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Thanks Greve. Yes, I mean that the moveable is completely black. How should I continue from here? If the registration is so far off that it is out of the field of view, what should I do next?
Thanks
Dani
El mié., 16 ene. 2019 a las 22:54, Greve, Douglas N.,Ph.D. (< DGREVE@mgh.harvard.edu>) escribió:
when you say it does not load, do you mean that the moveable is blank/black? The terminal output indicates that it is being loaded. It is probably the case that the registration is so far off that it is out of the field of view
On 1/16/19 11:30 AM, Daniel Ferreira wrote:
External Email - Use CautionHi 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 mailto: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 Caution 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 <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=f...
Wed, 09 Jan 2019 10:22:05 -0800 <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=d...
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 20:09:47UTC 2018
x86_64 x86_64 x86_64 GNU/Linux* *recon-all -s 0e63e2e7-d1e1-4e78-9106-150994a32c44 exited withERRORS 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 ona 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, CareSciences
and Society Karolinska Institutet (Sweden) *Address: **Blickagången 16, 141 52 Huddinge | phone: +46 720128047|
email:daniel.ferreira.padi...@ki.se <mailto:daniel.ferreira.padi...@ki.se> <daniel.ferreira.padi...@ki.se mailto: 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)
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