[FieldTrip] I think you solved the problem

Hanneke van Dijk Hanneke.vanDijk at med.uni-duesseldorf.de
Fri Apr 15 11:34:20 CEST 2011


Dear Jan and Jan-Mathijs,

Thanks for working on this problem! I'm testing it for data recorded with
the 'old' neuromag 122 system. I'm using the script that Jan attached to a
previous e-mail, and the fieldtrip version that was released yesterday. The
first question that I have is:

What to do if you don't have fiducial information from the neuromag
software? I could use ft_volume_realign with cfg.method = 'interactive' and
point the fiducials out and swap the y and x axes. But in what coordinate
system am I then, and in what coordinate system should I move on?

second,

My 'vol' , headmodel, seems to end up in a factor 10 (or more(?)) smaller
unit then the grid and grad. You can't even see it in the headmodelplot (it
is a small dot somewhere in the middle). I don't know what happened there.

third,

If you look at the picture I attached the grid is not in the centre of the
helmet (pic1 from the top down), and very low (pic2 looking from the left).
I don't know how to solve that. I at least think the subject was not in the
helmet that way!

Groetjes Hanneke

--------------------------------------------------
Dr. Hanneke van Dijk
Institut für Klinische Neurowissenschaften und Medizinische Psychologie
Gebäude-Nr.: 23.02
Ebene: 03 Zimmer-Nr.: 47
Tel.:  +49 211-81-13074
Mail : hanneke.vandijk at med.uni-duesseldorf.de
http://www.uniklinik-duesseldorf.de/deutsch/unternehmen/institute/KlinNeurowiss/Team/HannekevanDijk/page.html

On Thu, Apr 14, 2011 at 9:31 AM, <Jan.Hirschmann at med.uni-duesseldorf.de>wrote:

