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SPM  February 2011

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Subject:

Re: New Segmentation Out of Memory Error

From:

John Ashburner <[log in to unmask]>

Reply-To:

John Ashburner <[log in to unmask]>

Date:

Thu, 17 Feb 2011 16:33:07 +0000

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (217 lines)

The best possible workaround would be the following.  In principle, if
you have scans from other subjects that have additional information
(eg structure label images etc), then you can align these scans to the
population average images, using Dartel.  Once you have done this, the
information can be warped so that it overlays on your individuals'
scans via a procedure described towards the end of the "Using Dartel"
chapter of the SPM8 manual.

Alternatively, you could create a copy of the MNI-space image of
labels, and tweak the matrix in its header, so that it is in alignment
with the population average.  This is untested, but I think you'd set
the matrix to M3*inv(M2)*M1, where:

M1 = voxel-to-world matrix of your MNI-space labels
M2 = voxel-to-world matrix of the population average space Template_6
M3 = matrix in the Template_6_2mni.mat

If this works, you should be able to use one of the options in the
Dartel toolbox (or the Deformations Utility) to warp the data on to
your original scans.

Best  regards,
-John

On 16 February 2011 19:45, michel grothe <[log in to unmask]> wrote:
> Thanks, this would be great.
>
> Meanwhile, I have some questions regarding a possible work-around:
>
> Would it be OK to use an affine transform calculated with the
> Normalise-Button to approximate the affine transform from 'DARTEL-Normalise
> to MNI' in order to be able to generate the mentioned composition
> 'native->DARTEL->MNI'. Does the affine alignment step in 'DARTEL-Normalise
> to MNI' register the DARTEL-GM template to the GM-apriori map (or the GM map
> in TPM.nii,1?) or does it also use the respective WM-maps?
> How much does the affine alignment in 'DARTEL-Normalise to MNI' differ from
> the one in 'Normalise', when registering DARTEL-GM to GM-apriori map (or
> TPM.nii,1) and setting non-linear iterations to 0?
>
> Thanks again for your help.
> Best regards,
> Michel
>
>> Date: Wed, 16 Feb 2011 17:16:00 +0000
>> From: [log in to unmask]
>> Subject: Re: [SPM] New Segmentation Out of Memory Error
>> To: [log in to unmask]
>>
>> > I haven´t seen such a file in my version of SPM8 (the penultimate
>> > update,
>> > run on win32). Is it possible that this file is just generated during
>> > estimation of the affine transform and not stored permanently on disk?
>> > Or
>> > does it come with the latest update?
>>
>> This change occurred in SPM8 r3727, so should be in the current
>> updates, which are to r4010.
>>
>>
>> > It would be very helpful to have such a file, mainly for the reasons
>> > Richard
>> > mentioned, i.e. use it to compose the complete transform
>> > 'native->DARTEL-mean->MNI'. The inverse of such a composition could be
>> > used
>> > to warp Atlas-labels in MNI space to native space.
>>
>> There's no easy way to use the file yet, but I'll try to code
>> something up for a future version of SPM8.
>>
>> Best regards,
>> -John
>>
>>
>> >> Date: Wed, 16 Feb 2011 15:58:16 +0000
>> >> From: [log in to unmask]
>> >> Subject: Re: [SPM] New Segmentation Out of Memory Error
>> >> To: [log in to unmask]
>> >>
>> >> This file does indeed contain an affine transform, and is generated
>> >> when the affine registration between population average and MNI space
>> >> is estimated.
>> >>
>> >> There's no script to do what you're after yet, but if the demand is
>> >> high enough I could introduce the option. Can I ask how you plan to
>> >> use the transforms?
>> >>
>> >> Best regards,
>> >> -John
>> >>
>> >>
>> >> On 16 February 2011 15:44, Richard Binney
>> >> <[log in to unmask]>
>> >> wrote:
>> >> > ......I've just spotted that running normalise-to-mni now spits out a
>> >> > 'Template_6_2mni.mat' file. I don't recall seeing this before - would
>> >> > this
