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NEUROMEG  August 2014

NEUROMEG August 2014

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Subject:

Skipping

From:

Rik Henson <[log in to unmask]>

Reply-To:

Rik Henson <[log in to unmask]>

Date:

Tue, 12 Aug 2014 08:28:53 +0000

Content-Type:

text/plain

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Parts/Attachments

text/plain (146 lines)

Dear NeuroMEG

We have some raw FIF datasets in which cHPI was only switched on between 30 and 100s after data recording started (lab policy, to allow initial checking of data quality before cHPI activated). Using a "full monty" MF2.2 command like:

/neuro/bin/util/maxfilter-2.2 -f infile_raw.fif -o outfile.fif  -ctc /neuro/databases/ctc/ct_sparse.fif   -cal /neuro/databases/sss/sss_cal.dat -autobad on  -frame head -origin 17.576 9.671 41.64 -st 10 -corr 0.98  -linefreq 50 -hpistep 10 -hpisubt amp -hpicons -movecomp inter -hp posfile.pos -trans default -frame head -origin 17.576 -3.329 47.64 -v | tee logfile.log

produces a core dump on some files like in example output appended below.  I wondered whether this is because the cHPI  is turned on later (interacting perhaps with length of tSSS buffer, or something?), so I added " -skip 0 X", and execution then works fine (where X = 60 for example). 

My problem is determining X. Because different raw files (different subjects) have variable delays before cHPI turne don, X varies across subjects (eg X=60 leads to a core dump for a subject whose recording seems to start later, but then works for X=100...). Ideally, I would like all output files to start at the same point (ie onset of cHPI). Is there an easy way to automatically determine X (other than running once, examining MF2.2 logfile, selecting X, etc, since I have 100s of subjects!) - eg can I extract the cHPI onset time from an initial show_fiff command? (Or is there another way to avoid these crashes?)

