[Mne_analysis] mne_make_movie and centOS 6

Fri Aug 1 05:12:27 EDT 2014

Hi Burke,

The reason for this failure is that png and jpg conversions need the following programs somewhere on your PATH:

tifftopnm
pnmtojpeg
pnmtopng

They are obviously missing in your CentOS 6 installation.

- Matti

On Jul 31, 2014, at 5:47 PM, Burke Rosen <bqrosen at ucsd.edu> wrote:

> update: 
> 
> Using the --tif instead of the --png option works. --jpg also does not work. I am not sure why this is the case, but using the .tif files is a usable work-around. 
> 
> -Burke
> 
> 
> On 07/28/14 12:04, Burke Rosen wrote:
>> Hello, I am trying to save images with the following command:
>> 
>> mne_make_movie \
>> --pick 383 \
>> --integ 100 \
>> --subject fsaverage \
>> --fthresh 0.08 \
>> --fmid 0.11 \
>> --fmax 0.17 \
>> --stcin /home/bqrosen/projects/simon/MEG/group/TF/SC/groupavg_maps_n15/stcfiles/SC_groupavg_group_a_cond_21_mean-ico7 \
>> --png /home/bqrosen/projects/simon/MEG/group/TF/SC/groupavg_maps_n15/pngfiles_nolabel/test_ip82_SC_cong_a_0.08_0.11_0.17_mean_275_375 \
>> --view med \
>> --rh \
>> --qual 100 \
>> --nocomments \
>> --noscalebar \
>> --snr 5 \
>> --spm \
>> --smooth 10
>> 
>> When I run on my code on a centOS 5 machine it executes as expected and produces the intended .png file. However, when I run the same code on a centOS 6 machine, the output terminates with "system : No such file or directory". Interestingly, an output file is created with the correct name in the correct directory, but this file is empty.
>> 
>> It appear a similar issue was reported once before, though it was not resolved (and the OS comparison not made):
>> https://mail.nmr.mgh.harvard.edu/pipermail//mne_analysis/2012-December/001314.html
>> 
>> Below is the centOS 5 and centOS 6 output.
>> 
>> Thank you for your insight.
>> 
>> -Burke
>> 
>> centOS5:
>> mne_make_movie version 1.34 compiled at Dec 21 2009 19:48:23
>> Create movies and tif, rgb, jpeg, png, or w files  using a precomputed inverse operator decomposition
>> 
>> stc input file         : /home/bqrosen/projects/simon/MEG/group/TF/SC/groupavg_maps_n15/stcfiles/SC_groupavg_group_a_cond_21_mean-ico7
>> PNG output             : /home/bqrosen/projects/simon/MEG/group/TF/SC/groupavg_maps_n15/pngfiles_nolabel/test_ip82_SC_cong_a_0.08_0.11_0.17_mean_275_375
>>                          The input stc file will be assumed to contain dSPM data
>> Subject                : fsaverage
>> Visualization surface  : inflated
>>                          Process right hemisphere only
>> Magnification factor   : 1.00  
>> Time integration       : 100.0  ms
>> Thresholding:
>>     fthresh           : 0.08   
>>     fmid              : 0.11   
>>     fslope            : 16.67  
>>     fmax              : 0.17   
>> 
>> -------------------------------------------------------------------
>> 
>> 600 x 400 off-screen rendering initialized.
>> Selected view called 'med'
>> 
>> -------------------------------------------------------------------
>> 
>> read stc file /home/bqrosen/projects/simon/MEG/group/TF/SC/groupavg_maps_n15/stcfiles/SC_groupavg_group_a_cond_21_mean-ico7-lh.stc
>> read stc file /home/bqrosen/projects/simon/MEG/group/TF/SC/groupavg_maps_n15/stcfiles/SC_groupavg_group_a_cond_21_mean-ico7-rh.stc
>> 
>> -------------------------------------------------------------------
>> 
>> Loading inflated surfaces for subject fsaverage...
>> 
>> Triangle file : created by nicks on Wed Aug 15 21:20:39 2007 nvert = 163842 ntri = 327680
>>     Triangle and vertex normals and neighboring triangles...[done]
>>     Vertex neighbors...[done]
>>     Distances between neighboring vertices...[983040 distances done]
>> Triangle file : created by nicks on Wed Aug 15 21:20:57 2007 nvert = 163842 ntri = 327680
