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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:
External Email - Use CautionDear 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 https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Daniel+Ferreira%22 Wed, 09 Jan 2019 10:22:05 -0800 https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20190109
External Email - Use CautionDear 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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