[FieldTrip] difficulty with nifti format and ft_write_volume
Jen Whitman
jenwhitman at gmail.com
Thu Feb 24 19:07:23 CET 2011
Great, thanks!
I'll start the analysis with your new script today and will let you know how
it works out.
Jen
On Thu, Feb 24, 2011 at 4:44 AM, jan-mathijs schoffelen <
jan.schoffelen at donders.ru.nl> wrote:
> Dear Jen,
>
> I managed to reproduce your problem. The code was rather buggy and indeed
> ft_volumewrite did not behave as it should have. I now fixed it in the code
> and it should run fine now. Please find the updated file attached. It will
> be available on our ftp-server as of tonight. Please note that I updated the
> documentation, and changed the names of some of the options a bit. If you
> want to save your data in analyze-format, you should specify cfg.filetype =
> 'analyze_spm'. If you specify cfg.filetype = 'nifti', it should write out a
> volume to nifti-format, using SPM8.
>
> Best wishes,
>
> Jan-Mathijs
>
>
>
>
>
> On Feb 23, 2011, at 7:44 PM, Jen Whitman wrote:
>
>
> Dear Jan,
>
> Thanks for the quick reply. Yes, I have tried it out quite a few times now,
> experimenting with different settings in the cfgs. Below I'll paste the code
> I've been using to write images - first the code that successfully created
> spm2 images that produced good results, then the code used for creating
> nifti format images from the same data. The comments in this second part are
> at this point a bit of a maze of cfg options I've been changing back &
> forth. Any insights/suggestions regarding how to set up my cfgs to make this
> work would be greatly appreciated.
>
> Jen
>
>
> %%%%%%%% this code generated spm2-compatible images which did work
> (producing results that made sense).
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>
> sourcetemp.avg.pow = (sourcetemp.avg.pow - sourcePre.avg.pow) ./
> sourcePre.avg.pow;
>
> cfg = [];
> cfg.downsample = 2;
> sourcetempInt = sourceinterpolate(cfg, sourcetemp , mri);
>
> % projecting the plot onto a surface...
> cfg = [];
> cfg.coordinates = 'ctf';
> cfg.template = '/home/common/matlab/spm2/templates/T1.mnc'; %this
> template is in MNI coordinates
> sourcetempIntN = volumenormalise(cfg, sourcetempInt);
>
> filename=[subj 'run' int2str(r) 'cond' int2str(cond) '_' int2str(f)
> 'HzWin' int2str(win) 'width750ms'];
> cfg=[];
> cfg.parameter = 'avg.pow'; % string, describing the functional data
> to be processed, e.g. 'pow', 'coh' or 'nai'
> cfg.filename = [filename '.img']; %'testimageoutput_alphafreq'; %
> filename without the extension
> cfg.filetype = 'spm'; %'analyze', 'spm', 'vmp' or 'vmr'
> cfg.coordinates = 'spm'; %'spm, 'ctf' or empty for interactive
> (default = [])
> cfg.datatype = 'double'; %'float'; %'double'; %'bit1', 'uint8',
> 'int16', 'int32', 'float' or 'double'
>
> volumewrite(cfg, sourcetempIntN)
>
>
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> %%%%% this code below hasn't worked yet...
>
> % I added cfg.spmversion = 'spm8';
> % in the cfgs for the calls to ft_prepare_leadfield and ft_sourceanalysis,
> % and in the call to prepare_singleshell after calling volumesegment
>
> % I've also ensured that spm8 is the only spm version in my path, even in
> % the fieldtrip/external folder, and ensured that spm8 is installed
> properly
> % (files compiled correctly, etc..)
>
> sourcetemp.avg.pow = (sourcetemp.avg.pow - sourcePre.avg.pow) ./
> sourcePre.avg.pow;
>
> filename=[subj 'run' int2str(r) 'cond' int2str(cond) '_' int2str(f)
> 'Hzspm8_FIXv9_Win' int2str(win) 'width750ms.img'];
>
> cfg = [];
> % cfg.coordinates = 'spm'; % changed for version 5
> % cfg.spmversion = 'spm8'; % changed for version 5
> cfg.downsample = 4;
> sourcetempInt = ft_sourceinterpolate(cfg, sourcetemp , mri);
>
>
> % projecting the plot onto a surface...
