[Mne_analysis] a junior question on mne_setup_source_space
peng
prion.w at gmail.com
Tue Apr 29 12:44:05 EDT 2014
Hi dgw,
First thanks you for help in previous discussions, also thanks alex,
martin, junpeng and many others for helps.
I have played with the commands for a while and now understand more.
However, I am still not sure how this "morph" works. For example, in the
following command,
mne_setup_source_space --subject fsaverage --ico 2 --morph subj1
--overwrite
Previously, I thought with this command, it would took some locations in
the template fsaverage, and then projected them into subj1 based on their
anatomical similarity (e.g. shape of white matter). Or in another words, I
expected that if I repeated this command many times by changing the
subjects, I would have all subjects share the same or at least very close
locations (in cortex level) for the same vertex id. This is interesting for
me because it would give much convenience in later group analysis. e.g.
location #100 of subject 1 and location #100 of subject 2 means the same
thing in group level. However, later I applied the labels in freesurfer and
found out that for the same id (e.g. #100) may belong to different brain
areas (as indicated by labels). I am a little confused then. Is this
difference cause by small variations; or I was wrong in the root : This
morph does not grantee a one-to-one mapping between template and each
subject?
Thanks a lot for the help!
best
Peng
On Fri, Mar 28, 2014 at 3:08 PM, dgw <dgwakeman at gmail.com> wrote:
> That certainly is the basic workflow in terms of commands, but I don't
> think you want to use the "tmp" subject. You also don't morph the data
> until later in the process.
>
> Can I recommend that you start off by doing the example in the
> "Cookbook" chapter? It does not take very long, and it will help you
> be more familiar with how the process works in one individual. Then
> you can try to take what you learn from that and apply it directly to
> your data.
>
> HTH,
> D
> .
>
> On Fri, Mar 28, 2014 at 9:52 AM, 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
> >>> > _______________________________________________
> >>> > Mne_analysis mailing list
> >>> > Mne_analysis at nmr.mgh.harvard.edu
> >>> > <mailto:Mne_analysis at nmr.mgh.harvard.edu>
> >>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> >>> >
> >>> >
> >>> > The information in this e-mail is intended only for the person to
> >>> > whom it is
> >>> > addressed. If you believe this e-mail was sent to you in error
> and
> >>> > the e-mail
> >>> > contains patient information, please contact the Partners
> >>> > Compliance
> >>> > HelpLine at
> >>> > http://www.partners.org/complianceline . If the e-mail was sent
> to
> >>> > you in error
> >>> > but does not contain patient information, please contact the
> sender
> >>> > and properly
> >>> > dispose of the e-mail.
> >>> >
> >>> >
> >>> >
> >>> >
> >>> > _______________________________________________
> >>> > Mne_analysis mailing list
> >>> > Mne_analysis at nmr.mgh.harvard.edu
> >>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> >>> >
> >>>
> >>> _______________________________________________
> >>> Mne_analysis mailing list
> >>> Mne_analysis at nmr.mgh.harvard.edu
> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> >>
> >>
> >
> >
> > _______________________________________________
> > Mne_analysis mailing list
> > Mne_analysis at nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> >
> >
> > The information in this e-mail is intended only for the person to whom
> it is
> > addressed. If you believe this e-mail was sent to you in error and the
> > e-mail
> > contains patient information, please contact the Partners Compliance
> > HelpLine at
> > http://www.partners.org/complianceline . If the e-mail was sent to you
> in
> > error
> > but does not contain patient information, please contact the sender and
> > properly
> > dispose of the e-mail.
> >
> _______________________________________________
> Mne_analysis mailing list
> Mne_analysis at nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20140429/aa7f265d/attachment.html
More information about the Mne_analysis
mailing list