[Mne_analysis] Mne_analysis Digest, Vol 96, Issue 21
Eric Larson
larson.eric.d at gmail.com
Thu Jan 21 09:34:41 EST 2016
Actually yeah, you could do that. It could lead to a lot of wasted
computation time to have to redo such a static, anatomy-(only)-dependent
step, but it would be doable. I'd still prefer running the 5120 version,
unless there is a good reason to suspect the 20480 will give better
results. It will also make forward solution calculation faster.
Eric
On Thu, Jan 21, 2016 at 9:31 AM, dgw <dgwakeman at gmail.com> wrote:
> Eric,
>
> What if he calculates it in mne-python on the fly and doesn't write to
> disk?
>
> d
>
> On Thu, Jan 21, 2016 at 9:26 AM, Eric Larson <larson.eric.d at gmail.com>
> wrote:
> > I suspect creating a 3-layer BEM solution with 20480 triangles will end
> up
> > using too much space -- to limit it would mean cutting off some data from
> > the solution, rendering it unusable.
> >
> > Have you tried using 5120 triangles (the default, ico 4)?
> >
> > Eric
> >
> >
> > On Thu, Jan 21, 2016 at 9:22 AM, Tadeusz W. Kononowicz
> > <t.w.kononowicz at icloud.com> wrote:
> >>
> >> Hello,
> >>
> >> Is there a quick fix to that limit that I could use locally?
> >>
> >> T
> >>
> >> On 21 Jan, 2016,at 03:16 PM, mne_analysis-request at nmr.mgh.harvard.edu
> >> wrote:
> >>
> >> Send Mne_analysis mailing list submissions to
> >> mne_analysis at nmr.mgh.harvard.edu
> >>
> >> To subscribe or unsubscribe via the World Wide Web, visit
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> >> or, via email, send a message with subject or body 'help' to
> >> mne_analysis-request at nmr.mgh.harvard.edu
> >>
> >> You can reach the person managing the list at
> >> mne_analysis-owner at nmr.mgh.harvard.edu
> >>
> >> When replying, please edit your Subject line so it is more specific
> >> than "Re: Contents of Mne_analysis digest..."
> >>
> >>
> >> Today's Topics:
> >>
> >> 1. Re: Mne_analysis Digest, Vol 96, Issue 19 (Eric Larson)
> >>
> >>
> >> ----------------------------------------------------------------------
> >>
> >> Message: 1
> >> Date: Thu, 21 Jan 2016 09:15:58 -0500
> >> From: Eric Larson <larson.eric.d at gmail.com>
> >> Subject: Re: [Mne_analysis] Mne_analysis Digest, Vol 96, Issue 19
> >> To: Discussion and support forum for the users of MNE Software
> >> <mne_analysis at nmr.mgh.harvard.edu>
> >> Message-ID:
> >> <CAGu2niXcWvm2XfpCuN1h9-EJmJo-nM=
> NNHTynN2PUstUOkYRmA at mail.gmail.com>
> >> Content-Type: text/plain; charset="utf-8"
> >>
> >> Ahh, that's likely the problem. There is a 2GB file size limit on FIF
> >> files, so the pointer to the next tag is invalid (probably overflows and
> >> goes negative?). Do you need 20480 triangles instead of 5120?
> >>
> >> Eric
> >>
> >>
> >> On Thu, Jan 21, 2016 at 9:13 AM, Tadeusz W. Kononowicz <
> >> t.w.kononowicz at icloud.com> wrote:
> >>
> >> Hi Alex,
> >>
> >>
> >> Not sure how we can do it as the file is 3G big.
> >>
> >> Do you have an access to Neurospin server?
> >>
> >>
> >> T.
> >>
> >>
> >> On 21 Jan, 2016,at 03:05 PM, mne_analysis-request at nmr.mgh.harvard.edu
> >>
> >> wrote:
> >>
> >>
> >> Send Mne_analysis mailing list submissions to
> >>
> >> mne_analysis at nmr.mgh.harvard.edu
> >>
> >>
> >> To subscribe or unsubscribe via the World Wide Web, visit
> >>
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> >>
> >> or, via email, send a message with subject or body 'help' to
> >>
> >> mne_analysis-request at nmr.mgh.harvard.edu
> >>
> >>
> >> You can reach the person managing the list at
> >>
> >> mne_analysis-owner at nmr.mgh.harvard.edu
> >>
> >>
> >> When replying, please edit your Subject line so it is more specific
> >>
> >> than "Re: Contents of Mne_analysis digest..."
