[FieldTrip] difficulty with nifti format and ft_write_volume
jan-mathijs schoffelen
jan.schoffelen at donders.ru.nl
Thu Feb 24 07:58:24 CET 2011
Hi Jen,
Thanks for sending the code.
What is the actual error message you are getting?
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
>
> _______________________________________________
> 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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20110224/52ea01f5/attachment-0002.html>
More information about the fieldtrip
mailing list