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 (dgreve@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