[Mne_analysis] a junior question on mne_setup_source_space
dgw
dgwakeman at gmail.com
Thu May 1 10:12:35 EDT 2014
Hi Peng,
I think the basic point here is you have the logic reversed. The idea
behind the morph option is that you would use --subject subj1 and
--morph fsaverage. You would then do this for all of your subjects.
Although with such a tiny number of sources (--ico 2), I wouldn't
expect to get very good results.
HTH,
D
On Tue, Apr 29, 2014 at 12:44 PM, peng <prion.w at gmail.com> wrote:
> 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
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