Hi Steve,
Thank you very much for your response. I'm asking our system administrator about the Mac version. In the meantime, I ran the two lines in your last e-mail, and the following is what I got:
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$FSLDIR/bin/gnuplot
G N U P L O T
version 3.7
patchlevel 1
last modified Fri Oct 22 18:00:00 BST 1999
Copyright(C) 1986 - 1993, 1998, 1999
Thomas Williams, Colin Kelley and many others
Type `help` to access the on-line reference manual
The gnuplot FAQ is available from
<http://www.ucc.ie/gnuplot/gnuplot-faq.html>
Send comments and requests for help to <[log in to unmask]>
Send bugs, suggestions and mods to <[log in to unmask]>
plot.c:630: failed assertion `p >= home && p <= (home + sizeof(home) - 1 - 2)'
Abort
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$FSLDIR/bin/convert
Version: @(#)ImageMagick 5.4.0 11/01/01 Q:16 http://www.imagemagick.org
Copyright: Copyright (C) 2001 ImageMagick Studio
Usage: convertb [options ...] file [ files... ] output_file
Where options include:
-adjoin join images into a single multi-image file
-affine matrix drawing transform matrix
-antialias remove pixel-aliasing
-append append an image sequence
-average average an image sequence
-background color background color
-blur geometry blur the image
-border geometry surround image with a border of color
-bordercolor color border color
-box color color for annotation bounding box
-cache threshold megabytes of memory available to the pixel cache
-channel type extract a particular color chanell from image
-charcoal radius simulate a charcoal drawing
-coalesce merge a sequence of images
-colorize value colorize the image with the fill color
-colors value preferred number of colors in the image
-colorspace type alternate image colorspace
-comment string annotate image with comment
-compress type type of image compression
-contrast enhance or reduce the image contrast
-crop geometry preferred size and location of the cropped image
-cycle amount cycle the image colormap
-delay value display the next image after pausing
-deconstruct break down an image sequence into constituent parts
-density geometry vertical and horizontal density of the image
-depth value depth of the image
-despeckle reduce the speckles within an image
-display server obtain image or font from this X server
-dispose method GIF disposal method
-dither apply Floyd/Steinberg error diffusion to image
-draw string annotate the image with a graphic primitive
-edge radius apply a filter to detect edges in the image
-emboss radius emboss an image
-enhance apply a digital filter to enhance a noisy image
-equalize perform histogram equalization to an image
-fill color color to use when filling a graphic primitive
-filter type use this filter when resizing an image
-flatten flatten a sequence of images
-flip flip image in the vertical direction
-flop flop image in the horizontal direction
-font name font for rendering text
-frame geometry surround image with an ornamental border
-fuzz distance colors within this distance are considered equal
-gamma value level of gamma correction
-geometry geometry perferred size or location of the image
-gaussian geometry gaussian blur an image
-gravity type vertical and horizontal text placement
-implode amount implode image pixels about the center
-intent type Absolute, Perceptual, Relative, or Saturation
-interlace type None, Line, Plane, or Partition
-label name assign a label to an image
-level value adjust the level of image contrast
-list type Color, Delegate, Format, Magic, Module, or Type
-loop iterations add Netscape loop extension to your GIF animation
-map filename transform image colors to match this set of colors
-matte store matte channel if the image has one
-median radius apply a median filter to the image
-modulate value vary the brightness, saturation, and hue
-monochrome transform image to black and white
-morph value morph an image sequence
-mosaic create an mosaic from an image sequence
-negate replace every pixel with its complementary color
-noise radius add or reduce noise in an image
-normalize transform image to span the full range of colors
-opaque color change this color to the fill color
-page geometry size and location of an image canvas
-paint radius simulate an oil painting
-ping efficiently determine image attributes
-pointsize value pointsize of Postscript font
-preview type image preview type
-profile filename add ICM or IPTC information profile to image
-quality value JPEG/MIFF/PNG compression level
-raise value lighten/darken image edges to create a 3-D effect
-region geometry apply options to a portion of the image
-roll geometry roll an image vertically or horizontally
-rotate degrees apply Paeth rotation to the image
-sample geometry scale image with pixel sampling
-scale geometry resize image
-scene value image scene number
-segment values segment an image
-seed value pseudo-random number generator seed value
-shade degrees shade the image using a distant light source
-sharpen geometry sharpen the image
-shave geometry shave pixels from the image edges
-shear geometry slide one edge of the image along the X or Y axis
-size geometry width and height of image
-solarize threshold negate all pixels above the threshold level
-spread amount displace image pixels by a random amount
-stroke color color to use when stoking a graphic primitive
-strokewidth value width of stroke
-swirl degrees swirl image pixels about the center
-texture filename name of texture to tile onto the image background
-threshold value threshold the image
-tile filename tile image when filling a graphic primitive
-transparent color make this color transparent within the image
-treedepth value depth of the color tree
-type type image type
-units type PixelsPerInch, PixelsPerCentimeter, or Undefined
-unsharp geometry sharpen the image
-verbose print detailed information about the image
-view FlashPix viewing transforms
-wave geometry alter an image along a sine wave
By default, the image format of `file' is determined by its magic
number. To specify a particular image format, precede the filename
with an image format name and a colon (i.e. ps:image) or specify the
image type as the filename suffix (i.e. image.ps). Specify 'file' as
'-' for standard input or output.
