Re: [Freesurfer] Error with Talairach Transform during recon-all

Do you have a subject called "tal_before"?

Janani Dhinakaran wrote:

I also checked without the '--surf orig'. Still not found.

On 8 March 2010 14:22, Janani Dhinakaran <janinthesky@gmail.com mailto:janinthesky@gmail.com> wrote:

Here is how I checked if it was done okay
Looks like it wasn't.

s0964091@CRIC-0012:~$ export SUBJECTS_DIR=~/Desktop/Newdata
s0964091@CRIC-0012:~$ tkregister2 --mgz --s tal_before --fstal
--surf orig
tkregister_tcl /usr/local/freesurfer/lib/tcl/tkregister2.tcl
surfname set to orig
INFO: no target volume specified, assuming FreeSurfer orig volume.
target  volume orig
movable volume (null)
reg file       (null)
LoadVol        1
ZeroCRAS       1
$Id: tkregister2.c,v 1.86.2.12 2009/03/19 22:04:20 greve Exp $
Diagnostic Level -1


WARNING: cannot write to
/home/s0964091/Desktop/Newdata/tal_before/mri/transforms.
You will not be able to save any edits.
Hit Enter to continue:
 ... continuing

regio_read_mincxfm: No such file or directory
ERROR: could not read
/home/s0964091/Desktop/Newdata/tal_before/mri/transforms/talairach.xfm




On 8 March 2010 14:09, Douglas N Greve <greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>> wrote:

    That is a message from the routine that we use to
    automatically check the tal transform. Sometimes it is too
    conservative. You should check the transform manually with
    tkregister2. If it looks ok, then you can run recon-all with
    -notal-check. See
    http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
    for more info.

    doug

    Janani Dhinakaran wrote:

        Any idea what this means and what I can do about it?

        Mon Mar  8 12:46:58 GMT 2010
        talairach_avi done
        #--------------------------------------------
        #@# Talairach Failure Detection Mon Mar  8 12:46:58 GMT 2010
        /home/s0964091/Desktop/Newdata/JS/mri

         talairach_afd -T 0.005 -xfm transforms/talairach.xfm

        ERROR: talairach_afd: Talairach Transform:
        transforms/talairach.xfm ***FAILED*** (p=0.0000,
        pval=0.0000 < threshold=0.0050)
        Linux CRIC-0012 2.6.31-20-generic #57-Ubuntu SMP Mon Feb 8
        09:02:26 UTC 2010 x86_64 GNU/Linux

        recon-all exited with ERRORS at Mon Mar  8 12:46:58 GMT 2010

        Thank you
        Jan
        -- 
        I am the Sun, I know no darkness.
        ------------------------------------------------------------------------

        _______________________________________________
        Freesurfer mailing list
        Freesurfer@nmr.mgh.harvard.edu
        <mailto:Freesurfer@nmr.mgh.harvard.edu>
        https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


    -- 
    Douglas N. Greve, Ph.D.
    MGH-NMR Center
    greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
    Phone Number: 617-724-2358 Fax: 617-726-7422

    Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
    <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
    FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
    <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>




-- 
I am the Sun, I know no darkness.

-- I am the Sun, I know no darkness.