Sorry, orig.mgz should exist in mri not mri/orig
On 7/10/2022 4:04 PM, Douglas N. Greve wrote:
Does orig.mgz exist in /usr/local/freesurfer/7.2.0/subjects/home/mri/orig? Also be aware that we are phasing out register.dat files in favor or using lta files. Also, the tk tools (tkregister2, tkmedit, tksurfer) are officially depricated. Try using tkregisterfv instead.
On 6/28/2022 4:38 PM, Rachel Wagner wrote:
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Oh thank you, good catch! I am now encountering the issue below:
developer@developer-VirtualBox:~$ tkregister2 --s home --mov updated.mgz --regheader --reg register.dat --surf orig
tkregister_tcl /usr/local/freesurfer/7.2.0/tktools/tkregister2.tcl
surfname set to orig
INFO: no target volume specified, assuming FreeSurfer orig volume.
target volume orig
movable volume updated.mgz
reg file register.dat
LoadVol 1
ZeroCRAS 0
$Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $
Diagnostic Level -1
ERROR: could not find orig as either mgz or COR
/usr/local/freesurfer/7.2.0/subjects/home/mri/orig
Could this be another typo on my part or should I be using a different path?
Thanks again!
Rachel
*From: *Wighton, Paul mailto:PWIGHTON@mgh.harvard.edu *Sent: *June 28, 2022 4:36 PM *To: *freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu *Subject: *Re: [Freesurfer] Command Not Found
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Hi Rachel,
Are you trying to run tkregister2? Looks like you forgot the t at the start of the command.
-Paul
*From:*freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Rachel Wagner rwagne2@uwo.ca *Sent:* Tuesday, June 28, 2022 4:29 PM *To:* freesurfer@nmr.mgh.harvard.edu Freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Command Not Found
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Hello,
Thank you for your help! I am trying to register my spm image and am getting the following error:
developer@developer-VirtualBox:~$ kregister2 --s home --mov updated.mgz --regheader --reg register.dat --surf orig
kregister2: command not found
Is my path not set correctly?
Thanks again,
Rachel Wagner
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
