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Hi Greve,

Thanks for your quick reply. 

I mean that tkregister2 loads the target volume (I think the original T1 it is) but it does not load the moveable volume as stated in  https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach_freeview: "You will see the subject's volume as the TARGET volume and your Talairach volume as a fuzzy MOVEABLE volume ...".

Below you will find the terminal output from tkregister2. Thanks in advance.

>>

tkregister2 --mgz --s 0e63e2e7-d1e1-4e78-9106-150994a32c44 --fstal
tkregister_tcl /usr/local/freesurfer-6.0.0/tktools/tkregister2.tcl
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 1.132.2.1 2016/08/02 21:17:29 greve Exp $
Diagnostic Level -1

%Tue Dec 11 11:32:27 2018>>> /usr/local/freesurfer-6.0.0/mni/bin/minctracc -clobber -debug /tmp/5039.1.all.q/mritotal_2474//src_8_dxyz.mnc /usr/local/freesurfer-6.0.0/mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc transforms/talairach.auto.xfm -transformation /tmp/5039.1.all.q/mritotal_2474//src_8tmp2c.xfm -lsq9 -xcorr -model_mask /usr/local/freesurfer-6.0.0/mni/bin/../share/mni_autoreg/average_305_8_mask.mnc -center -3.237066 24.478743 -30.435196 -step 4 4 4 -tol 0.004 -simplex 2

talairach.xfm ---------------------
 0.58327   0.88352  -0.65294  -43.57153;
-1.09786   0.44137  -0.38347  -72.94266;
-0.04069   0.75613   0.98680   212.60657;
 0.00000   0.00000   0.00000   1.00000;
INFO: loading target /home/daniel/FreeSurfer/0e63e2e7-d1e1-4e78-9106-150994a32c44/mri/orig.mgz
Zeroing CRAS of target
new xfm -----------------
 0.58327   0.88352  -0.65294  -25.73127;
-1.09786   0.44137  -0.38347  -65.12145;
-0.04069   0.75613   0.98680   228.56956;
 0.00000   0.00000   0.00000   1.00000;
---------------------
INFO: changing target type to float
Ttarg: --------------------
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
INFO: loading movable /usr/local/freesurfer-6.0.0/average/mni305.cor.mgz
INFO: changing move type to float
Tmov: --------------------
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
mkheaderreg = 0, float2int = 0
---- Input registration matrix --------
 0.58327   0.88352  -0.65294  -25.73127;
-1.09786   0.44137  -0.38347  -65.12145;
-0.04069   0.75613   0.98680   228.56956;
 0.00000   0.00000   0.00000   1.00000;
Determinant 1.92442
subject = 0e63e2e7-d1e1-4e78-9106-150994a32c44
Zoom Factor = 2, SQR() = 4
FOV = 256
Opening window 0e63e2e7-d1e1-4e78-9106-150994a32c44
Opening 0e63e2e7-d1e1-4e78-9106-150994a32c44, xnum = 256, xdim = 512
Setting scale
tkregister2: interface: /usr/local/freesurfer-6.0.0/tktools/tkregister2.tcl
tkregister.tcl: startup done
tkregister.tcl: default macro interface (to change: macro,mini,micro)
tkregister.tcl: or: setenv tkregisterinterface {macro,mini,micro}
% ------------------------------------------------------------
  Screen:  249 340 (28,28,28), inorm = 1, mov_frame = 0 
  Anat:    (124  85 127)   (   4.0   -1.0   43.0)   32.0000    27.7
  Func:    (180 -142  42)   ( -52.4  -86.4  270.1)  OutOfBounds
--------------------------------------------------------------





El mié., 16 ene. 2019 a las 15:35, Greve, Douglas N.,Ph.D. (<DGREVE@mgh.harvard.edu>) escribió:
What do you mean that the tal volume does not load as a mov volume? Can you send the terminal output from tkregister2?

On 1/16/19 10:01 AM, Daniel Ferreira wrote:

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Dear Bruce, Martin, and experts,


I posted an issue a few days ago. I have been looking through the archives but can not figure out the solution myself. I was wondering if you would have any suggestion on how to fix the issue described further down?

Thank you very much in advance

Dani

----

Daniel Ferreira Wed, 09 Jan 2019 10:22:05 -0800

        External Email - Use Caution        

Dear experts,
I am processing some data and one of my cases failed. I checked the
recon-all.log and found the following:


*#@# Talairach Failure Detection tis 11 dec 2018 11:32:31 CET*
*/home/daniel/FreeSurfer/0e63e2e7-d1e1-4e78-9106-150994a32c44/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)*

*Manual Talairach alignment may be necessary, or*
*include the -notal-check flag to skip this test,*
*making sure the -notal-check flag follows -all*
*or -autorecon1 in the command string.*
*See:*

*http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
<http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach>*

*ERROR: Talairach failed!*

*Linux siv 4.4.0-140-generic #166-Ubuntu SMP Wed Nov 14 20:09:47 UTC 2018
x86_64 x86_64 x86_64 GNU/Linux*

*recon-all -s 0e63e2e7-d1e1-4e78-9106-150994a32c44 exited with ERRORS at
tis 11 dec 2018 11:32:31 CET*



Next, I tried to fix the issue by using tkregister:
 tkregister2 --mgz --s tal_before --fstal

However, the Talairach volume does not load as a MOVEABLE volume.

When I check the available recon-all output I only have:

orig/001 --> looks good
rawavg --> looks good
orig --> its awful (it looks like millions of white tiny voxels on a black
background)
nu --> it is empty
transforms/talairach.xfm --> is available

I was wondering if you would know about any way to fix this?

Thank you in advance,

Dani

-- 

*Daniel Ferreira, PhD, Assistant Professor*

Division of Clinical Geriatrics; Department of Neurobiology, Care Sciences
and Society

Karolinska Institutet (Sweden)

*Address: **Blickagången 16, 141 52 Huddinge | phone: +46 720128047 |
email: daniel.ferreira.padi...@ki.se <daniel.ferreira.padi...@ki.se>*

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--

Daniel Ferreira, PhD, Assistant Professor

Division of Clinical Geriatrics; Department of Neurobiology, Care Sciences and Society

Karolinska Institutet (Sweden)

Address: Blickagången 16, 141 52 Huddinge | phone: +46 720128047 | email: daniel.ferreira.padilla@ki.se