>  Dear Jan-Mathijs,
>
>
>
> sure, I will do that. I have tested one head model with
> ft_dipole_simulation and beamforming and it looks good (at least when I
> simulate two conditions and subtract sources the right location comes out).
> So I guess we (and maybe others) will use the new procedure now.
>
>
>
> Best,
>
> jan
>
>
>  ------------------------------
>
> *Von:* fieldtrip-bounces at donders.ru.nl [mailto:
> fieldtrip-bounces at donders.ru.nl] *Im Auftrag von *jan-mathijs schoffelen
> *Gesendet:* Mittwoch, 13. April 2011 16:57
> *An:* Email discussion list for the FieldTrip project
> *Betreff:* Re: [FieldTrip] I think you solved the problem
>
>
>
> Dear Jan,
>
>
>
> No problem. Thanks for the script. If you feel up to it, you are kindly
> invited to update the documentation on the fieldtrip wiki as well. If I
> recall correctly, at some point Hanneke added some documentation about how
> to create MNI-based dipole grids for neuromag data. A lot of the
> intermediate steps have now become obsolete and this part of the wiki can be
> substantially cleaned.
>
>
>
> Thanks,
>
>
>
> Jan-Mathijs
>
>
>
>
>
> On Apr 13, 2011, at 2:31 PM, <Jan.Hirschmann at med.uni-duesseldorf.de> <
> Jan.Hirschmann at med.uni-duesseldorf.de> wrote:
>
>
>
>   Dear Jan-Mathijs,
>
>
>
> I think we solved the problem. Everthing is like you said in the first
> place. ft_volumerealign and ft_volumesegment should be called with
> cfg.coordsys=’neuromag’. The only thing that was wrong is that for the voxel
> coordinates read from the Neuromag GUI x and y should be swapped. For anyone
> interested I attach a script that is meant to be easy-to-use for beginners.
>
>
>
> Thank you very much for your time!
>   ------------------------------
>
> *Von:* fieldtrip-bounces at donders.ru.nl [
> mailto:fieldtrip-bounces at donders.ru.nl <fieldtrip-bounces at donders.ru.nl>]
> *Im Auftrag von *jan-mathijs schoffelen
> *Gesendet:* Dienstag, 12. April 2011 21:18
> *An:* Email discussion list for the FieldTrip project
> *Betreff:* Re: [FieldTrip] I think you solved the problem
>
>
>
> Dear Jan,
>
>
>
> I suspect that your mri, as it comes out of ft_read_mri is already
> coregistered in neuromag space. After your realignment and after replacing
> mri.transform with real_mri.transform, the coordinate axes in your pic1 look
> strange. This I think causes the 'dropped pocket change'.
>
> What happens if you skip the ft_volumerealign step and call
> ft_volumesegment directly on the mri (with cfg.coordsys = 'neuromag', or,
> for what it's worth, without cfg.coordsys; in this case you will be able to
> verify the coordinate system)?
>
> Alternatively, if this doesn't work, could you replace mri.transform by
> eye(4) prior to calling ft_volumerealign and ft_volumesegment (both with
> cfg.coordsys = 'neuromag' and no further tampering with transformation
> matrices?).
>
>
>
> Thanks
>
>
>
> JM
>
>
>
>
>
> On Apr 12, 2011, at 8:49 PM, <Jan.Hirschmann at med.uni-duesseldorf.de> <
> Jan.Hirschmann at med.uni-duesseldorf.de> wrote:
>
>
>
>
>    Dear Jan-Mathijs,
>
>
>
> sorry, I think I was a bit too enthusiastic when I said everything worked
> out wonderfully. It worked only once. After an afternoon of confusion I
> concluded that on my first try I must have misspelled
> cfg.coordsys=’neuromag’ on my calls to ft_volumerealign and
> ft_volumesegment. In fact, the segmentation looks really bad with these
> settings. What works for me is written underneath:
>
>
>
> mri  = ft_read_mri('….fif');
>
> hdr=ft_read_header('…fif');
>
> mri.anatomy=double(mri.anatomy);
>
>
>
> %this is taken from the Neuromag GUI for MRI-MEG Integration
>
> cfg=[];
>
> cfg.fiducial.rpa=[136.35   142.80    31.96];
>
> cfg.fiducial.nas=[47.84   101.80   100.10];
>
> cfg.fiducial.lpa=[139.22   146.17   162.69];
>
>
>
> %go from neuromag voxel to neuromag head coordinates
>
> cfg.coordsys='neuromag';
>
> cfg.method='fiducial';
>
> real_mri=ft_volumerealign(cfg,mri);
>
>
>
> %taking real_mri with its coordsys field will not work, so I take mri
>
> mri.transform=real_mri.transform;
>
>
>
> cfg                = [];
>
> cfg.keepintermediate = 'no';
>
> cfg.write = 'no';
>
> segmentedmri   = ft_volumesegment(cfg, mri);
>
>
>
>
>
> Before segmentation the function shows some kind of brain (pic 1). When
> segmentation is done the segmented brain looks good (pic 2) but the brain
> does not fit the helmet (pic 3). It is looking at its feet as if it dropped