> >>
> >>
> >>
> >> Today's Topics:
> >>
> >>
> >> 1. reading bem solution (Tadeusz W. Kononowicz)
> >>
> >> 2. Re: reading bem solution (Alexandre Gramfort)
> >>
> >>
> >>
> >> ----------------------------------------------------------------------
> >>
> >>
> >> Message: 1
> >>
> >> Date: Thu, 21 Jan 2016 13:33:52 +0000 (GMT)
> >>
> >> From: "Tadeusz W. Kononowicz" <t.w.kononowicz at icloud.com>
> >>
> >> Subject: [Mne_analysis] reading bem solution
> >>
> >> To: mne_analysis at nmr.mgh.harvard.edu
> >>
> >> Message-ID: <0eea2f05-e157-40f6-bd2b-d08d4257c789 at me.com>
> >>
> >> Content-Type: text/plain; charset="us-ascii"
> >>
> >>
> >> Hello Mne Users,
> >>
> >>
> >>
> >> This code works fine:
> >>
> >> bem1 = path + '-20480-20480-20480-bem-sol.fif'
> >>
> >> surfaces = mne.read_bem_surfaces(bem1)
> >>
> >>
> >> But when I want to read another solution I got that. Any hints?
> >>
> >>
> >>
> >> bem2 = path + '-5120-5120-5120-bem-sol.fif'
> >>
> >> surfaces = mne.read_bem_surfaces(bem2)
> >>
> >>
> >>
> >>
> ---------------------------------------------------------------------------
> >>
> >> IOError Traceback (most recent call last)
> >>
> >> <ipython-input-10-5b41654e22f2> in <module>()
> >>
> >> ----> 1 surfaces = mne.read_bem_surfaces(sub_name_bem)
> >>
> >>
> >>
> >>
> /home/tkononow/anaconda2/lib/python2.7/site-packages/mne-0.11.0-py2.7.egg/mne/bem.pyc
> >>
> >> in read_bem_surfaces(fname, patch_stats, s_id, verbose)
> >>
> >>
> >>
> >>
> /home/tkononow/anaconda2/lib/python2.7/site-packages/mne-0.11.0-py2.7.egg/mne/utils.pyc
> >>
> >> in verbose(function, *args, **kwargs)
> >>
> >> 549 finally:
> >>
> >> 550 set_log_level(old_level)
> >>
> >> --> 551 return function(*args, **kwargs)
> >>
> >> 552
> >>
> >> 553
> >>
> >>
> >>
> >>
> /home/tkononow/anaconda2/lib/python2.7/site-packages/mne-0.11.0-py2.7.egg/mne/bem.pyc
> >>
> >> in read_bem_surfaces(fname, patch_stats, s_id, verbose)
> >>
> >> 1063 coord_frame = FIFF.FIFFV_COORD_MRI
> >>
> >> 1064 # Open the file, create directory
> >>
> >> -> 1065 f, tree, _ = fiff_open(fname)
> >>
> >> 1066 with f as fid:
> >>
> >> 1067 # Find BEM
> >>
> >>
> >>
> >>
> /home/tkononow/anaconda2/lib/python2.7/site-packages/mne-0.11.0-py2.7.egg/mne/io/open.pyc
> >>
> >> in fiff_open(fname, preload, verbose)
> >>
> >>
> >>
> >>
> /home/tkononow/anaconda2/lib/python2.7/site-packages/mne-0.11.0-py2.7.egg/mne/utils.pyc
> >>
> >> in verbose(function, *args, **kwargs)
> >>
> >> 549 finally:
> >>
> >> 550 set_log_level(old_level)
> >>
> >> --> 551 return function(*args, **kwargs)
> >>
> >> 552
> >>
> >> 553
> >>
> >>
> >>
> >>
> /home/tkononow/anaconda2/lib/python2.7/site-packages/mne-0.11.0-py2.7.egg/mne/io/open.pyc
> >>
> >> in fiff_open(fname, preload, verbose)
> >>
> >> 144 directory.append(tag)
> >>
> >> 145
> >>
> >> --> 146 tree, _ = make_dir_tree(fid, directory)
> >>
> >> 147
> >>
> >> 148 logger.debug('[done]')
> >>
> >>
> >>
> >>
> /home/tkononow/anaconda2/lib/python2.7/site-packages/mne-0.11.0-py2.7.egg/mne/io/tree.pyc
