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. >>>> >>> >>> >>> >>> > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
