This looks wrong: W = TalXFM * Norig * inv(Torig); If RAS = A.vox2ras1 * [i;j;k;1]; (Note: vox2ras = Norig), then just mni305 = TalXFM*A.vox2ras1 * [i;j;k;1]
One way to check is to display the MNI305 and ScannerRAS in the tkmedit control window. Take the RAS from the control window, put it into your formula and see if you the MNI305value. doug On 04/24/2013 12:00 PM, Garikoitz Lerma-Usabiaga wrote: > Hi Doug, > I try to make the question shorter, hopefully you will be able to give > me a hint: > > Do you think this method to cut every subjects hippo-subfield > according to their MNI305 Y coordinate could be accurate? > > (for every voxel in every subfield for every subject, do: ) > > > RAS = A.vox2ras1 * [i;j;k;1]; > > > MNI305 = W * RAS; % W = TalXFM * Norig * inv(Torig); > > > if MNI305(2) < -20 then A.vol(i,j,k) = 0; > > > I find that every subject is cut very differently (the Y plane goes > usually to the head), where do you think could be the error, in the > within subject vox2ras or in the MNI305 transformation? Shouldn't I > use this method at all? > > > many many thanks again, > Gari > > > ---------- Forwarded message ---------- > From: *Garikoitz Lerma-Usabiaga* <gariko...@gmail.com > <mailto:gariko...@gmail.com>> > Date: Sat, Apr 20, 2013 at 2:31 AM > Subject: Conversion > To: Douglas N Greve <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > > > Hi Doug, > sorry to bother you again with a direct message, one of your > colleagues has been helping out but I don't think he got it right and > before posting it publicly I would like to know your opinion. > > *OBJECTIVE*: > I want to cut hippo-subfields with a vertical plane in Y. That plane > is defined by a MNI305 coordinate (Y = -20). > > > *METHOD*: > I created a script in Matlab that reads (per every subject): > > TalXFM = xfm_read('talairach.xfm'); > > ORIG = MRIread('orig.mgz'); > > Norig = ORIG.vox2ras; > > Torig = ORIG.tkrvox2ras; > > W = TalXFM * Norig * inv(Torig); > > And reads every hippo_subfield: > > A = MRIread('posterior_left_CA1.mgz'); > > A.vol=permute(A.vol,[2 1 3]); > > Then I just loop through every voxel to set to zero all voxels one > side of that MNI305 coordinate: > > > RAS = A.vox2ras1 * [i;j;k;1]; > > > MNI305 = W * RAS; > > > if MNI305(2) < -20 then A.vol(i,j,k) = 0; > > Then I permute and write it again (afterwards I can sum the modified > volumes per every subfield). > > > A.vol=permute(A.vol,[2 1 3]); > > > MRIwrite(A, 'new_posterior_left_CA1.mgz'); > > > *PROBLEM*: > the vertical plane is not ok, usually it goes out of the hippocampus > or just touches a bit of it (it should separate the head, so be a > quarter of it). But it is a vertical plane. > > > *QUESTIONS*: > > RAS = A.vox2ras1 * [i;j;k;1]; >> Is this Scanner_RAS or Volume_RAS? > > In any case, it gives wrong results (when I compare to freeview or > tkmedit), is this method of calculating RAS coordinates ok? Is there > any other method? > > MNI305 = W * RAS; >> What RAS coordinate should I use here? The > obtained in the previous step is OK? > > Do you think that these methods are accurate enough to accomplish > what I am trying to do or I should try another approach? > > > > Many many thanks again for your help, I will be happy to make the > results available for everybody if this works (I think this makes the > second Samuel Adams :) ) > br, > Gari > > -- 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 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.