> >>
> >> in make_dir_tree(fid, directory, start, indent, verbose)
> >>
> >>
> >>
> >>
> /home/tkononow/anaconda2/lib/python2.7/site-packages/mne-0.11.0-py2.7.egg/mne/utils.pyc
> >>
> >> in verbose(function, *args, **kwargs)
> >>
> >> 549 finally:
> >>
> >> 550 set_log_level(old_level)
> >>
> >> --> 551 return function(*args, **kwargs)
> >>
> >> 552
> >>
> >> 553
> >>
> >>
> >>
> >>
> /home/tkononow/anaconda2/lib/python2.7/site-packages/mne-0.11.0-py2.7.egg/mne/io/tree.pyc
> >>
> >> in make_dir_tree(fid, directory, start, indent, verbose)
> >>
> >> 76 if directory[this].kind == FIFF_BLOCK_START:
> >>
> >> 77 if this != start:
> >>
> >> ---> 78 child, this = make_dir_tree(fid, directory, this, indent + 1)
> >>
> >> 79 tree['nchild'] += 1
> >>
> >> 80 tree['children'].append(child)
> >>
> >>
> >>
> >>
> /home/tkononow/anaconda2/lib/python2.7/site-packages/mne-0.11.0-py2.7.egg/mne/io/tree.pyc
> >>
> >> in make_dir_tree(fid, directory, start, indent, verbose)
> >>
> >>
> >>
> >>
> /home/tkononow/anaconda2/lib/python2.7/site-packages/mne-0.11.0-py2.7.egg/mne/utils.pyc
> >>
> >> in verbose(function, *args, **kwargs)
> >>
> >> 549 finally:
> >>
> >> 550 set_log_level(old_level)
> >>
> >> --> 551 return function(*args, **kwargs)
> >>
> >> 552
> >>
> >> 553
> >>
> >>
> >>
> >>
> /home/tkononow/anaconda2/lib/python2.7/site-packages/mne-0.11.0-py2.7.egg/mne/io/tree.pyc
> >>
> >> in make_dir_tree(fid, directory, start, indent, verbose)
> >>
> >> 55
> >>
> >> 56 if directory[start].kind == FIFF_BLOCK_START:
> >>
> >> ---> 57 tag = read_tag(fid, directory[start].pos)
> >>
> >> 58 block = tag.data
> >>
> >> 59 else:
> >>
> >>
> >>
> >>
> /home/tkononow/anaconda2/lib/python2.7/site-packages/mne-0.11.0-py2.7.egg/mne/io/tag.pyc
> >>
> >> in read_tag(fid, pos, shape, rlims)
> >>
> >> 480 if tag.next != FIFF.FIFFV_NEXT_SEQ:
> >>
> >> 481 # f.seek(tag.next,0)
> >>
> >> --> 482 fid.seek(tag.next, 1) # XXX : fix? pb when tag.next < 0
> >>
> >> 483
> >>
> >> 484 return tag
> >>
> >>
> >> IOError: [Errno 22] Invalid argument
> >>
> >>
> >>
> >> Thank you for your help,
> >>
> >>
> >> Tadeusz W. Kononowicz
> >>
> >> -------------- next part --------------
> >>
> >> An HTML attachment was scrubbed...
> >>
> >> URL:
> >>
> >>
> >>
> http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20160121/55269845/attachment-0001.html
> >>
> >>
> >> ------------------------------
> >>
> >>
> >> Message: 2
> >>
> >> Date: Thu, 21 Jan 2016 15:05:02 +0100
> >>
> >> From: Alexandre Gramfort <alexandre.gramfort at telecom-paristech.fr>
> >>
> >> Subject: Re: [Mne_analysis] reading bem solution
> >>
> >> To: Discussion and support forum for the users of MNE Software
> >>
> >> <mne_analysis at nmr.mgh.harvard.edu>
> >>
> >> Message-ID:
> >>
> >> <CADeotZohizT9KWWhA5H8zWJ5uQt3=u8ZYKg47XTu5Qtz4L1bwg at mail.gmail.com>
> >>
> >> Content-Type: text/plain; charset="utf-8"
> >>
> >>
> >> hi Tadeusz,
> >>
> >>
> >> can you share the problematic file.
