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<DIV><FONT color=#000000 size=4 face=宋体>Hi Peng, </FONT></DIV>
<DIV> </DIV>
<DIV>Please read carefully chapter 12 of the manual, and you will master how to
</DIV>
<DIV>process MEG data. After you know it, you can try to process data following
your</DIV>
<DIV>imagination. Of course, each time you encounter problems, please read the
</DIV>
<DIV>associated chapters of the manual. </DIV>
<DIV> </DIV>
<DIV>Best wishes, </DIV>
<DIV>Junpeng </DIV>
<DIV> </DIV>
<DIV align=left><FONT color=#c0c0c0 size=2 face=Verdana>2014-03-28</FONT></DIV>
<DIV align=left><FONT size=2 face=Verdana>
<HR style="WIDTH: 122px; HEIGHT: 2px" id=SignNameHR align=left SIZE=2>
</FONT></DIV>
<DIV align=left><FONT color=#c0c0c0 size=2 face=Verdana><SPAN
id=_FlashSignName>junpeng.zhang</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Verdana>
<HR>
</FONT></DIV>
<DIV><FONT size=2 face=Verdana><STRONG>发件人：</STRONG>dgw
<dgwakeman@gmail.com></FONT></DIV>
<DIV><FONT size=2
face=Verdana><STRONG>发送时间：</STRONG>2014-03-28 22:08</FONT></DIV>
<DIV><FONT size=2 face=Verdana><STRONG>主题：</STRONG>Re: [Mne_analysis] a junior
question on mne_setup_source_space</FONT></DIV>
<DIV><FONT size=2 face=Verdana><STRONG>收件人：</STRONG>"Discussion and support
forum for the users of MNE
Software"<mne_analysis@nmr.mgh.harvard.edu></FONT></DIV>
<DIV><FONT size=2 face=Verdana><STRONG>抄送：</STRONG></FONT></DIV>
<DIV><FONT size=2 face=Verdana></FONT> </DIV>
<DIV><FONT size=2 face=Verdana>
<DIV>That certainly is the basic workflow in terms of commands, but I don't </DIV>
<DIV>think you want to use the "tmp" subject. You also don't morph the data </DIV>
<DIV>until later in the process. </DIV>
<DIV> </DIV>
<DIV>Can I recommend that you start off by doing the example in the </DIV>
<DIV>"Cookbook" chapter? It does not take very long, and it will help you </DIV>
<DIV>be more familiar with how the process works in one individual. Then </DIV>
<DIV>you can try to take what you learn from that and apply it directly to </DIV>
<DIV>your data. </DIV>
<DIV> </DIV>
<DIV>HTH, </DIV>
<DIV>D </DIV>
<DIV>. </DIV>
<DIV> </DIV>
<DIV>On Fri, Mar 28, 2014 at 9:52 AM, peng <prion.w@gmail.com> wrote: </DIV>
<DIV>> Dear Alex, Martin and other MNE users, </DIV>
<DIV>> </DIV>
<DIV>> I have my MEG raw data in CTF .ds format and raw MRI image with dicom </DIV>
<DIV>> format. I wish to use MNE to compute the leadfield (source space based on </DIV>
<DIV>> surface). </DIV>
<DIV>> With your help, I wish to summarise a possible pipeline as a following: </DIV>
<DIV>> 1. recon-all --subject test1 #use in freesurfer to generate the brain </DIV>
<DIV>> surfaces and other needed files. </DIV>
<DIV>> 2. mne_watershed_bem --subject test1 --overwrite --atlas #generate surfaces </DIV>
<DIV>> for bem model </DIV>
<DIV>> 3. mne_ctf2fiff --ds test1.ds --fif test1.fif --infoonly #generate MEG </DIV>
<DIV>> information (sensor locations etc.) </DIV>
<DIV>> 4. #use MNE_analyze with test1.fif and inflated.surf to generate </DIV>
<DIV>> test1-trans.fif which contains the transformation matrix; </DIV>
<DIV>> #or use a previous calculated transformation matrix and convert it to </DIV>
<DIV>> fif format </DIV>
<DIV>> 5. mne_setup_source_space --subject tmp --ico 5 --morph test1 #tmp is name </DIV>
<DIV>> of a template, could be fsaverage or icbm152... </DIV>
<DIV>> #This is to use locations on the surface of the template cortex (white </DIV>
<DIV>> matter?) as source space. </DIV>
<DIV>> #These locations was morphed to subject <test1> to generate leadfield for </DIV>
<DIV>> this subject later </DIV>
<DIV>> 6. mne_do_forward_solution --subject test1 \ </DIV>
<DIV>> --src test1-fsaverage-ico-5-src.fif \ </DIV>
<DIV>> --meas test1.fif \ </DIV>
<DIV>> --trans test1-trans.fif \ </DIV>
<DIV>> --megonly --overwrite \ </DIV>
<DIV>> --fwd test1-oct-5-fwd.fif </DIV>
<DIV>> # I can then find my leadfield (MxNx3 matrix, M=number of locations, N = </DIV>
<DIV>> number of sensors) by importing test1-oct-5-fwd.fif into matlab. </DIV>
