Many thanks for your answers! 


I have another question: 
Usually we work with 1 mm3 T1-s, but we have a 0.7 mm3 sequence as well. Lüsebrink et al (2013) say that: "FreeSurfer is not designed to process data with a spatial resolution other than 1 mm and was modified to avoid this limitation." 

When running 0.7 mm3 T1-s with the recon-all standard stream we observe the following in recon-all.log:
"Original Data has (0.35, 0.35, 0.7) mm size and (640, 640, 256) voxels.
Data is conformed to 1 mm size and 256 voxels for all directions"

> Will FS 5.2 work with other resolutions different to 1 mm3?
> With the current limitation, can we expect any gain in cortical thickness (or other) measurements using lower voxel size-s, if at the end everything is conformed to 1 mm3?

many thanks again for your responses!
Gari


On Thu, Mar 7, 2013 at 4:38 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
and 1mm isotropic

On Thu, 7 Mar 2013, Nick Schmansky wrote:

see:

http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferWiki?action=AttachFile&do=get&target=FreeSurfer_Suggested_Morphometry_Protocols.pdf


Hi Gari

we use a bandwidth and readout matched (to our multi-echo mprage) T2-SPACE
with a FLAIR inversion pulse. Andre (ccd) can give you the details

cheers
Bruce


On Thu, 7 Mar 2013, Garikoitz Lerma-Usabiaga wrote:

Hi Bruce,is there any recommended protocol for T2 acquisition to be used
in the 5.2 recon-all stream?

Should we used the same voxel size as the T1? (we are using  1 mm3 right
now).

If it is going to improve the skull striping and pial surface creation,
we might acquire specific T2 images just to be
used in the recon-all stream.

many thanks,
Gari 


On Wed, Feb 27, 2013 at 2:44 PM, Bruce Fischl
<fischl@nmr.mgh.harvard.edu> wrote:
      Hi Nicola

      the T2 might in 5.2, but it is pretty thick slices so might hurt
more
      than it helps. Not sure, but you can try it out

      cheers
      Bruce
      On Wed, 27 Feb 2013, Nicola
      Toschi wrote:

     > Hello List,
     >
     > on out 3T scanner, in addition to MPRAGE images (1 mm^3), we
usually
     > acquire T2 and PD images - however they are at 1x1x5 mm
resolution.
     >
     > Would you recommend passing these (T2+PD) to the recon-all
stream anyway
     > - would they add value/accuracy to the segmentation/parcellation
(or
     > would they possibly decrease accuracy)?
     >
     > Thanks in advance,
     >
     > Nicola
     >
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