[FieldTrip] I think you solved the problem
Jen Whitman
jenwhitman at gmail.com
Mon Feb 28 22:32:16 CET 2011
I just checked, and when I re-ran my segmentation script with the new
Fieldtrip in order to use an spm8 template image, coordinates got reversed.
When I take out the calls to flipdim, they look fine (see attached
screenshots). That certainly explains the meaningless results I was getting!
Thanks for figuring that out,
Jen
On Mon, Feb 28, 2011 at 12:36 PM, jan-mathijs schoffelen <
jan.schoffelen at donders.ru.nl> wrote:
> Hi Jen,
>
> At first glance I have a comment on your script. You may need to explicitly
> check the alignment of your segmented volume and the original anatomy. A
> while a go some changes were made to ft_volumesegment, taking away the need
> to do the flipdim(flipdim... operations. I have posted this on the
> discussion list last January, but you may not have noticed.
> Anyway, if you now have used a recent version of FieldTrip for your
> segmentation both the location of your dipole grid, and the volume conductor
> model will not be adequately coregistered with the data, which may lead to
> funky results to begin with. That's most likely not related to the filetype
> in which the volumes are saved for later use.
>
> Best wishes,
>
> Jan-Mathijs
>
>
>
> On Feb 28, 2011, at 8:59 PM, Jen Whitman wrote:
>
> Hello Jan,
>
> When calling volumesegment, I specified 'ctf' as the coordinate system. The
> function I wrote to call volumesegment and prepare_singleshell for each
> subject and save the results is pasted below, with a couple of comments
> added for clarity.
> Over the weekend I tried specifying the coordinate system in the call to
> ft_volumenormalise as 'ctf' rather than 'spm', and commented out all the
> lines that said cfg.spmversion = 'spm8'; before calling a function. However,
> that created worse results, as each plot involved stripes of activation and
> empty voxels, suggesting that 'ctf' was not the correct coordinate system to
> specify.
>
> Thanks for the attached script. Looking in that the comments in that, I
> suspect that the solution to my problems will be to specify my filetype as
> nifti_img rather than nifti. I'll let you know how that goes.
>
> Jen
>
>
> ------------------------------------------------------------------------------------------------------------
> % the variable subj is simply a string consisting of a subject number (e.g.
> 's05') which can be a folder name or part of a filename
> function [vol mri segmentedmri
> segmentedmriF]=call_volume_segment_function_spm8(subj)
> cfg.spmversion = 'spm8';
> cfg.template = '/home/woodwardlab/spm8/templates/EPI.nii';
> %cfg.template='/home/common/matlab/spm2/templates/T1.mnc';
> cfg.name=[subj '_volseg'];
> cfg.write='yes';
> cfg.smooth='no';
> cfg.coordinates='ctf';
> mri=read_mri([subj '/mri/' subj 'head.mri']); % made with CTF mriConverter
> and mriViewer software, after fiducials were marked
> segmentedmri = volumesegment(cfg, mri);
> segmentedmriF = segmentedmri;
> segmentedmriF.gray = flipdim(flipdim(flipdim(segmentedmriF.gray,3),2),1);
> segmentedmriF.white = flipdim(flipdim(flipdim(segmentedmriF.white,3),2),1);
> segmentedmriF.csf = flipdim(flipdim(flipdim(segmentedmriF.csf,3),2),1);
> segmentedmriF.transform = mri.transform;
> segmentedmriF.anatomy = mri.anatomy;
> cfg = [];
> cfg.spmversion = 'spm8';
> vol = prepare_singleshell(cfg, segmentedmriF);
> eval(['save ' subj '/meg/mrisegmented.mat mri segmentedmri segmentedmriF
> vol'])
>
>
>
> On Sat, Feb 26, 2011 at 5:26 AM, jan-mathijs schoffelen <
> jan.schoffelen at donders.ru.nl> wrote:
>
>> Dear Jen,
>>
>> I do not manage to reproduce your issue, when only focussing on the
>> ft_volumewrite and visualization part of your pipeline. See attached script,
>> and yet an updated version of ft_volumewrite which you need to (hopefully)
>> draw the same conclusion as I did.
>> Yet, I only now realize that your question may pertain to the entire
>> pipeline. It could be that something is going wrong there.
>> I only see now that in the part of your script of which you reported that
>> it gave 'good' results, you specify cfg.coordinates = 'ctf' before calling
>> ft_volumenormalise. I assume this is correct, because the coordinate system
>> your source-reconstructed data lives in, is according to the CTF-convention,
>> and not according to the SPM-convention. On the other hand, the template for
>> the spatial normalization lives in the SPM-coordinate system. In order for
>> the spatial normalization to work OK, Fieldtrip tries to convert from one
>> coordinate system to the other (once again, this is appropriate behaviour),
>> before doing the actual normalization. It seems that at least in the script
>> you sent along, in the final (not working version), you specified
>> cfg.coordinates = 'spm' prior to calling ft_volumenormalise. This is
>> probably wrong.
>> Another important point that should be mentioned, is that the coordinate
>> systems in which the functional data and the anatomical data live should be
>> the same for the ft_sourceinterpolate to make sense. In other words, if your
>> source reconstructed images are defined on a 3D grid of positions in
>> CTF-space, the mri.transform of your anatomy should describe a
>> transformation from voxel to CTF-space.
>> I think you may want to revisit step by step this part of the pipeline; I
>> don't think the problem lies in the writing.
>> A final possibility of course is that Mricron is misbehaving...
>>
>> Best,
>>
>> Jan-Mathijs
>>
>>
>>
>>
>>
>>
>> On Feb 25, 2011, at 9:44 PM, Jen Whitman wrote:
>>
>> Hi Jan,
>>
>> I tried re-running the analysis with the new script you sent me, and the
>> latest version of fieldtrip (since I needed ft_get_opt as well), but the
>> spm8 images being written are still producing flawed results. It's the same
>> problem as I mentioned briefly in my previous post. I am not getting any
>> error messages when writing these images. Rather, my problem is that the
>> spm8 and spm2 results from the same data ought to be identical when viewed
>> in mricron, but they're far from it. When I use mricron to look at the
>> results from the spm8-format images, combined across participants to create
>> a t-image, I just get a single 'blob' spanning roughly half the brain. In
>> contrast, when I used spm2-format previously on the same data, the t-image
>> was much more meaningful; a posterior alpha power decrease in a set of
>> regions corresponding to the 'task-positive network' (a network found in the
>> results of an fMRI version of my experiment, and widely reported in the fMRI
>> literature).
>>
>> This failure to replicate the spm2 results when using spm8 images from the
>> same data leads me to suspect that something is wrong with the coordinates
>> for spm8 format. However, after experimenting extensively with different cfg
>> options I still haven't identified the problem. If I my structural MRIs have
>> been saved to .mri files using CTF's MRIConverter program, which cfg
>> options, particularly for coordinates, template images, and filetypes,
>> should I specify before calling the ft_volumesegment,
>> ft_prepare_singleshell, ft_sourceinterpolate, ft_volumenormalise, and
>> ft_volumewrite functions? Or should I be calling a different set of
>> functions now?
>>
>> Thanks again for your help,
>>
>> Jen
>>
>> On Thu, Feb 24, 2011 at 10:07 AM, Jen Whitman <jenwhitman at gmail.com>wrote:
>>
>>> 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
>>>>>
>>>>
>>>> _______________________________________________
>>>> 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
>>
>>
>> _______________________________________________
>> 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
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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