A modified version of the manual should now appear with the next set of
spm8 updates.
Best regards,
-John
On Tue, 2010-02-16 at 09:48 -0600, Manuel De La Cruz Gutierrez wrote:
> May I suggest having this bit of information on the New Segmentation
> documentation/SPM manual? I spent days trying to figure out why I ran out of
> memory when trying to write the deformation fields on a 32-bit Linux virtual
> machine hosted on Win XP 32-bit.
>
> All the best!
>
> Manuel
> -------------
> Manuel de la Cruz Gutierrez, PhD
> Developmental Psychology Lab
> Dept. of Psychology, U of Houston
>
>
>
> On 2/15/10 7:45 AM, "John Ashburner" <[log in to unmask]> wrote:
>
> > On a 32 bit computer, the most memory that SPM or any other program can
> > use at any time is 4Gbytes (or sometimes only 2Gbytes). This is because
> > the largest number that can be represented with 32 bits is
> > 4,294,967,295. A 150Mbyte file probably has 2 bytes per voxel, so is
> > probably about 512x512x300 in size. Then add a bunch of deformations
> > and their inverses, a few tissue class images etc, and the amount of
> > memory needed soon adds up.
> >
> > 64-bit computers can handle images of these dimensions, but it seems
> > that 32 bit computers simply do not have enough memory to run this part
> > of SPM.
> >
> > You are essentially searching for the model that most accurately
> > characterises the anatomical patterns of difference among the
> > populations. I have my own preferred model for doing this, but most
> > investigators want to use a method that localises volumetric differences
> > of grey matter to specific regions. To make interpretations in terms of
> > localised volume differences, then the pre-processed data should
> > accurately reflect the tissue volumes you are interested in. The more
> > accurate the models used for pre-processing, then the more
> > straight-forward is the interpretation. I wouldn't have the first clue
> > about trying to assign any physiological interpretation to patterns of
> > difference that did not account for the stretching and shrinking that
> > occurs through spatially normalising the data.
> >
> > Best regards,
> > -John
> >
> > On Mon, 2010-02-15 at 11:43 +0000, Dennis Chung Ming-Tak wrote:
> >> On Fri, 12 Feb 2010 17:15:36 +0000, John Ashburner wrote:
> >>> Realign, Coreg, Normalise and the old Segment are pretty much the same
> >>> as in SPM5. However, SPM8 has a new version of the segmentation (see my
> >>> email from a few minutes ago) that I think will achieve more accurate
> >>> spatial normalisation than the older versions.
> >>
> >> Given the improvements you listed in the other post, does this dramatically
> >> change the structure of the output files? I only ask because my system (1GB
> >> physical + 3GB virtual memory in 32 bit XP) reports "out of memory" when I
> >> try
> >> to import certain new segmented images - specifically 150ish megabyte
> >> MPRAGE files - into DARTEL. The new segmented images (i.e. c1 to c5) were
> >> produced and can be viewed but this "out of memory" seemed to pop up when
> >> the program tries to produce the DARTEL files (i.e. rc1 etc.).
> >>
> >> I should note that the old segmented files of these MPRAGE images were
> >> processed through DARTEL without trouble and the 50ish megabyte SPGR files,
> >> which were segmented using the new method, could also be successfully
> >> imported into DARTEL.
> >>
> >>> Dartel is a still more accurate approach to spatial normalisation,
> >>> although it is a bit more complicated to use.
> >>
> >> I've been following this modulated vs. unmodulated debate here on the mailing
> >> list. I understand that Dr. Ashburner's position is that an unmodulated
> >> comparison merely reflects registration error but others such as Mechelli
> >> 2005
> >> and Gaser etc. suggest that unmodulated analyses reveal brain matter
> >> density/concentration. Now, with the improvement of registration through the
> >> use of new segmentation and DARTEL, does this change the debate in any
> >> way? If not, I'm sorry for beating a dead horse. Of course, I am assuming
> >> we
> >> are not studying subjects with significant deformation or volume reduction
> >> which would interfere with registration.
> >>
> >> Thank you for your attention.
> >>
> >> Sincerely,
> >> Dennis
> >>
> >>
> >
>
--
John Ashburner <[log in to unmask]>
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