Hi Fred, sorry for the delay. How are you running tkregister2 to produce a new lta? Is the only difference between the lta files the matrix? Or did the src and dst geometry and/or type change?
doug On 05/02/2013 05:52 AM, Fred Dick wrote: > Hi Doug > > sorry to nudge - any thoughts on lta tweaking? > > cheers, > Fred > > > On 30 Apr 2013, at 16:44, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > >> Hi Fred, >> >> I'll have to defer to Doug on this >> Bruce >> On Tue, 30 Apr 2013, Fred Dick wrote: >> >>> Hi Bruce >>> >>> >>> On 30 Apr 2013, at 13:36, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: >>> >>>> Hi Fred >>>> >>>> I know it's a silly question but are you sure that file exists and is >>>> readable by you? The fact that it's calling GCAread means it's doing the >>>> right thing and support gca files. >>> Totally not a silly question. With tkregister tho it looks like the path to >>> gca is hard coded somewhere (but not in tkregister.tcl). So after finally >>> engaging my brain I realized I could just make a symlink to the path >>> tkregister is looking for (e.g., >>> /usr/local/freesurfer-5.0.0-cent4-64/average/RB_all_2008-03-26.gca) and >>> then it works. >>> >>> So that's great - and then if I use an --ltaout flag, tkregister helpfully >>> writes out the .lta. Which mysteriously is different than the original >>> talairach.lta. >>> >>> Is it the inverse transform with an offset, perhaps? >>> >>> The reason I ask is that it looks like you can tweak non-ideal .lta with >>> tkregister. I think Matt Glasser wrote something related a while back, but >>> not sure. >>> >>> Thanks as always, >>> >>> Fred >>> >>> >>> >>> >>> >>>> You can also extra the mean of the highest prob label (-nth 0) and the >>>> label itself (-nth 1) using mri_convert: >>>> >>>> mri_convert -nth 0 \ >>>> /usr/local/freesurfer-5.0.0-cent4-64/average/RB_all_2008-03-26.gca \ >>>> label_means.mgz >>>> >>>> mri_convert -nth 1 \ >>>> /usr/local/freesurfer-5.0.0-cent4-64/average/RB_all_2008-03-26.gca \ >>>> labels.mgz >>>> >>>> >>>> cheers >>>> Bruce >>>> >>>> >>>> On Tue, 30 Apr 2013, Fred Dick wrote: >>>> >>>>> Hi again >>>>> >>>>> different weighting sorta kinda worked better. It might be a dud brain. >>>>> >>>>> But on this topic - I realized I wasn't quite sure of a couple of things, >>>>> and had some errors pop up with some tkregister2 options. >>>>> >>>>> [btw, running stable 5.2.0 on snow leopard] >>>>> >>>>> 1) I first tried to check the reg to the gca, and got the following error >>>>> message. It looks like maybe this is an old/deprecated option given the >>>>> hard-coded path to the 5.0.0 linux version (I saw a posting from Doug >>>>> from a few years ago on this) >>>>> >>>>> >>>>> ------------------------------------------------------------------------------------------------------------------------------------------ >>>>> [rancate:/Applications/freesurfer/subjects] fred% tkregister2 --check-reg >>>>> --gca dancar >>>>> tkregister_tcl /Applications/freesurfer/tktools/tkregister2.tcl >>>>> INFO: LTA input is not RAS to RAS...converting... >>>>> target volume /Applications/freesurfer/subjects/dancar/mri/T1.mgz >>>>> movable >>>>> volume/usr/local/freesurfer-5.0.0-cent4-64/average/RB_all_2008-03-26.gca >>>>> reg file /tmp/reg.tmp.1367946635.dat >>>>> LoadVol 1 >>>>> ZeroCRAS 0 >>>>> $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ >>>>> Diagnostic Level -1 >>>>> GCAread(/usr/local/freesurfer-5.0.0-cent4-64/average/RB_all_2008-03-26.gca): >>>>> could not open file >>>>> No such file or directory >>>>> ERROR: could not read >>>>> /usr/local/freesurfer-5.0.0-cent4-64/average/RB_all_2008-03-26.gca as 22 >>>>> ------------------------------------------------------------------------------------------------------------------------------------------ >>>>> >>>>> 2) I also tried