> >>
> >>
> >> Alex
> >>
> >>
> >>
> >> On Thu, Jan 21, 2016 at 2:33 PM, Tadeusz W. Kononowicz <
> >>
> >> t.w.kononowicz at icloud.com> wrote:
> >>
> >>
> >> Hello Mne Users,
> >>
> >>
> >>
> >>
> >>
> >> This code works fine:
> >>
> >>
> >>
> >> bem1 = path + '-20480-20480-20480-bem-sol.fif'
> >>
> >>
> >>
> >> surfaces = mne.read_bem_surfaces(bem1)
> >>
> >>
> >>
> >>
> >> But when I want to read another solution I got that. Any hints?
> >>
> >>
> >>
> >>
> >>
> >> bem2 = path + '-5120-5120-5120-bem-sol.fif'
> >>
> >>
> >>
> >> surfaces = mne.read_bem_surfaces(bem2)
> >>
> >>
> >>
> >>
> >>
> >>
> ---------------------------------------------------------------------------
> >>
> >>
> >>
> >> IOError Traceback (most recent call last)
> >>
> >>
> >>
> >> <ipython-input-10-5b41654e22f2> in <module>()
> >>
> >>
> >>
> >> ----> 1 surfaces = mne.read_bem_surfaces(sub_name_bem)
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> /home/tkononow/anaconda2/lib/python2.7/site-packages/mne-0.11.0-py2.7.egg/mne/bem.pyc
> >>
> >>
> >> in read_bem_surfaces(fname, patch_stats, s_id, verbose)
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> /home/tkononow/anaconda2/lib/python2.7/site-packages/mne-0.11.0-py2.7.egg/mne/utils.pyc
> >>
> >>
> >> in verbose(function, *args, **kwargs)
> >>
> >>
> >>
> >> 549 finally:
> >>
> >>
> >>
> >> 550 set_log_level(old_level)
> >>
> >>
> >>
> >> --> 551 return function(*args, **kwargs)
> >>
> >>
> >>
> >> 552
> >>
> >>
> >>
> >> 553
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> /home/tkononow/anaconda2/lib/python2.7/site-packages/mne-0.11.0-py2.7.egg/mne/bem.pyc
> >>
> >>
> >> in read_bem_surfaces(fname, patch_stats, s_id, verbose)
> >>
> >>
> >>
> >> 1063 coord_frame = FIFF.FIFFV_COORD_MRI
> >>
> >>
> >>
> >> 1064 # Open the file, create directory
> >>
> >>
> >>
> >> -> 1065 f, tree, _ = fiff_open(fname)
> >>
> >>
> >>
> >> 1066 with f as fid:
> >>
> >>
> >>
> >> 1067 # Find BEM
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> /home/tkononow/anaconda2/lib/python2.7/site-packages/mne-0.11.0-py2.7.egg/mne/io/open.pyc
> >>
> >>
> >> in fiff_open(fname, preload, verbose)
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> /home/tkononow/anaconda2/lib/python2.7/site-packages/mne-0.11.0-py2.7.egg/mne/utils.pyc
> >>
> >>
> >> in verbose(function, *args, **kwargs)
> >>
> >>
> >>
> >> 549 finally:
> >>
> >>
> >>
> >> 550 set_log_level(old_level)
> >>
> >>
> >>
> >> --> 551 return function(*args, **kwargs)
> >>
> >>
> >>
> >> 552
> >>
> >>
> >>
> >> 553
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> /home/tkononow/anaconda2/lib/python2.7/site-packages/mne-0.11.0-py2.7.egg/mne/io/open.pyc
> >>
> >>
> >> in fiff_open(fname, preload, verbose)
> >>
> >>
> >>
> >> 144 directory.append(tag)
> >>
> >>
> >>
> >> 145
> >>
> >>
> >>
> >> --> 146 tree, _ = make_dir_tree(fid, directory)
> >>
> >>
> >>
> >> 147
> >>
> >>
> >>
> >> 148 logger.debug('[done]')
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> /home/tkononow/anaconda2/lib/python2.7/site-packages/mne-0.11.0-py2.7.egg/mne/io/tree.pyc
> >>
> >>
> >> in make_dir_tree(fid, directory, start, indent, verbose)
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> /home/tkononow/anaconda2/lib/python2.7/site-packages/mne-0.11.0-py2.7.egg/mne/utils.pyc
> >>
> >>
> >> in verbose(function, *args, **kwargs)
> >>
> >>
> >>
> >> 549 finally:
> >>
> >>
> >>
> >> 550 set_log_level(old_level)
