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. 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