> some pocket change. Do you know what is going on?
>
>
>
> Thanks,
>
> jan
>
>
>   ------------------------------
>
> *Von:* fieldtrip-bounces at donders.ru.nl [
> mailto:fieldtrip-bounces at donders.ru.nl <fieldtrip-bounces at donders.ru.nl>]
> *Im Auftrag von *jan-mathijs schoffelen
> *Gesendet:* Dienstag, 12. April 2011 12:11
> *An:* Email discussion list for the FieldTrip project
> *Betreff:* Re: [FieldTrip] I think you solved the problem
>
>
>
> Dear Jan,
>
>
>
> Apart from not being properly aligned, the segmentation looks a bit strange
> to me. I suspect that not everything went well here ;o).
>
> Could you try the following:
>
>
>
> specify cfg.coordsys = 'neuromag', both in your call to ft_volumerealign
> and in your call to ft_volumesegment. The cfg.coordinates for
> ft_volumesegment has to be removed (actually it is a deprecated option). The
> idea now is that mri-structures in fieldtrip can have a coordsys field,
> which allows for more transparent use of the different head coordinate
> system conventions. This takes away the need for intermediately
> coregistering the MRI in 'ctf'-convention, and would also take away your
> need to call headcoordinates later on.
>
>
>
> Best wishes,
>
>
>
> Jan-Mathijs
>
>
>
>
>
> On Apr 12, 2011, at 11:07 AM, <Jan.Hirschmann at med.uni-duesseldorf.de> <
> Jan.Hirschmann at med.uni-duesseldorf.de> wrote:
>
>
>
>
>
>     Dear fieldtrip experts,
>
>
>
> I have two questions regarding head model creation. As noted on this
> thread, the volumesegment function was updated and I tested it for our
> Neuromag data. The segmentation is performed, but unfortunately it is not
> aligned with the MRI in my case. Here is the code I am using, the fieldtrip
> is from 9th April 2011.
>
>
>
> %read mri
>
> mri                = ft_read_mri(subject_files.fiff_mri);
>
> mri.anatomy=double(mri.anatomy);
>
>
>
> %these are the fiducials for this subject taken from the Neuromag GUI for
> coregistration
>
> cfg=[];
>
> cfg.fiducial.rpa=[136.35   142.80    31.96];
>
> cfg.fiducial.nas=[47.84   101.80   100.10];
>
> cfg.fiducial.lpa=[139.22   146.17   162.69];
>
>
>
> %define the head coordinate system according to CTF conventions
>
> cfg.method='fiducial';
>
> real_mri=ft_volumerealign(cfg,mri);
>
>
>
> %segment
>
> cfg                = [];
>
> cfg.template       = '/data/apps/spm/spm8/templates/T1.nii';
>
> cfg.coordinates    = 'ctf';
>
> cfg.keepintermediate = 'no';
>
> segmentedmri     = ft_volumesegment(cfg, real_mri);
>
>
>
> %plot white matter
>
> test=segmentedmri;
>
> test.anatomy=real_mri.anatomy;
>
> cfg=[];
>
> cfg.funparameter='white';
>
> ft_sourceplot(cfg,test); %see attached picture
>
>
>
> The other issue regards back-transformation from CTF to Neuromag
> coordinates, which is necessary to make the head model fit the sensors. My
> idea was to create an appropriate transformation matrix like this.
>
>
>
> cd /net/avidya/storage/home/jan/fieldtrip-20110409/private
>
> ctfmat=headcoordinates(nas,lpa,rpa,'ctf');
>
> nmmat=headcoordinates(nas,lpa,rpa,'neuromag');
>
> ctf_to_nm=nmmat/ctfmat;
>
>
>
>
>
> And then to use it on the head model to bring it back into Neuromag
> coordinates:
>
>
>
> %create single shell, realistic headmodel
>
> cfg                = [];
>
> hdm                = ft_prepare_singleshell(cfg,segmentedmri);
>
>
>
> % transformation of headmodel into Neuromag space
>
> hdm.bnd.pnt=warp_apply(ctf_to_nm,hdm.bnd.pnt,'homogeneous');
>
>
>
> Does this survive a sanity check?
>
>
>
> Best regards and thanks a lot,
>
>
>
> Jan
>
>
>
>
>    ------------------------------
>
> *Von:* fieldtrip-bounces at donders.ru.nl [
> mailto:fieldtrip-bounces at donders.ru.nl <fieldtrip-bounces at donders.ru.nl>]
> *Im Auftrag von *Jen Whitman
> *Gesendet:* Montag, 28. Februar 2011 22:32
> *An:* Email discussion list for the FieldTrip project
> *Betreff:* [FieldTrip] I think you solved the problem
>
>
>
> 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
>
>
>
> <misalignment.png>
>
> _______________________________________________
> 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
>
>
>
> <pic1.png><pic2.png><pic3.png>
>
> _______________________________________________
> 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
>
>
>
> <headmodel_with_neuromag.m>
>
> _______________________________________________
> 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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