[Mne_analysis] a junior question on mne_setup_source_space
Alexandre Gramfort
alexandre.gramfort at telecom-paristech.fr
Fri Mar 28 11:30:40 EDT 2014
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
>>> > _______________________________________________
>>> > 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.
>
More information about the Mne_analysis
mailing list