[Mne_analysis] a junior question on mne_setup_source_space

peng prion.w at gmail.com
Fri Mar 28 11:49:27 EDT 2014
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Thanks alex for your help with the scripts.
However in both scripts, it was not specified how -trans.fif was
obtained...
I tried the GUI as described in the manual section 12.11, but it did not
work well. Thus I wish to import the transformation matrix obtained from
other software, but errors happened again(please check my previous posts on
this)...




On Fri, Mar 28, 2014 at 4:30 PM, Alexandre Gramfort <
alexandre.gramfort at telecom-paristech.fr> wrote:

> Dear Peng,
>
> you have here full scripts to analyze CTF data:
>
> for the anatomy pipeline:
>
> https://github.com/mne-tools/mne-scripts/tree/master/spm_face
>
> for MEG data analysis:
>
>
> http://martinos.org/mne/dev/auto_examples/datasets/plot_spm_faces_dataset.html
>
> HTH
> A
>
>
> On Fri, Mar 28, 2014 at 2:52 PM, peng <prion.w at gmail.com> wrote:
> > Dear Alex, Martin and other MNE users,
> >
> > I have my MEG raw data in CTF .ds format and raw MRI image with dicom
> > format. I wish to use MNE to compute the leadfield (source space based on
> > surface).
> > With your help, I wish to summarise a possible pipeline as a following:
> > 1. recon-all --subject test1 #use  in freesurfer to generate the brain
> > surfaces and other needed files.
> > 2. mne_watershed_bem --subject test1 --overwrite --atlas #generate
> surfaces
> > for bem model
> > 3. mne_ctf2fiff --ds test1.ds --fif test1.fif --infoonly #generate MEG
> > information (sensor locations etc.)
> > 4. #use MNE_analyze with test1.fif and inflated.surf to generate
> > test1-trans.fif which contains the transformation matrix;
> >     #or use a previous calculated transformation matrix and convert it to
> > fif format
> > 5. mne_setup_source_space --subject tmp --ico 5 --morph test1 #tmp is
> name
> > of a template, could be fsaverage or icbm152...
> > #This is to use locations on the surface of the template cortex (white
> > matter?) as source space.
> > #These locations was morphed to subject <test1> to generate leadfield for
> > this subject later
> > 6. mne_do_forward_solution --subject test1 \
> >    --src test1-fsaverage-ico-5-src.fif \
> >   --meas test1.fif \
> >   --trans test1-trans.fif \
> >   --megonly --overwrite \
> >   --fwd test1-oct-5-fwd.fif
> > # I can then find my leadfield (MxNx3 matrix, M=number of locations, N =
> > number of sensors) by importing test1-oct-5-fwd.fif into matlab.
> >
> > Did I miss something?
> > Thanks a lot for the help.
> >
> >
> >
> > On Fri, Mar 28, 2014 at 2:14 PM, peng <prion.w at gmail.com> wrote:
> >>
> >> Thank you Martin for the help.
> >> 1. I re-run the command "mne_setup_forward_model" and it seemed working
> >> this time (maybe I did not set the environment correctly). Sorry for the
> >> confusion.
> >> 2. I tried with MNE_analyze GUI and it was not easy for me. But I saved
> >> results from one subject successfully and it could be load by
> MNE_analyze.
> >> However I wanted to read it in matlab to check the real contents (which
> I
> >> assume is a structure with the transformation matrix). I failed with "x
> =
> >> fiff_read_mri(fname, 0). It complained "Could not find MRI data"...
> Would
> >> please let me know the function name to read and write *-src.fif file in
> >> matlab?
> >>
> >>
> >>
> >> On Wed, Mar 26, 2014 at 9:28 PM, Martin Luessi
> >> <mluessi at nmr.mgh.harvard.edu> wrote:
> >>>
> >>> On 03/26/14 16:00, peng wrote:
> >>> > Thank you for the answers.
> >>> > 1. Surprisingly I did not find any files were generated/saved after
> >>> > running mne_setup_forward_model.
> >>>
> >>> I assume there was an error, can you post the program output?
> >>>
> >>> > 2. I don't have a -trans.fif file. I tried to do it in GUI of
> >>> > MNE_analyze, it was quite complicated. If I have a co-registered mri
> >>> > file (generated by CTF software with .mri extension), can it be
> >>> > converted to fif format? If not, I can read the 4x4 head2mri matrix
> via
> >>> > matlab, can this information be written to fif format with certain
> >>> > tools
> >>> > in MNE?
> >>>
> >>> There is also a coreg GUI in MNE-Python, have a look here
> >>>
> >>> http://www.slideshare.net/mne-python/mnepython-coregistration
> >>>
> >>> You could write a .fif file with the transform in Matlab, but it seems
> >>> to me that this wouldn't be easier than using the coregistration tools
> >>> in mne_analyze or MNE-Python.
> >>>
> >>> HTH,
> >>>
> >>> Martin
> >>>
> >>>
> >>> > Thanks again!
> >>> >
> >>> >
> >>> > On Tue, Mar 25, 2014 at 11:39 PM, Alexandre Gramfort
> >>> > <alexandre.gramfort at telecom-paristech.fr
> >>> > <mailto:alexandre.gramfort at telecom-paristech.fr>> wrote:
> >>> >
> >>> >     hi,
> >>> >
> >>> >     >  Some additional questions.
> >>> >     > 1 After I ran mne_setup_forward_model, I have no feedback from
> >>> > the
> >>> >     command
> >>> >     > line, is it normal?
> >>> >
> >>> >     it should print that it saved a file to disk
> >>> >
> >>> >     > 2 I am using CTF data, thus I converted the .ds folder from CTF
> >>> > to fif
> >>> >     > format with mne_ctf2fiff command, with option --infoonly. Here
> I
> >>> >     only want
> >>> >     > to get the Leadfield thus I suppose data is not necessary.
> >>> > However
> >>> >     when I
> >>> >     > try mne_do_forward_solution, it asked for mri description file,
> >>> >     which I
> >>> >     > haven't. I have only a series of dicom files or the .mri file
> >>> >     generated by
> >>> >     > ctf software from them. Can I still move on?
> >>> >
> >>> >     you need to do the coregistration and get a -trans.fif file.
> >>> >
> >>> >     A
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