[Mne_analysis] a junior question on mne_setup_source_space

peng prion.w at gmail.com
Thu May 1 16:00:36 EDT 2014
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Thank you for the suggestion, dgw.

best
Peng


On Thu, May 1, 2014 at 8:53 PM, dgw <dgwakeman at gmail.com> wrote:

> Unless someone can track down what the problem is you ran into (it may
> be related to the extremely low ico number, which I mentioned in my
> previous email: feel free to try some others), I would stick to the
> following analysis (mostly because I believe this is the more common
> workflow, and I am unfamiliar with that option in
> mne_setup_source_space):
>
> Do the inverse on all of your subjects without using the --morph
> option including setting up the source space.
>
> Next, create the morph maps for each subject to something like
> fsaverage (or even an individual from your analysis).
>
> Next, morph the stcs to whichever you created the morph maps to.
>
> Then you can perform whatever steps you originally wanted to on that
> morphed data (which will have a one to one correspondence).
>
> HTH,
> D
>
> On Thu, May 1, 2014 at 2:38 PM, peng <prion.w at gmail.com> wrote:
> > Thank you for the reply. I have attached the message on the screen as a
> txt
> > file after implementing the line below. Hope it helps.
> >
> > mne_setup_source_space --subject sub03 --ico 2 --morph fsaverage
> >
> > I read the chapter and I guess in the above line, it should be FROM sub3
> TO
> > fsaverage in morphing.
> >
> > If I wish to set all source space points anatomically equivalent,
> <--subject
> > fsaverage --morph subxx> shall work better. Because the locations with
> same
> > id in different subjects are at exactly same position in fsaverage, and
> then
> > morphed to various subjects, being different because of different
> morphing
> > matrix. Or I am wrong because in mne_setup_source_space there are other
> > components not explained in the chapter?
> >
> >
> > best
> >
> > Peng
> >
> >
> >
> > On Thu, May 1, 2014 at 5:29 PM, dgw <dgwakeman at gmail.com> wrote:
> >>
> >> Hi Peng,
> >>
> >> Please see response in text.
> >>
> >> On Thu, May 1, 2014 at 11:05 AM, peng <prion.w at gmail.com> wrote:
> >> > Thanks for the reply, dgw. Do you mean the segmentation is made in
> >> > fsaverage
> >> > and then project to subject by
> >> > ====
> >> > mne_setup_source_space --subject subj1 --ico 2 --morph fsaverage
> >> > ====
> >> > I tried this way before and it always failed with the error message
> that
> >> > vertex XXX was used multiple times, no matter which resolution I use
> >> > (ico 2,
> >> > 3, 4 or 5). It seemed the resolution of fsaverage is not so high (2
> mm),
> >> > thus I tried icbm152 and colin27 (both 1 mm resolution), and it did
> not
> >> > work
> >> > either. Do you have any idea on possible reasons?
> >>
> >> Well, we would need to get an error report to try and track this down.
> >> There is a useful chart in the morphing and averaging chapter which
> >> describes the pipeline you are trying to use. Essentially, it is a
> >> multistep process. Because MNE tries to provide you the best possible
> >> estimates, you first analyze the data in the individuals space
> >> (vertices don't match). Then you morph that data for each individual
> >> to a shared space (e.g. fsaverage). Each individuals morphed data will
> >> then have a one to one mapping.
> >>
> >> > I just made ico 2 here as an example. Of course I am also interested
> to
> >> > know
> >> > what is the minimum number you think appropriate for reasonable
> mapping?
> >>
> >> This depends on your application of the "loose" ness of your
> >> orientation constraint. Something like --ico 5 and --loose .2
> >>
> >> >
> >> > btw: I hope it is OK when I address you as dgw; that's what I saw as
> the
> >> > email sender. Please correct me if it is not what you like.
> >> >
> >> > best
> >> > Peng
> >> >
> >> >
> >> > On Thu, May 1, 2014 at 4:12 PM, dgw <dgwakeman at gmail.com> wrote:
> >> >>
> >> >> 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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> >> >> >> >>> >
> >> >> >> >>> >
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