> cfg = [];
> %cfg.coordinates = 'spm'; % changed for version 5
> %cfg.coordinates = 'ctf'; % changed for version 5
> cfg.coordinates = 'spm'; % changed back to spm for version 9
> cfg.downsample = 4;
> %cfg.spmversion = 'spm8'; % changed for version 6 (because this gets
> specified in volumewrite)
> cfg.template = 'Hmatrix/mask.nii.nii'; % basically equivalent to using
> spm8/templates/EPI.nii, except that mask.nii (produced from fmri data) has
> the desired voxel size
> % cfg.name = [filename]; % changed for version 6
> %cfg.write= 'yes'; % changed for version 6 (when this was set to 'yes'
> there was no subsequent call to volumewrite)
> cfg.write= 'no'; % changed for version 6
> sourcetempIntN = ft_volumenormalise(cfg, sourcetempInt);
>
> % this whole cfg and function call added for version 6
> cfg=[];
> % cfg.parameter = string, describing the functional data to be
> processed, e.g. 'pow', 'coh' or 'nai'
> % cfg.filename = filename without the extension
> % cfg.filetype = 'analyze', 'spm', 'vmp' or 'vmr'
> % cfg.vmpversion = 1 or 2 (default) version of the vmp-format to use
> % cfg.coordinates = 'spm, 'ctf' or empty for interactive (default = [])
> cfg.parameter='pow';
> cfg.filename=filename;
> cfg.filetype = 'spm';
> cfg.spmversion = 'SPM8'; % capitalized after first error message from
> vers 6
> % cfg.dataformat='nifti'; % added after first error message from vers 6
> % commented out after 2nd error message
> from vers 6
> %cfg.vmpversion=2; % this is a filetype, like spm, so don't need to
> specify unless cfg.filetyp='vmp'
> cfg.coordinates='spm';
> ft_volumewrite(cfg,sourcetempIntN);
>
>
>
>
>
> On Wed, Feb 23, 2011 at 7:50 AM, jan-mathijs schoffelen <
> jan.schoffelen at donders.ru.nl> wrote:
>
>> Dear Jen,
>>
>> I notice that indeed in the documentation section of ft_write_volume there
>> is a FIXME behind nifti. Yet, nifti format seems to be supported by
>> ft_write_volume (at least in a recent version of fieldtrip). Did you try it
>> at all (and ran into problems) or were you held back by the FIXME statement?
>> Could you just try it out using a recent fieldtrip function?
>>
>> Thanks and best wishes
>>
>> Jan-Mathijs
>>
>>
>>
>> On Feb 23, 2011, at 2:21 AM, Jen Whitman wrote:
>>
>> Hello,
>>>
>>> While writing beamformed images to spm2 format in a previous version of
>>> fieldtrip (now lost due to a computer crash), I was able to get nice-looking
>>> results; networks of brain regions consistent with existing literature. When
>>> I try to write images from the same dataset and the same analysis to spm8
>>> format, my results (t-images computed across subjects) end up being single
>>> clusters spanning large sections of the brain (e.g. a 'blob' spanning all of
>>> one hemisphere but not the other). Unfortunately, some aspects of my planned
>>> data analyses cannot be performed on spm2 images, so I have to find a way of
>>> writing to successfully to nifti format.
>>>
>>> I just noticed that in the comments in the ft_write_volume function,
>>> which I am calling via ft_volumewrite, it says 'FIXME' next to nifti under
>>> the list of supported dataformats. Is there by any chance a patch out there
>>> for writing nifti images?
>>>
>>> Thanks!
>>>
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>
>>
>> Dr. J.M. (Jan-Mathijs) Schoffelen
>> Donders Institute for Brain, Cognition and Behaviour,
>> Centre for Cognitive Neuroimaging,
>> Radboud University Nijmegen, The Netherlands
>> J.Schoffelen at donders.ru.nl
>> Telephone: 0031-24-3614793
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>
> _______________________________________________
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> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
> Dr. J.M. (Jan-Mathijs) Schoffelen
> Donders Institute for Brain, Cognition and Behaviour,
> Centre for Cognitive Neuroimaging,
> Radboud University Nijmegen, The Netherlands
> J.Schoffelen at donders.ru.nl
> Telephone: 0031-24-3614793
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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