<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif; "><div>Matti and Eric,</div><div><br></div><div>I have it working now. I was modifying my local bash profile, but out sysadmin told me to not do that as the "master" profile was doing things correctly. Good suggestion on Eric's part to try FreeSurfer by itself.</div><div><br></div><div>-Jeff</div><div><br></div><span id="OLK_SRC_BODY_SECTION"><div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt"><span style="font-weight:bold">From: </span> Matti Hamalainen <<a href="mailto:msh@nmr.mgh.harvard.edu">msh@nmr.mgh.harvard.edu</a>><br><span style="font-weight:bold">To: </span> Jeff Eriksen <<a href="mailto:eriksenj@ohsu.edu">eriksenj@ohsu.edu</a>><br><span style="font-weight:bold">Cc: </span> Eric Larson <<a href="mailto:larson.eric.d@gmail.com">larson.eric.d@gmail.com</a>>, "<a href="mailto:mne_analysis@nmr.mgh.harvard.edu">mne_analysis@nmr.mgh.harvard.edu</a>" <<a href="mailto:mne_analysis@nmr.mgh.harvard.edu">mne_analysis@nmr.mgh.harvard.edu</a>><br><span style="font-weight:bold">Subject: </span> Re: [Mne_analysis] mne_analyze inverse display problem<br></div><div><br></div><div><meta http-equiv="Content-Type" content="text/html; charset=utf-8"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><br></div><div>Jeff,</div><div><br></div><div>The subject name is coded into the source space, forward solution, and inverse operator files. This means that the directory structure under SUBJECTS_DIR has to remain intact. Otherwise, the location does not matter as long as SUBJECTS_DIR is set correctly.
HOWEVER, if you have used media with a windows file system on it to transfer files, strange things may happen because symbolic links are not supported. </div><div><br></div><div>- Matti</div><br><div><div>On Jun 28, 2012, at 3:49 AM, Jeff Eriksen wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Eric et al.,<br><br>
I moved my files from Mac to Linux. I can open the averaged EEG, but when<br>
I try to open the surfaces they cannot be found. I am sure this is because<br>
their location was hard-coded in the fif files. Is there any way to change<br>
this? Otherwise I seem to have two options.<br><br>
Set up identical directory structure on Linux to match Mac folders<br>
Or<br>
Re-run the part of the MNE analysis that code the locations of surface<br>
(and other?) files into the fif files.<br><br>
I have set the appropriate FreeSurfer environmental variables, thinking<br>that would be enough, but apparently not.<br><br>
Thanks,<br>
-Jeff<br><br>
On 6/27/12 10:51 AM, "Eric Larson" <<a href="mailto:larson.eric.d@gmail.com">larson.eric.d@gmail.com</a>> wrote:<br><br><blockquote type="cite">Are you using OSX? I've had an issue with the display not working<br></blockquote><blockquote type="cite">appropriately sometimes (alternates between blank/maybe white and some<br></blockquote><blockquote type="cite">fixed image even when it should be updating). I chalked it up to an<br></blockquote><blockquote type="cite">improper implementation of OpenGL/XWindows on OSX since I have never<br></blockquote><blockquote type="cite">run into the same issue on linux x86_64 or i686.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Eric<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">On Wed, Jun 27, 2012 at 10:47 AM, Jeff Eriksen <<a href="mailto:eriksenj@ohsu.edu">eriksenj@ohsu.edu</a>> wrote:<br></blockquote><blockquote type="cite"><blockquote type="cite">Alex,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">I did mark the VREF channel as bad.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">I used the --diagnoise switch so as not to have to worry about the<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">actually noise-cov matrix at this point.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">The problem is not a scaling issue - it is a severe display issue/bug -<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">the entire pane goes completely white, no surface displayed, nothing,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">and<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">at that point I can not even get back to any of the three types of<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">inverses. The only way to continue is to exit mne_analyse and restart<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">it.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Thanks,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">-Jeff<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">On 6/26/12 11:50 PM, "Alexandre Gramfort" <<a href="mailto:gramfort@nmr.mgh.harvard.edu">gramfort@nmr.mgh.harvard.edu</a>><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">wrote:<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">hi,<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">I tried ico-4 and ico-5, and still get the same results poor<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">correlation<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">between scalp and cortical sources. I have not tried the ‹loose option<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">yet,<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">will do that this afternoon. I did try ‹diagnoise, and that seemed to<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">improve matters (though I do not know why the manual says most users<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">never<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">need to use this), but I am experiencing issues with mne_analyse in<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">trying<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">to display the three different estimates.<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">did you correct for the bad channel like matti suggested? did you take a<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">look<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">at the noise covariance you estimated from the data? Ideally it should<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">be<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">as diagonal as possible with similar values along the diagonal. See e.g.<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><a href="http://martinos.org/mne/auto_examples/plot_estimate_covariance_matrix_ra">http://martinos.org/mne/auto_examples/plot_estimate_covariance_matrix_ra</a><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">w.<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">html<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">for an example of noise covariance plot.<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">As I change from dSPM, which comes<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">up as defult, to MNE, the inflated brain pane goes white, and I cannot<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">get<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">it back until I exit and go back in. Ever seen this before?<br></blockquote></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">you certainly need to adjust the scaling of the colorbar.<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">do you see something like this:<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><a href="http://martinos.org/mne/_images/MNE_preferences.png">http://martinos.org/mne/_images/MNE_preferences.png</a><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">taken from :<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><a href="http://martinos.org/mne/manual/analyze.html#ch-interactive-analysis">http://martinos.org/mne/manual/analyze.html#ch-interactive-analysis</a><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Alex<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">The information in this e-mail is intended only for the person to whom<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">it<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">is<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">addressed. If you believe this e-mail was sent to you in error and the<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">e-mail<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">contains patient information, please contact the Partners Compliance<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">HelpLine at<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><a href="http://www.partners.org/complianceline">http://www.partners.org/complianceline</a> . If the e-mail was sent to you<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">in<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">error<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">but does not contain patient information, please contact the sender and<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">properly<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">dispose of the e-mail.<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">_______________________________________________<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Mne_analysis mailing list<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><a href="mailto:Mne_analysis@nmr.mgh.harvard.edu">Mne_analysis@nmr.mgh.harvard.edu</a><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><a href="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis">https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis</a><br></blockquote></blockquote><br><br>
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<a href="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis">https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis</a><br><br><br></div></blockquote></div><br><div apple-content-edited="true"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>---------</div><div><br></div><div>Matti Hamalainen, Ph.D.</div><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" style="font: normal normal normal 12px/normal Helvetica; ">Athinoula A. Martinos Center for Biomedical Imaging</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" style="font: normal normal normal 12px/normal Helvetica; ">Massachusetts General Hospital</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><br></div></div><div><a href="mailto:msh@nmr.mgh.harvard.edu">msh@nmr.mgh.harvard.edu</a></div></div></span></div></span></div></span></div></span></div></span><div><a href="mailto:mhamalainen@partners.org">mhamalainen@partners.org</a></div><div><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "></span></div><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"></span><br class="Apple-interchange-newline"></div><br></div></div></span></body></html>