[FieldTrip] I think you solved the problem
Jan.Hirschmann at med.uni-duesseldorf.de
Jan.Hirschmann at med.uni-duesseldorf.de
Tue Apr 12 13:08:55 CEST 2011
Dear JM,
thanks a lot. I have actually just realized a few minutes ago that
volumesegment and volumerealign are now supporting neuromag this way. It
works just fine.
I was already surprised that headcoordinates has a flag for neuromag
now, and it should have occured to me that this means that also the
higher-level functions were changed. Could I ask you to include this new
feature in the help? I could also put an example script online if that
is helpful for communicating this aspect (in case it hasn't been
communicated long ago and I just missed it).
Best,
jan
________________________________
Von: fieldtrip-bounces at donders.ru.nl
[mailto: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] 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
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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
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