to load up the gca in tkmedit using the appropriate gui >>>>> option, but nothing happened (no error messages either) >>>>> >>>>> 3) Then tried another trick that Doug suggested a while ago on the >>>>> message boards: >>>>> >>>>> tkregister2 --mov $FREESURFER_HOME/average/RB_all_2008-03-26.gca --targ >>>>> $SUBJECTS_DIR/dancar/mri/brain.mgz --lta-inv >>>>> $SUBJECTS_DIR/dancar/mri/transforms/talairach.lta --check-reg >>>>> >>>>> and got "ERROR: Option --lta-inv unknown" >>>>> >>>>> 4) I finally tried using the talairach.lta as a transform to the fsl >>>>> target, using some old default-processed brains to make sure it was >>>>> correct-ish: >>>>> >>>>> tkregister2 --check-reg --lta transforms/talairach.lta --mov ./T1.mgz >>>>> --fsl-targ >>>>> >>>>> This seemed in the ballpark - except when I looked at bert, who I assumed >>>>> would be canonical, and transform was clearly not correct. (Given Doug's >>>>> earlier command, it seemed like talairach.lta was the inverse transform >>>>> of what I thought it was, e.g., sub => standard). >>>>> >>>>> So I'm slightly stymied. >>>>> >>>>> Thanks tons, >>>>> >>>>> Fred >>>>> >>>>> >>>>> >>>>> >>>>> On 29 Apr 2013, at 15:06, Fred Dick <ubjt...@mail.bbk.ac.uk> wrote: >>>>> >>>>>> Aha, I shall quickly try with the non -w weighting and see what happens. >>>>>> Thanks! >>>>>> On 29 Apr 2013, at 15:05, Bruce Fischl <fis...@nmr.mgh.harvard.edu> >>>>>> wrote: >>>>>> >>>>>>> yes, the -w will create an optimal weighting to maximize gray/white >>>>>>> contrast. The image it generates won't in general be physically >>>>>>> realizable in an real MR acquisition. Not surprising that the tal stuff >>>>>>> fails >>>>>>> On Mon, 29 Apr 2013, Fred Dick wrote: >>>>>>> >>>>>>>> Hi Bruce >>>>>>>> >>>>>>>> I'm using TR=20, flip=30, TE=5 - but possibly irrelevant as also have >>>>>>>> the -w flag on. >>>>>>>> >>>>>>>> I originally thought this was from a bad brainmask, but then generated >>>>>>>> a good one and same thing happening. >>>>>>>> >>>>>>>> >>>>>>>> On 29 Apr 2013, at 14:27, Bruce Fischl <fis...@nmr.mgh.harvard.edu> >>>>>>>> wrote: >>>>>>>> >>>>>>>>> Hi Fred >>>>>>>>> >>>>>>>>> we don't have much experience with this. Which synthesis are you >>>>>>>>> using? You might need to use a different one for the talairaching to >>>>>>>>> more closely match the atlas (maybe a TR=20,TE=2.5,flip=20-30 one) >>>>>>>>> >>>>>>>>> >>>>>>>>> On Mon, 29 Apr 2013, Fred Dick wrote: >>>>>>>>> >>>>>>>>>> Dear all >>>>>>>>>> >>>>>>>>>> I'm having difficulties getting correct Talairach.lta's from >>>>>>>>>> synthetic flash volumes (Bruce, you are probably sorry you ever told >>>>>>>>>> me about this!). Basically the brain is over-scaled (bigger than it >>>>>>>>>> should be), which I think is happening because the contrast is so >>>>>>>>>> good (gm much darker than wm). >>>>>>>>>> >>>>>>>>>> Is there an example of how to use the -flash_parms flag, and what >>>>>>>>>> mri_em_register is expecting in the parameter file? >>>>>>>>>> >>>>>>>>>> Thanks, >>>>>>>>>> >>>>>>>>>> Fred >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>>> Freesurfer mailing list >>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>> >>>>>>>>> The information in this e-mail is intended only for the person to >>>>>>>>> whom it is >>>>>>>>> addressed. If you believe this e-mail was sent to you in error and >>>>>>>>> the e-mail >>>>>>>>> contains patient information, please contact the Partners Compliance >>>>>>>>> HelpLine at >>>>>>>>> http://www.partners.org/complianceline . If the e-mail was sent to >>>>>>>>> you in error >>>>>>>>> but does not contain patient information, please contact the sender >>>>>>>>> and properly >>>>>>>>> dispose of the e-mail. >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>> >>>>> >>>>> >>> >>> >>> > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
