External Email - Use Caution
The first thing to do is to check your input data to make sure that
something is not really wrong. Eg, a large artifact or unusual anatomy.
On 1/17/19 5:35 AM, Daniel Ferreira wrote:
>
> External Email - Use Caution
>
> 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 <mailto: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 Caution
> >
> > 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 <mailto:DGREVE@mgh.harvard.edu>
> <mailto: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=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 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
> <mailto:email%3Adaniel.ferreira.padi...@ki.se>
> <mailto:daniel.ferreira.padi...@ki.se
> <mailto:daniel.ferreira.padi...@ki.se>>
> <daniel.ferreira.padi...@ki.se
> <mailto:daniel.ferreira.padi...@ki.se>
> <mailto:daniel.ferreira.padi...@ki.se
> <mailto:daniel.ferreira.padi...@ki.se>>>*
> >>
> >> _______________________________________________
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> <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
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> >
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> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> >
> > --
> >
> > *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
> <mailto:daniel.ferreira.padilla@ki.se>
> > <mailto:daniel.ferreira.padilla@ki.se
> <mailto:daniel.ferreira.padilla@ki.se>>/
> >
> >
> > _______________________________________________
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>
>
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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
> <mailto:daniel.ferreira.padilla@ki.se>/
>
>
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_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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