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I also noticed that the motion correction reports are also missing the plots. When I checked the tsplot directory of a couple of runs from different subjects, none of the .gif files had been created. Also several of the .txt files (tsplotc_zstat3.txt, ps_tsplotc_zstat3_ev1.txt, etc.) were missing in one of the runs but not in the other.
I'll get back to you as soon as I find out about the OS version.
Thank you again for your help!
-Yoshiko
On Thu, 11 Jan 2007 17:23:18 +0000, Steve Smith <[log in to unmask]> wrote:
> Hi - it sounds like you might be running the wrong Mac version. Did
> you definitely take the version for G5?
> If you got the activation images then the analysis definitely did
> complete - it looks like the program "gnuplot" isn't running - what
> happens if you type
> $FSLDIR/bin/gnuplot
> $FSLDIR/bin/convert
> Cheers.
>
>
>
>
> On 10 Jan 2007, at 19:31, Yoshiko Yamada wrote:
>
> > Hi,
> >
> > We are running FSL (v 3.3; FEAT v 5.63) on Mac Dual 2.5 GHz PowerPC
> > G5 with OS X (10.4.8).
> > Wen we ran FSL on PC, the versions of FSL and FEAT were the same as
> > above.
> > Thank you for your input!
> >
> > -Yoshiko
> >
> >
> >
> > On Wed, 10 Jan 2007 17:04:01 +0000, Steve Smith
> > <[log in to unmask]> wrote:
> >> Hi - it looks like gnuplot is the problem here - are you running on a
> >> slightly unusual (or incomplete) platform? What OS are you running
> >> and what version of FSL?
> >> Cheers.
> >>
> >>
> >> On 10 Jan 2007, at 03:16, Yoshiko Yamada wrote:
> >>
> >>> Hi,
> >>>
> >>> I searched in the archives but didn't find exactly the same problem
> >>> I've been having.
> >>> In report.htmls of the 1st level analyses I ran recently, I see no
> >>> time series plots. Instead, there are
> >>> icons with a question mark. Unlike the problem posted earlier by
> >>> others, I do have threshold
> >>> activation images. In report.htmls of the 1st level analyses I ran
> >>> awhile ago do show time series
> >>> plots.
> >>>
> >>> One of the differences between the earlier and more recent analyses
> >>> is that earllier ones were
> >>> done on a PC (in cygwin window) whereas the more recent ones were
> >>> done on a mac.
> >>> I checked design.fsf from the earlier and recent analyses and
> >>> compared (using "compare
> >>> document" command in Word). The differences were the following:
> >>>
> >>> - Absolute path name (I needed to change this when I moved from PC
> >>> to mac.)
> >>> - DOF for regstration to main stractural (changed from 7 to 12)
> >>>
> >>> I've attached the design. fsf and report.log (both from mac). I
> >>> hope they help.
> >>> Does absence of time series plots suggest that the analysis was not
> >>> completed?
> >>>
> >>> Thank you for your advice.
> >>>
> >>> -Yoshiko
> >>>
> >>>
> >>>
> >>>
> >>> <design.fsf>
> >>> <report.log>
> >>
> >>
> >> ---------------------------------------------------------------------
> >> ---
> >> ---
> >> Stephen M. Smith, Professor of Biomedical Engineering
> >> Associate Director, