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:

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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