[Mne_analysis] Mne_analysis Digest, Vol 96, Issue 21

dgw dgwakeman at gmail.com
Thu Jan 21 09:31:10 EST 2016
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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
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>> or, via email, send a message with subject or body 'help' to
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>>
>> 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
>>
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