<DIV>> </DIV>
<DIV>> Did I miss something? </DIV>
<DIV>> Thanks a lot for the help. </DIV>
<DIV>> </DIV>
<DIV>> </DIV>
<DIV>> </DIV>
<DIV>> On Fri, Mar 28, 2014 at 2:14 PM, peng <prion.w@gmail.com> wrote: </DIV>
<DIV>>> </DIV>
<DIV>>> Thank you Martin for the help. </DIV>
<DIV>>> 1. I re-run the command "mne_setup_forward_model" and it seemed working </DIV>
<DIV>>> this time (maybe I did not set the environment correctly). Sorry for the </DIV>
<DIV>>> confusion. </DIV>
<DIV>>> 2. I tried with MNE_analyze GUI and it was not easy for me. But I saved </DIV>
<DIV>>> results from one subject successfully and it could be load by MNE_analyze. </DIV>
<DIV>>> However I wanted to read it in matlab to check the real contents (which I </DIV>
<DIV>>> assume is a structure with the transformation matrix). I failed with "x = </DIV>
<DIV>>> fiff_read_mri(fname, 0). It complained "Could not find MRI data"... Would </DIV>
<DIV>>> please let me know the function name to read and write *-src.fif file in </DIV>
<DIV>>> matlab? </DIV>
<DIV>>> </DIV>
<DIV>>> </DIV>
<DIV>>> </DIV>
<DIV>>> On Wed, Mar 26, 2014 at 9:28 PM, Martin Luessi </DIV>
<DIV>>> <mluessi@nmr.mgh.harvard.edu> wrote: </DIV>
<DIV>>>> </DIV>
<DIV>>>> On 03/26/14 16:00, peng wrote: </DIV>
<DIV>>>> > Thank you for the answers. </DIV>
<DIV>>>> > 1. Surprisingly I did not find any files were generated/saved after </DIV>
<DIV>>>> > running mne_setup_forward_model. </DIV>
<DIV>>>> </DIV>
<DIV>>>> I assume there was an error, can you post the program output? </DIV>
<DIV>>>> </DIV>
<DIV>>>> > 2. I don't have a -trans.fif file. I tried to do it in GUI of </DIV>
<DIV>>>> > MNE_analyze, it was quite complicated. If I have a co-registered mri </DIV>
<DIV>>>> > file (generated by CTF software with .mri extension), can it be </DIV>
<DIV>>>> > converted to fif format? If not, I can read the 4x4 head2mri matrix via </DIV>
<DIV>>>> > matlab, can this information be written to fif format with certain </DIV>
<DIV>>>> > tools </DIV>
<DIV>>>> > in MNE? </DIV>
<DIV>>>> </DIV>
<DIV>>>> There is also a coreg GUI in MNE-Python, have a look here </DIV>
<DIV>>>> </DIV>
<DIV>>>> http://www.slideshare.net/mne-python/mnepython-coregistration </DIV>
<DIV>>>> </DIV>
<DIV>>>> You could write a .fif file with the transform in Matlab, but it seems </DIV>
<DIV>>>> to me that this wouldn't be easier than using the coregistration tools </DIV>
<DIV>>>> in mne_analyze or MNE-Python. </DIV>
<DIV>>>> </DIV>
<DIV>>>> HTH, </DIV>
<DIV>>>> </DIV>
<DIV>>>> Martin </DIV>
<DIV>>>> </DIV>
<DIV>>>> </DIV>
<DIV>>>> > Thanks again! </DIV>
<DIV>>>> > </DIV>
<DIV>>>> > </DIV>
<DIV>>>> > On Tue, Mar 25, 2014 at 11:39 PM, Alexandre Gramfort </DIV>
<DIV>>>> > <alexandre.gramfort@telecom-paristech.fr </DIV>
<DIV>>>> > <mailto:alexandre.gramfort@telecom-paristech.fr>> wrote: </DIV>
<DIV>>>> > </DIV>
<DIV>>>> > hi, </DIV>
<DIV>>>> > </DIV>
<DIV>>>> > > Some additional questions. </DIV>
<DIV>>>> > > 1 After I ran mne_setup_forward_model, I have no feedback from </DIV>
<DIV>>>> > the </DIV>
<DIV>>>> > command </DIV>
<DIV>>>> > > line, is it normal? </DIV>
<DIV>>>> > </DIV>
<DIV>>>> > it should print that it saved a file to disk </DIV>
<DIV>>>> > </DIV>
<DIV>>>> > > 2 I am using CTF data, thus I converted the .ds folder from CTF </DIV>
<DIV>>>> > to fif </DIV>
<DIV>>>> > > format with mne_ctf2fiff command, with option --infoonly. Here I </DIV>
<DIV>>>> > only want </DIV>
<DIV>>>> > > to get the Leadfield thus I suppose data is not necessary. </DIV>
<DIV>>>> > However </DIV>
<DIV>>>> > when I </DIV>
<DIV>>>> > > try mne_do_forward_solution, it asked for mri description file, </DIV>
<DIV>>>> > which I </DIV>
<DIV>>>> > > haven't. I have only a series of dicom files or the .mri file </DIV>
<DIV>>>> > generated by </DIV>
<DIV>>>> > > ctf software from them. Can I still move on? </DIV>
<DIV>>>> > </DIV>
<DIV>>>> > you need to do the coregistration and get a -trans.fif file. </DIV>
<DIV>>>> > </DIV>
<DIV>>>> > A </DIV>
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