Dear Mark,
Dear Ivana,
Thank you for the helpful reply. The reason why i try to implement my
possum data into SPM, is because i am currently learning both packages.
I should consider it 'progress' if i can simulate data in fsl and not
only analyze them with FEAT (which works nicely already), but also get
the same/similar result in SPM. This does not work yet. My activation in
SPM is completely different than in FEAT, so i'm working out why this is
the case...step by step.
Bjorn
Mark Jenkinson wrote:
> Hi Bjorn,
>
> Just to add to this.
> POSSUM is designed to simulate EPI data for FMRI simulations.
> So I'm not quite sure why you would be trying to run segmentation
> on this EPI data. If you want a structural image as well as your EPI data
> then you can synthesize one easily from the tissue-type maps used
> in POSSUM. Just extract each separate tissue-type volume with fslroi,
> and then, with fslmaths, weight them and sum them up. Alternatively,
> you can use the structural images from BrainWeb as this is the
> same subject as the default model that comes with POSSUM.
>
> All the best,
> Mark
>
>
>
>
>
> Ivana Drobnjak wrote:
>> Dear Bjorn,
>>
>> When using POSSUM you get an output directory in with a file called
>> brain.nii.gz . This file consists of three different volumes one for
>> each tissue type. This is the input to POSSUM and not a structural
>> image. It is a segmented digital brain which consists of three volumes
>> (one for gray, one for white and one for CSF). So if you are using
>> this file to segment it you would get the kind of errors you are
>> complaining of.
>>
>> Similarly, when you want to simulate an image you do not use a
>> structural image as your input, but as explained above, a segmented
>> version of the structural (one volume per tissue type, all merged
>> together). It is important to keep in mind that the MR parameters
>> (file called MRpar) need to be in the same order as the tissue types.
>> If you are using MR parameters given by default with POSSUM, they are
>> ordered as: first row is grey matter, second is white, and the third
>> is CSF so try to keep the order of your segmented volumes the same.
>> Once you finish the simulation this input file will be present in your
>> output directory and will be called brain.nii.gz.
>>
>> The actual output of POSSUM is called image_abs.nii.gz and this is the
>> image you should be segmenting. fslview always helps to see your data
>> so that you can see these things easier. In addition there is a very
>> straightforward explanation of the files on the website:
>> http://www.fmrib.ox.ac.uk/fsl/possum/index.html . I highly recommend
>> you to read this website.
>>
>> Hope this helps,
>> Ivana
>>
>>
>>
>>
>> On 18 Mar 2008, at 10:32, Bjorn Roelstraete wrote:
>>
>>> dear all,
>>>
>>> when i try to analyze my simulated possum data with SPM, i get stuck
>>> at the segmentation part. the default "structural" image in possum is
>>> brain.nii, but when i use this file as the structural image in SPM,i
>>> get errors ("Matrix is singular to working precision").
>>> And when i try to use another structural file in possum
>>> (e.g.structural_brain.nii), it won't simulate! how do i solve this?
>>> is there a file in fsl or fsl-feeds that is suited for simulating
>>> with possum AND analyzing with SPM at the same time?
>>>
>>> thanks in advance,
>>>
>>> --
>>> Bjorn Roelstraete
>>> Ghent University
>>> Department of Data-analysis
>>> H. Dunantlaan 1, B-9000 Gent, Belgium
>>> Tel: 32-9-2646434
>>> E-mail: [log in to unmask]
>>>
>>
--
Bjorn Roelstraete
Ghent University
Department of Data-analysis
H. Dunantlaan 1, B-9000 Gent, Belgium
Tel: 32-9-2646434
E-mail: [log in to unmask]
