Dear Avi, thank you for your reply, probably I didn't make my point clear enough. Our high resolution quantitative T1-maps (derived from multispectral FLASH) have excellent GM-WM contrast and once autorecon1 (talairach-avi) gets over this tricky coregistration into standard space all other following steps look very fine (including the subcortical segmentation which I'm interested in). Since registration is often more robust when images are approximately realigned from the beginning, I thought to use SPM (or fsl) affine coregistration parameters (to MNI space) as a guess in talairach_avi would be worth a try (I think the problem lies in a somewhat different contrast of the neck and skull which appear brighter in our qT1 maps compared to MPRAGE). I could use SPM-coregistered T1 maps instead an put them into the freesurfer pipeline which, however, would mean an additional interpolation (which is not what I want). Is there another workaround? ( I read that in tkregister2 there is the option to apply fsl transformation matrices - something like that would be needed - but I'm no too familiar with the way freesurfer handels and stores those transformations). As my doctorate fellow sees himself manually segmenting all the subcortical structurs any help would be greatly appreciated -:)
Thanks, Simon Baudrexel Brain Imaging Center Goethe University Frankfurt ________________________________ Von: Snyder, Avi [a...@npg.wustl.edu] Gesendet: Donnerstag, 12. Juli 2012 01:58 Bis: Baudrexel, Simon; Bruce Fischl Cc: freesurfer@nmr.mgh.harvard.edu Betreff: Re: AW: [Freesurfer] Using SPM transformation matrices as initial guess in talairach_avi Simon, The standard Talairach atlas transform module in FreeSurfer was designed for T1W high-resolution structural images (e.g., MP-RAGE or SPGR). This is a design choice partly driven by the fact that the FreeSurfer segmentation algorithm assumes high-resolution T1 weighting. Reliable atlas transformation with any other contrast mechanism would be highly uncertain. Atlas transformation modules theoretically could be produced for other contrast mechanisms, e.g., R1 or FA. However, it is not clear that, even if this were done, that the tissue classification part of FreeSurfer would work. If you have R1 and/or FA images that need to be analyzed using FreeSurfer segmentations, I would think that you should submit a minimally processed high-resolution T1W image to FreeSurfer and then use the generated results as ROIs in subsequent analyses. Of course, this strategy requires that the images containing the contrast to be evaluated are co-registered to the segmented MP-RAGE. I hope I have correctly understood your scientific objectives. Avi Snyder ------------ On 7/10/12 4:20 AM, "Baudrexel, Simon" <simon.baudre...@kgu.de> wrote: >Hi Bruce, > >I'm using freesurfer version 5.1.0. I currently try to process >quantitative T1 (R1) maps derived from 4 and 18 deg. FLASH images and FA >maps. Interestingly, transformation appears to fail less often when using >single (16 deg.) FLASH images, only. SPM segmentation routine on the >other hand works pretty well on both T1 and FLASH images (probably >because of using header origin information - which was set to the >anterior commissure- as first guess in the registration). > >Thanks >Simon >________________________________________ >Von: Bruce Fischl [fis...@nmr.mgh.harvard.edu] >Gesendet: Montag, 9. Juli 2012 20:03 >Bis: Baudrexel, Simon >Cc: freesurfer@nmr.mgh.harvard.edu; Avi Snyder >Betreff: Re: [Freesurfer] Using SPM transformation matrices as initial >guess in talairach_avi > >Hi Simon > >what version are you using? Avi Snyder (ccd) has been tracking down some >interactions between his talairach code and our intensity normalization >that seem to have made it more fragilie, particularly in 5.1. He has some >suggested fixes that may improve things for you. > >cheers >Bruce > >On Mon, 9 Jul 2012, Baudrexel, Simon >wrote: > >> Hello, >> >> since I experienced a high rate of registration errors using >>talairach_avi >> in the conventional recon-all processing stream (more than 50% >> misregistration), I would like to incorporate SPM affine registration >> parameters (as provided in the seg_inv_sn.mat file obtained from the >> segmentation routine) as initial guess "to help" talairach-avi. Is >>there a >> possibility to do this? How do I have to adjust the transformation >>matrix >> that it can be handled by freesurfer? >> >> I also tried to circumvent the registration-problem using skull-stripped >> images, which unfortunately also did not improve the results (I think a >> template made from skull-stripped images has to be used in that case) >> >> Any help would be much appreciated >> >> Regards, >> Simon _______________________________________________ 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.
