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