Hi Simon I'm also puzzled about your "quantitative T1 maps". Are these T1 values in ms? If so, the image won't have "T1-weighted contrast" as WM will be darker (shorter T1) than GM, in which case everything would fail. I assume that what you are going to FreeSurfer (and Avi's code) is instead the larger flip angle FLASH image.
cheers Bruce On Thu, 12 Jul 2012, Snyder, Avi wrote: > I don't see that it is possible to avoid double resampling if you use > FreeSurfer to segment. As far as I can tell, the problem with your dataset > is that a substantial fraction of cases results a clearly poor Talarrach > atlas transform, e.g., too "fat" or too "thin" or distorted. There is no > provision, as far as I am aware, to, initialize the Talairach transform > module based on a prior computations. There are two main possibilities > that underly bad Talairach transforms (1) input images very displaced or > rotated from standard acquisitions (2) mismatch between contrast > mechanisms in the sample T1W and the atlas representative target. It is > possible to correct error mechanism 2. A dialog regarding this possibility > is ongoing with the FreeSurfer developers. > > Avi > ----------------------------------- > On 7/12/12 5:09 AM, "Baudrexel, Simon" <simon.baudre...@kgu.de> wrote: > >> 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 . 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