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. (< dgr...@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 <daniel.ferreira.padi...@ki.se>* > > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > 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.padi...@ki.se <daniel.ferreira.padi...@ki.se>*
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