Hi Bjorn,
POSSUM output files are in NIFTI format and input files are in either
NIFTI or ANALYZE. I thought SPM deals with these file formats?
Best,
Ivana
On 11 Feb 2008, at 10:43, Bjorn Roelstraete wrote:
> Hi,
>
> i'm trying to analyze some POSSUM simulated images with SPM, but i
> get stuck at the segmentation step. apparently, the structural
> image used in POSSUM is incompatible with the structural image
> needed by SPM. conversely, i can't run POSSUM with the structural
> images provided by SPM or FSL/feeds. does this sound familiar to
> anyone? does anyone have a compatible structural image for POSSUM
> AND SPM?
>
> thanks,
> bjorn
>
> Mark Jenkinson wrote:
>> Hi,
>> It sounds like you haven't got your setup right.
>> You can check this by doing the following in your terminal:
>> echo $FSLDIR
>> If this is blank then there is a basic setup problem.
>> If this is ok but "echo $PATH" does not include any directory
>> like the $FSLDIR one then this is also a problem.
>> If you have a problem then check whether you followed the
>> installation instructions carefully - especially the bit about
>> environment variables. If you used the installer script
>> it is possible that it did not set your configuration files up
>> properly.
>> If this is the case try modifying your shell startup file manually
>> as described in the installation instructions.
>> All the best,
>> Mark
>> On 7 Feb 2008, at 22:35, Bjorn Roelstraete wrote:
>>> nope, i see the fslsplit-file in the fsl\bin folder, but i can't
>>> use it. my fsl version is 4.0.
>>>
>>> . Quoting Matt Glasser <[log in to unmask]>:
>>>
>>>> What version of FSL do you have? If you have an older version,
>>>> it may be
>>>> avwsplit.
>>>>
>>>> Peace,
>>>>
>>>> Matt.
>>>>
>>>> -----Original Message-----
>>>> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]]
>>>> On Behalf
>>>> Of Bjorn Roelstraete
>>>> Sent: Thursday, February 07, 2008 11:08 AM
>>>> To: [log in to unmask]
>>>> Subject: Re: [FSL] multiple volume simulation
>>>>
>>>> i get 'command not found'
>>>>
>>>> Matthew Webster wrote:
>>>>> Hi,
>>>>> If FSL is installed normally on your machine, then typing
>>>>> fslsplit
>>>>> at the command line should give you the usage text - does that
>>>>> happen or
>>>>> is the command not found?
>>>>>
>>>>> Matthew
>>>>>
>>>>>> ok, but how do i use fslsplit? can i use it with the gui or do
>>>>>> i have
>>>>>> to type in the command line? in the second case, where do i
>>>>>> type it? i
>>>>>> tried my linux shell, but it doesn't work there, neither does
>>>>>> it in
>>>>>> matlab.
>>>>>>
>>>>>> Matthew Webster wrote:
>>>>>>> Hello,
>>>>>>> the fslsplit tool can be used to break a
>>>>>>> multivolume file
>>>>>>> into separate ones...
>>>>>>> Regards
>>>>>>> Matthew
>>>>>>>> dear all,
>>>>>>>>
>>>>>>>> i just finished an fmri simulation with possum. i simulated 10
>>>>>>>> volumes,
>>>>>>>> which i can look at with the fslview. however, i expected the
>>>>>>>> simulator to
>>>>>>>> produce 10 .nii files. instead i only have one, containing
>>>>>>>> all of
>>>>>>>> the 10
>>>>>>>> volumes. when i open the file in SPM, for example, it looks
>>>>>>>> like my 10
>>>>>>>> volumes are treated as one image. so my question is this:
>>>>>>>> can i make 10
>>>>>>>> separate .nii files from the original one containing the 10
>>>>>>>> volumes?
>>>>>>>> thank
>>>>>>>> you. bjorn
>>>>>>>>
>>>>>>
>>>>>> --
>>>>>> 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]
>>>>
>>>
>>>
>>>
>>> --
>>> 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]
>
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