[Mne_analysis] Mne_analysis Digest, Vol 96, Issue 19

[Eric Larson]

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:
>
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> 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...
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>
> ------------------------------
>
> 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
>
>
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