Thanks
Rik


************************************************************
*** This is Elekta Neuromag MaxFilter(TM) version 2.2.10  ***
*** Compilation date: Oct 11 2010 14:45:43               ***
*** Please report problems to [log in to unmask]     ***
************************************************************
No processing records found.
SSS origin (head) 17.6, -3.3, 47.6 mm.
Time scale: #f = 43.000 s, #l = 607.000 s  (initial skip #s = 43.000 s)
Using the default virtual transformation.
Applying the fine-calibration in /neuro/databases/sss/sss_cal.dat.
Using the cross-talk matrix in /neuro/databases/ctc/ct_sparse.fif.
Opened FIFF file infile_raw.fif (564 data buffers).
Started result FIFF file outfile.fif.
Signal Space Separation: Movement compensation for Elekta Neuromag data using tSSS.
HPIFIT: 5 coils digitized in order 2 3 5 1 4 
HPIFIT: 3 coils accepted: 1 3 4 
Coordinate transformations:
  0.9996  -0.0207   0.0213 !  1.0000   0.0000   0.0000
  0.0158   0.9774   0.2107 !  0.0000   1.0000   0.0000
 -0.0252  -0.2103   0.9773 !  0.0000   0.0000   1.0000
  0.6046  -0.1646  46.3373 ! 17.5760  -3.3290  47.6400
Rotation change -0.0, -0.2, -0.2 degrees
Position change (-17.0, 3.2, -1.3) = 17.3 mm
Found 338 total and 306 MEG channels.
Automatic bad channel detection is off.
SSS: 70/80 inside and 11/15 outside harmonic components.
CTC: Channel lists of the (306 x 306) matrix OK.
Using 5 HPI coils: 293 307 314 321 328 Hz
Line interference frequencies: 50 100 150 200 250 300 350 Hz
HPIFIT errors:  0.7, 14.6, 0.2, 0.5, 2.8 mm.
HP fitting limits: err = 5.0 mm, gval = 0.980.
Storing head positions to posfile.pos
--- Reading raw tag #b = 1/564 (#t = 43.000) ---
--- Reading raw tag #b = 2/564 (#t = 44.000) ---
--- Reading raw tag #b = 3/564 (#t = 45.000) ---
--- Reading raw tag #b = 4/564 (#t = 46.000) ---
--- Reading raw tag #b = 5/564 (#t = 47.000) ---
--- Reading raw tag #b = 6/564 (#t = 48.000) ---
--- Reading raw tag #b = 7/564 (#t = 49.000) ---
--- Reading raw tag #b = 8/564 (#t = 50.000) ---
--- Reading raw tag #b = 9/564 (#t = 51.000) ---
--- Reading raw tag #b = 10/564 (#t = 52.000) ---
--- Reading raw tag #b = 11/564 (#t = 53.000) ---
--- Reading raw tag #b = 12/564 (#t = 54.000) ---
All channels OK.
Time 43.000: cont HPI is off, using the previous head position!
   71.7  -30.8    0.4 /  72.0  -31.3    0.1 / g = 0.995 err =  0.7 mm / 1.000 -0.021  0.021
   -2.2  -36.7  124.3 /  -2.2  -36.7  124.3 / g = 0.998 err =  0.0 mm / 0.016  0.977  0.211
  -57.4   73.9   70.1 / -57.4   74.0   70.3 / g = 0.995 err =  0.2 mm /-0.025 -0.210  0.977
   61.1   69.2   74.8 /  60.8   69.6   75.1 / g = 0.997 err =  0.5 mm /   0.6   -0.2   46.3
  -71.9  -28.1   -0.2 / -71.9  -28.1   -0.2 / g = 0.997 err =  0.0 mm /
#t = 43.000, #e = 0.00 cm, #g = 0.000, #v = 0.00 cm/s, #r = 0.00 rad/s, #d = 0.00 cm
Time 44.000: cont HPI is off, using the previous head position!
   71.7  -30.8    0.4 /  72.0  -31.3    0.1 / g = 0.995 err =  0.7 mm / 1.000 -0.021  0.021
   -2.2  -36.7  124.3 /  -2.2  -36.7  124.3 / g = 0.998 err =  0.0 mm / 0.016  0.977  0.211
  -57.4   73.9   70.1 / -57.4   74.0   70.3 / g = 0.995 err =  0.2 mm /-0.025 -0.210  0.977
   61.1   69.2   74.8 /  60.8   69.6   75.1 / g = 0.997 err =  0.5 mm /   0.6   -0.2   46.3
  -71.9  -28.1   -0.2 / -71.9  -28.1   -0.2 / g = 0.997 err =  0.0 mm /
#t = 43.000, #e = 0.00 cm, #g = 0.000, #v = 0.00 cm/s, #r = 0.00 rad/s, #d = 0.00 cm
Time 45.000: cont HPI is off, using the previous head position!
   71.7  -30.8    0.4 /  72.0  -31.3    0.1 / g = 0.995 err =  0.7 mm / 1.000 -0.021  0.021
   -2.2  -36.7  124.3 /  -2.2  -36.7  124.3 / g = 0.998 err =  0.0 mm / 0.016  0.977  0.211
  -57.4   73.9   70.1 / -57.4   74.0   70.3 / g = 0.995 err =  0.2 mm /-0.025 -0.210  0.977
   61.1   69.2   74.8 /  60.8   69.6   75.1 / g = 0.997 err =  0.5 mm /   0.6   -0.2   46.3
  -71.9  -28.1   -0.2 / -71.9  -28.1   -0.2 / g = 0.997 err =  0.0 mm /
#t = 43.000, #e = 0.00 cm, #g = 0.000, #v = 0.00 cm/s, #r = 0.00 rad/s, #d = 0.00 cm
Time 46.000: cont HPI is off, using the previous head position!
   71.7  -30.8    0.4 /  72.0  -31.3    0.1 / g = 0.995 err =  0.7 mm / 1.000 -0.021  0.021
   -2.2  -36.7  124.3 /  -2.2  -36.7  124.3 / g = 0.998 err =  0.0 mm / 0.016  0.977  0.211
  -57.4   73.9   70.1 / -57.4   74.0   70.3 / g = 0.995 err =  0.2 mm /-0.025 -0.210  0.977
