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