>> >> > happen to be the affine transform I spoke of?
>> >> >
>> >> > R
>> >> >
>> >> > On Wed, Feb 16, 2011 at 3:39 PM, Richard Binney
>> >> > <[log in to unmask]> wrote:
>> >> >>
>> >> >> Ah, yes. I couldn't find the email you were refferring to, but I've
>> >> >> done
>> >> >> it and it makes a huge difference. Pretty obvious really.
>> >> >>
>> >> >> One more thing, John (or anybody else for that matter) - is there
>> >> >> now a
>> >> >> way in which one can easily create an inverse of the DARTEL
>> >> >> normalise-to-MNI
>> >> >> deformation composition (so from MNI --> study average -->
>> >> >> individual
>> >> >> subject space)? Is it possible (i.e., is there script) to have this
>> >> >> (forward
>> >> >> and/or backwards) written out for each subject or, alternatively, to
>> >> >> have
>> >> >> the affine template-to-TPM transform outputted such that one can
>> >> >> combine it
>> >> >> with a flow field, and subsequently inverse the composition using
>> >> >> the
>> >> >> deformations tool?
>> >> >>
>> >> >> All the best,
>> >> >>
>> >> >> Richard
>> >> >>
>> >> >> On Tue, Feb 15, 2011 at 5:42 PM, John Ashburner
>> >> >> <[log in to unmask]>
>> >> >> wrote:
>> >> >>>
>> >> >>> You may wish to change the voxel sizes and bounding box in order to
>> >> >>> obtain slightly lower resolution versions (other than the default
>> >> >>> 1.5mm isotropic with a large bounding box).  See the email I sent
>> >> >>> out
>> >> >>> recently.
>> >> >>>
>> >> >>> Best regards,
>> >> >>> -John
>> >> >>>
>> >> >>> On 15 February 2011 17:29, Richard Binney
>> >> >>> <[log in to unmask]>
>> >> >>> wrote:
>> >> >>> > Dear John (and other knowledgeable types),
>> >> >>> >
>> >> >>> > I used the deformation file (e.g., Y_p1_T1.nii) from Seg8 to
>> >> >>> > normalise
>> >> >>> > a
>> >> >>> > functional MRI timeseries. That worked fine - the anatomical
>> >> >>> > images that
>> >> >>> > I additionally warped in this way look great - but I now cannot
>> >> >>> > do
>> >> >>> > anything
>> >> >>> > with the timeseries.
>> >> >>> >
>> >> >>> > It is now almost 4Gb in size. I appreciate that using DARTEL to
>> >> >>> > warp
>> >> >>> > fMRI
>> >> >>> > data can result in massive files which are problematic (and thus
>> >> >>> > a
>> >> >>> > work
>> >> >>> > around is to apply the warp to contrast images), but I didn't
>> >> >>> > expect
>> >> >>> > the
>> >> >>> > segment deformation field to do the same.
>> >> >>> >
>> >> >>> > Does this sound about right for a timeseries with 465 volumes
>> >> >>> > (voxel
>> >> >>> > dim 2.5
>> >> >>> > x 2.5 x 3; matrix 96x96; numslices = 42)? Or have I made a
>> >> >>> > mistake
>> >> >>> > somewhere?
>> >> >>> >
>> >> >>> > so I'm supposing my inability to use the warped timeseries is a
>> >> >>> > memory
>> >> >>> > issue - I am running a 64-bit machine with 8Gb memory (I can see
>> >> >>> > all
>> >> >>> > this
>> >> >>> > being used in the task manager so doesn't seem to be a matlab
>> >> >>> > version
>> >> >>> > problem) but maybe this file is just way too big for the SPM
>> >> >>> > platform.....???? I could crop the image, etc I suppose but maybe
>> >> >>> > the
>> >> >>> > biggest problem is the shear number of volumes.
>> >> >>> >
>> >> >>> > Thanks in advance for your thoughts
>> >> >>> >
>> >> >>> > Richard
>> >> >>> >
>> >> >>> > On Thu, Feb 10, 2011 at 4:05 PM, William Pettersson-Yeo
>> >> >>> > <[log in to unmask]> wrote:
>> >> >>> >>
>> >> >>> >> Thanks John.
>> >> >>> >>
>> >> >>> >> It turns out the problem was due to the version of Matlab I was
>> >> >>> >> running.
>> >> >>> >>
>> >> >>> >> Matlab2007 was only running 32bit, whilst the 2010 version is
>> >> >>> >> 64.
>> >> >>> >>
>> >> >>> >> Having set up with Matlab2010, the new segmentation with DARTEL
>> >> >>> >> import
>> >> >>> >> now
>> >> >>> >> runs without any problem, without me having to alter/crop any of
>> >> >>> >> the
>> >> >>> >> images.
>> >> >>> >>
>> >> >>> >> All the best
>> >> >>> >> William
>> >> >>> >
>> >> >>> >
>> >> >>
>> >> >
>> >> >
>> >
>

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