>>     Triangle and vertex normals and neighboring triangles...[done]
>>     Vertex neighbors...[done]
>>     Distances between neighboring vertices...[983040 distances done]
>> 
>> -------------------------------------------------------------------
>> 
>> Parameters set.
>> 
>> -------------------------------------------------------------------
>> 
>> No movie production requested.
>> 
>> -------------------------------------------------------------------
>> 
>> Some timeframes selected. Outputting png files (from stc files)
>> 
>> dSPM at t =   383.0 ms...lh : -0.0202 .. 0.1664  ave = 0.03849 rh : -0.02223 .. 0.1747  ave = 0.04297 
>> produced png file /home/bqrosen/projects/simon/MEG/group/TF/SC/groupavg_maps_n15/pngfiles_nolabel/test_ip82_SC_cong_a_0.08_0.11_0.17_mean_275_375-00383.0-med-rh.png
>> 
>> -------------------------------------------------------------------
>> 
>> No labels to process
>> 
>> -------------------------------------------------------------------
>> 
>> 
>> I think I responded favorably to all your requests. Good bye.
>> 
>> centOS6:
>> mne_make_movie version 1.34 compiled at Dec 21 2009 19:48:23
>> Create movies and tif, rgb, jpeg, png, or w files  using a precomputed inverse operator decomposition
>> 
>> stc input file         : /home/bqrosen/projects/simon/MEG/group/TF/SC/groupavg_maps_n15/stcfiles/SC_groupavg_group_a_cond_21_mean-ico7
>> PNG output             : /home/bqrosen/projects/simon/MEG/group/TF/SC/groupavg_maps_n15/pngfiles_nolabel/test_ip50_SC_cong_a_0.08_0.11_0.17_mean_275_375
>>                          The input stc file will be assumed to contain dSPM data
>> Subject                : fsaverage
>> Visualization surface  : inflated
>>                          Process right hemisphere only
>> Magnification factor   : 1.00  
>> Time integration       : 100.0  ms
>> Thresholding:
>>     fthresh           : 0.08   
>>     fmid              : 0.11   
>>     fslope            : 16.67  
>>     fmax              : 0.17   
>> 
>> -------------------------------------------------------------------
>> 
>> 600 x 400 off-screen rendering initialized.
>> Selected view called 'med'
>> 
>> -------------------------------------------------------------------
>> 
>> read stc file /home/bqrosen/projects/simon/MEG/group/TF/SC/groupavg_maps_n15/stcfiles/SC_groupavg_group_a_cond_21_mean-ico7-lh.stc
>> read stc file /home/bqrosen/projects/simon/MEG/group/TF/SC/groupavg_maps_n15/stcfiles/SC_groupavg_group_a_cond_21_mean-ico7-rh.stc
>> 
>> -------------------------------------------------------------------
>> 
>> Loading inflated surfaces for subject fsaverage...
>> 
>> Triangle file : created by nicks on Wed Aug 15 21:20:39 2007 nvert = 163842 ntri = 327680
>>     Triangle and vertex normals and neighboring triangles...[done]
>>     Vertex neighbors...[done]
>>     Distances between neighboring vertices...[983040 distances done]
>> Triangle file : created by nicks on Wed Aug 15 21:20:57 2007 nvert = 163842 ntri = 327680
>>     Triangle and vertex normals and neighboring triangles...[done]
>>     Vertex neighbors...[done]
>>     Distances between neighboring vertices...[983040 distances done]
>> 
>> -------------------------------------------------------------------
>> 
>> Parameters set.
>> 
>> -------------------------------------------------------------------
>> 
>> No movie production requested.
>> 
>> -------------------------------------------------------------------
>> 
>> Some timeframes selected. Outputting png files (from stc files)
>> 
>> dSPM at t =   383.0 ms...lh : -0.0202 .. 0.1664  ave = 0.03849 rh : -0.02223 .. 0.1747  ave = 0.04297 
>> system : No such file or directory
>> 
>> 
> 
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