> >>
> >>
> >>
> >> --> 551 return function(*args, **kwargs)
> >>
> >>
> >>
> >> 552
> >>
> >>
> >>
> >> 553
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> /home/tkononow/anaconda2/lib/python2.7/site-packages/mne-0.11.0-py2.7.egg/mne/io/tree.pyc
> >>
> >>
> >> in make_dir_tree(fid, directory, start, indent, verbose)
> >>
> >>
> >>
> >> 76 if directory[this].kind == FIFF_BLOCK_START:
> >>
> >>
> >>
> >> 77 if this != start:
> >>
> >>
> >>
> >> ---> 78 child, this = make_dir_tree(fid, directory, this, indent + 1)
> >>
> >>
> >>
> >> 79 tree['nchild'] += 1
> >>
> >>
> >>
> >> 80 tree['children'].append(child)
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> /home/tkononow/anaconda2/lib/python2.7/site-packages/mne-0.11.0-py2.7.egg/mne/io/tree.pyc
> >>
> >>
> >> in make_dir_tree(fid, directory, start, indent, verbose)
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> /home/tkononow/anaconda2/lib/python2.7/site-packages/mne-0.11.0-py2.7.egg/mne/utils.pyc
> >>
> >>
> >> in verbose(function, *args, **kwargs)
> >>
> >>
> >>
> >> 549 finally:
> >>
> >>
> >>
> >> 550 set_log_level(old_level)
> >>
> >>
> >>
> >> --> 551 return function(*args, **kwargs)
> >>
> >>
> >>
> >> 552
> >>
> >>
> >>
> >> 553
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> /home/tkononow/anaconda2/lib/python2.7/site-packages/mne-0.11.0-py2.7.egg/mne/io/tree.pyc
> >>
> >>
> >> in make_dir_tree(fid, directory, start, indent, verbose)
> >>
> >>
> >>
> >> 55
> >>
> >>
> >>
> >> 56 if directory[start].kind == FIFF_BLOCK_START:
> >>
> >>
> >>
> >> ---> 57 tag = read_tag(fid, directory[start].pos)
> >>
> >>
> >>
> >> 58 block = tag.data
> >>
> >>
> >>
> >> 59 else:
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> /home/tkononow/anaconda2/lib/python2.7/site-packages/mne-0.11.0-py2.7.egg/mne/io/tag.pyc
> >>
> >>
> >> in read_tag(fid, pos, shape, rlims)
> >>
> >>
> >>
> >> 480 if tag.next != FIFF.FIFFV_NEXT_SEQ:
> >>
> >>
> >>
> >> 481 # f.seek(tag.next,0)
> >>
> >>
> >>
> >> --> 482 fid.seek(tag.next, 1) # XXX : fix? pb when tag.next < 0
> >>
> >>
> >>
> >> 483
> >>
> >>
> >>
> >> 484 return tag
> >>
> >>
> >>
> >>
> >> IOError: [Errno 22] Invalid argument
> >>
> >>
> >>
> >>
> >>
> >> Thank you for your help,
> >>
> >>
> >>
> >>
> >> Tadeusz W. Kononowicz
> >>
> >>
> >>
> >> _______________________________________________
> >>
> >>
> >> 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.
> >>
> >>
> >>
> >>
> >> -------------- next part --------------
> >>
> >> An HTML attachment was scrubbed...
> >>
> >> URL:
> >>
> >>
> >>
> http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20160121/4cd225c0/attachment.html
> >>
> >>
> >> ------------------------------
> >>
> >>
> >> _______________________________________________
> >>
> >> Mne_analysis mailing list
> >>
> >> Mne_analysis at nmr.mgh.harvard.edu
> >>
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> >>
> >>
> >> End of Mne_analysis Digest, Vol 96, Issue 19
> >>
> >> ********************************************
> >>
> >>
> >>
> >> _______________________________________________
> >>
> >> 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
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> >> HelpLine at
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> in
> >>
> >> error
> >>
> >> but does not contain patient information, please contact the sender and
> >>
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