<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><br></div>Hi again,<div><br><div><div>On Aug 19, 2011, at 1:27 PM, Matt Panichello wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Matti and Hari, thanks for explaining the summary waveform option. I removed the labeldir flag and can extract ~100 sources for each V1 ROI. <br><br>Dan, thanks also for your insight. Do you think that a highly decimated surface will undermine an analysis in any way? What is a more typical number of vertices for the entire brain?<br></blockquote><div><br></div>The about 11000 is the total number of sources which is ok. Nothing to worry about there.</div><div><br></div><div>- Matti</div><div><br></div><div> <br><blockquote type="cite">
<br>Thanks again!<br><br>Matt<br><br><br><br><div class="gmail_quote">On Fri, Aug 19, 2011 at 12:21 PM, Matti Hamalainen <span dir="ltr"><<a href="mailto:msh@nmr.mgh.harvard.edu">msh@nmr.mgh.harvard.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div bgcolor="#FFFFFF"><div>Hi,</div><div><br></div><div>With the labeldir option there will be only one summary waveform / label in the output file.</div>
<div><br></div><div><font color="#888888">- Matti</font><div><div></div><div class="h5"><br><br>On Aug 19, 2011, at 10:13 AM, Matt Panichello <<a href="mailto:panichem@nmr.mgh.harvard.edu" target="_blank">panichem@nmr.mgh.harvard.edu</a>> wrote:<br>
<br></div></div></div><div><div></div><div class="h5"><div></div><blockquote type="cite"><div><span style="font-family:arial, sans-serif;font-size:13px;background-color:rgb(255, 255, 255)"><div><span style="font-family:arial, sans-serif;font-size:13px;background-color:rgb(255, 255, 255)">Hi all,</span></div>
<div><span style="font-family:arial, sans-serif;font-size:13px;background-color:rgb(255, 255, 255)"><br></span></div><div><span style="font-family:arial, sans-serif;font-size:13px;background-color:rgb(255, 255, 255)">I am trying to extract the sources from labels using mne_compute_raw_inverse. The command finishes without error, but extracts extremely few sources for each label: 2 for a V1 label, and 3 for a rather large fusiform label. Both labels are based on the freesurfer parcellation of the surface and look fine in tksurfer. The exact command I am dropping looks like this:</span></div>
<div><span style="font-family:arial, sans-serif;font-size:13px;background-color:rgb(255, 255, 255)"><br></span></div><div><span style="font-family:arial, sans-serif;font-size:13px;background-color:rgb(255, 255, 255)">mne_compute_raw_invers --in (raw fif file) --inv (inverse solution) --labeldir (label directory) --picknormalcomp --align_z --snr 3 --out (outname)</span></div>
<div><span style="font-family:arial, sans-serif;font-size:13px;background-color:rgb(255, 255, 255)"><br></span></div><div><span style="font-family:arial, sans-serif;font-size:13px;background-color:rgb(255, 255, 255)">and my output is below. Any help would be appreciated! </span></div>
<div><span style="font-family:arial, sans-serif;font-size:13px;background-color:rgb(255, 255, 255)"><br></span></div><div><span style="font-family:arial, sans-serif;font-size:13px;background-color:rgb(255, 255, 255)">Thank you,</span></div>
<div><span style="font-family:arial, sans-serif;font-size:13px;background-color:rgb(255, 255, 255)"><br></span></div><div><span style="font-family:arial, sans-serif;font-size:13px;background-color:rgb(255, 255, 255)">Matt</span></div>
<div><span style="font-family:arial, sans-serif;font-size:13px;background-color:rgb(255, 255, 255)"><br></span></div><div><span style="font-family:arial, sans-serif;font-size:13px;background-color:rgb(255, 255, 255)"><br>
</span></div>mne_compute_raw_inverse version 1.15 compiled at Aug 19 2011 04:09:29<br><br>input file : S011/PM01_clean_raw.fif<br>inverse operator file : S011/ROI_freq/PM01_raw-5-meg-inv.fif<br>SNR : 3.000000<br>
Additional channels : 'STI 014'<br>All label files in S011/ROI_freq/ will be processed.<br>Source locations will be listed in head coordinates.<br><br>Reading the inverse operator...<br> Read 2 source spaces from S011/ROI_freq/PM01_raw-5-meg-inv.fif with a total of 11402 source locations<br>
Read the sensor covariance matrix (full)<br> Read the source covariance matrix (diagonal)<br> Measurement file id not found (omit matching).<br> Solution is based on MEG.<br> Inverse operator information was stored in head coordinates.<br>
Source orientation prior information read.<br> Depth-weighting prior information read.<br> Source orientations read.<br> Singular values read.<br> Eigenvectors read.<br> Number of channels = 305<br>
Number of sources = 11402<br> Free source orientations<br> Location information in head coordinates<br> Projection in effect:<br> # 1 : axial-PCA-01 : 1 vecs : 102 chs MEG active<br>
# 2 : axial-PCA-02 : 1 vecs : 102 chs MEG active<br> # 3 : axial-PCA-03 : 1 vecs : 102 chs MEG active<br> # 4 : axial-PCA-04 : 1 vecs : 102 chs MEG active<br><br>Adding derived data to the inverse operator (nave = 1)...<br>
Projection applied to the covariance matrix.<br> Decomposing the sensor noise covariance matrix...<br> Eigenvalue decomposition had been precomputed.<br> Eigenleads multiplied with Cholesky decomposition of the source covariance matrix.<br>
nave change: 1 -> 1<br><br>Raw data file S011/PM01_clean_raw.fif:<br><br>Processing label directory S011/ROI_freq/...<br>2 left-hemisphere labels in S011/ROI_freq/<br>1 right-hemisphere labels in S011/ROI_freq/<br>
Processing left-hemisphere labels...[done]<br>Processing right-hemisphere labels...[done]<br><br>Saving raw estimates...<br> Data will be split into <= 1907.3 MByte pieces<br> Processing raw data [2000 samples in each buffer] .........[1000 samples in each buffer] [done]<br>
393000 samples (including skips) saved to S011/ROI_freq/rh.V1.PM01.normal-mne_raw.fif ... closing...[done]<br></span><div><br></div><br>
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