Hi Gari
the post-hoc surface deformation will use whatever resolution you have,
and works quite nicely with .7mm scans.
cheers
Bruce
On Thu, 7 Mar 2013, Garikoitz
Lerma-Usabiaga wrote:
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 <fis...@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
<fis...@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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