
to look at a raw binary or image file in the terminal window or running
something that outputs non-standard
characters to the terminal (stdout). I would open a new terminal
window, source the freesurfer setup script, and try to identify if something
you run corrupts the display of text in the new terminal window.
- R.
On 10/26/22 10:21, Douglas N. Greve (dgr...@mgh.harvard.edu) wrote:
What is the error? The funny characters? Can you just send the
entire logs (recon-all and avi.log)?
On 10/25/2022 11:49 AM, Jonany, Vincent
Joe wrote:
External Email - Use
Caution
Dear FreeSurfer
Developers,
I am encountering a weird error in performing recon-all in
my dicom directory. I believe the problem is here (snippet
copied from talairach_avi.log. I have also attached here the
recon-all.log, as well as the talaraich_avi.log. Does anyone
know or have seen this problem before? I will appreciate any
kind of help, please let me know if I need to provide
anything else.
FreeSurfer version:
freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
Platform: MacOS Monterey (apple silicon)
$Id: imgreg_4dfp.c,v 1.4 2010/02/27 01:41:53 nicks Exp $
/Applications/freesurfer/6/average/3T18yoSchwartzReactN32_as_orig.4dfp.img
256 256 256 1
1.000000 1.000000 1.000000
orientation T byte_order littleendian
Reading image:
/Applications/freesurfer/6/average/3T18yoSchwartzReactN32_as_orig.4dfp.img
dimensions: 256 256 256
mmppix: 1.0000 -1.0000 -1.0000
center: 128.0000 -129.0000 -129.0000
talsrcimg_g11.4dfp.img
256 256 256 1
1.000000 1.000000 1.000000
orientation T byte_order littleendian
Reading image: talsrcimg_g11.4dfp.img
dimensions: 256 256 256
mmppix: 1.0000 -1.0000 -1.0000
center: 128.0000 -129.0000 -129.0000
t4_read:
talsrcimg_to_3T18yoSchwartzReactN32_as_orig_t4pupuÀþN
èEÑ�àÔ�àÔ7SÎ0°þN
#Öô>ÖxþN
°þN
�þN
SÎðþN
þN
Ñ@
àþN
�
Ñ read error
t4_read: transform initialized to I4
rotation matrix determinant 1.000000
Thank you in advance! I appreciate any help!
Best,
Vincent
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