[Mne_analysis] a junior question on mne_setup_source_space
junpeng.zhang
junpeng.zhang at gmail.com
Fri Mar 28 12:06:13 EDT 2014
Peng,
Please see the link
https://mail.nmr.mgh.harvard.edu/pipermail//mne_analysis/2012-October/001259.html
Part of the email as :
Kambiz,
What Dan meant is to read the fif file, change the transform, and write
the file back. I'm not very familiar with the matlab toolbox, but in
mne-python you could do it as follows:
--------------------------------------
import mne
raw = mne.fiff.Raw('raw.fif')
raw.info['dev_head_t']['trans'] = my_matrix
raw.save('raw_mytrans.fif')
--------------------------------------
where "my_matrix" is a 4x4 numpy array with your transform.
I hope this helps.
Best,
Martin
Hope it helps.
Junpeng
2014-03-29
junpeng.zhang
发件人：peng <prion.w at gmail.com>
发送时间：2014-03-28 23:40
主题：Re: [Mne_analysis] a junior question on mne_setup_source_space
收件人："Discussion and support forum for the users of MNE Software"<mne_analysis at nmr.mgh.harvard.edu>
抄送：
Thanks, dgw and junpeng for your feedback. I did read the manual before asking:)
I am sorry '-src.fif' was a typo, I wanted to read -trans.fif. I did not find a proper function in the manual.
To write it, <fiff_write_coord_trans> seem to be the correct function.
According to the manual, I set
==
t.from = 4 %(head);
t.to = 5 %(mri);
t.trans = M; %(4x4 matrix).
x = fopen('t.fif', 'w');
fiff_write_coord_trans(x, t);
fclose(x);
==
No complains from matlab in writing.
But mne_analyze complain that the file "does not start properly"...
On Fri, Mar 28, 2014 at 3:10 PM, dgw <dgwakeman at gmail.com> wrote:
Hi Peng,
The matlab toolbox chapter in the manual specifies how you read each
file type. The function to read a "-src.fif" file is
mne_read_source_spaces.
D
On Fri, Mar 28, 2014 at 9:14 AM, 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/20140329/0b47203c/attachment.html
More information about the Mne_analysis
mailing list