   61.1   69.2   74.8 /  60.8   69.6   75.1 / g = 0.997 err =  0.5 mm /   0.6   -0.2   46.3
  -71.9  -28.1   -0.2 / -71.9  -28.1   -0.2 / g = 0.997 err =  0.0 mm /
#t = 43.000, #e = 0.00 cm, #g = 0.000, #v = 0.00 cm/s, #r = 0.00 rad/s, #d = 0.00 cm
Time 47.000: cont HPI is off, using the previous head position!
   71.7  -30.8    0.4 /  72.0  -31.3    0.1 / g = 0.995 err =  0.7 mm / 1.000 -0.021  0.021
   -2.2  -36.7  124.3 /  -2.2  -36.7  124.3 / g = 0.998 err =  0.0 mm / 0.016  0.977  0.211
  -57.4   73.9   70.1 / -57.4   74.0   70.3 / g = 0.995 err =  0.2 mm /-0.025 -0.210  0.977
   61.1   69.2   74.8 /  60.8   69.6   75.1 / g = 0.997 err =  0.5 mm /   0.6   -0.2   46.3
  -71.9  -28.1   -0.2 / -71.9  -28.1   -0.2 / g = 0.997 err =  0.0 mm /
#t = 43.000, #e = 0.00 cm, #g = 0.000, #v = 0.00 cm/s, #r = 0.00 rad/s, #d = 0.00 cm
Time 48.000: cont HPI is off, using the previous head position!
   71.7  -30.8    0.4 /  72.0  -31.3    0.1 / g = 0.995 err =  0.7 mm / 1.000 -0.021  0.021
   -2.2  -36.7  124.3 /  -2.2  -36.7  124.3 / g = 0.998 err =  0.0 mm / 0.016  0.977  0.211
  -57.4   73.9   70.1 / -57.4   74.0   70.3 / g = 0.995 err =  0.2 mm /-0.025 -0.210  0.977
   61.1   69.2   74.8 /  60.8   69.6   75.1 / g = 0.997 err =  0.5 mm /   0.6   -0.2   46.3
  -71.9  -28.1   -0.2 / -71.9  -28.1   -0.2 / g = 0.997 err =  0.0 mm /
#t = 43.000, #e = 0.00 cm, #g = 0.000, #v = 0.00 cm/s, #r = 0.00 rad/s, #d = 0.00 cm
Time 49.000: cont HPI is off, using the previous head position!
   71.7  -30.8    0.4 /  72.0  -31.3    0.1 / g = 0.995 err =  0.7 mm / 1.000 -0.021  0.021
   -2.2  -36.7  124.3 /  -2.2  -36.7  124.3 / g = 0.998 err =  0.0 mm / 0.016  0.977  0.211
  -57.4   73.9   70.1 / -57.4   74.0   70.3 / g = 0.995 err =  0.2 mm /-0.025 -0.210  0.977
   61.1   69.2   74.8 /  60.8   69.6   75.1 / g = 0.997 err =  0.5 mm /   0.6   -0.2   46.3
  -71.9  -28.1   -0.2 / -71.9  -28.1   -0.2 / g = 0.997 err =  0.0 mm /
#t = 43.000, #e = 0.00 cm, #g = 0.000, #v = 0.00 cm/s, #r = 0.00 rad/s, #d = 0.00 cm
Time 50.000: cont HPI is off, using the previous head position!
   71.7  -30.8    0.4 /  72.0  -31.3    0.1 / g = 0.995 err =  0.7 mm / 1.000 -0.021  0.021
   -2.2  -36.7  124.3 /  -2.2  -36.7  124.3 / g = 0.998 err =  0.0 mm / 0.016  0.977  0.211
  -57.4   73.9   70.1 / -57.4   74.0   70.3 / g = 0.995 err =  0.2 mm /-0.025 -0.210  0.977
   61.1   69.2   74.8 /  60.8   69.6   75.1 / g = 0.997 err =  0.5 mm /   0.6   -0.2   46.3
  -71.9  -28.1   -0.2 / -71.9  -28.1   -0.2 / g = 0.997 err =  0.0 mm /
#t = 43.000, #e = 0.00 cm, #g = 0.000, #v = 0.00 cm/s, #r = 0.00 rad/s, #d = 0.00 cm
Time 51.000: cont HPI is off, using the previous head position!
   71.7  -30.8    0.4 /  72.0  -31.3    0.1 / g = 0.995 err =  0.7 mm / 1.000 -0.021  0.021
   -2.2  -36.7  124.3 /  -2.2  -36.7  124.3 / g = 0.998 err =  0.0 mm / 0.016  0.977  0.211
  -57.4   73.9   70.1 / -57.4   74.0   70.3 / g = 0.995 err =  0.2 mm /-0.025 -0.210  0.977
   61.1   69.2   74.8 /  60.8   69.6   75.1 / g = 0.997 err =  0.5 mm /   0.6   -0.2   46.3
  -71.9  -28.1   -0.2 / -71.9  -28.1   -0.2 / g = 0.997 err =  0.0 mm /
#t = 43.000, #e = 0.00 cm, #g = 0.000, #v = 0.00 cm/s, #r = 0.00 rad/s, #d = 0.00 cm
Time 52.000: cont HPI is off, using the previous head position!
   71.7  -30.8    0.4 /  72.0  -31.3    0.1 / g = 0.995 err =  0.7 mm / 1.000 -0.021  0.021
   -2.2  -36.7  124.3 /  -2.2  -36.7  124.3 / g = 0.998 err =  0.0 mm / 0.016  0.977  0.211
  -57.4   73.9   70.1 / -57.4   74.0   70.3 / g = 0.995 err =  0.2 mm /-0.025 -0.210  0.977
   61.1   69.2   74.8 /  60.8   69.6   75.1 / g = 0.997 err =  0.5 mm /   0.6   -0.2   46.3
  -71.9  -28.1   -0.2 / -71.9  -28.1   -0.2 / g = 0.997 err =  0.0 mm /
#t = 43.000, #e = 0.00 cm, #gProgram died due to signal 11, all output files were deleted!
Core dump disabled.


-------------------------------------------------------
Professor Richard Henson
Deputy Director
MRC Cognition & Brain Sciences Unit
15 Chaucer Road
Cambridge, CB2 7EF
England
EMAIL:  [log in to unmask]
URL:    http://www.mrc-cbu.cam.ac.uk/people/rik.henson/personal
TEL     +44 (0)1223 355 294 x501
FAX     +44 (0)1223 359 062
MOB     +44 (0)794 1377 345
-------------------------------------------------------

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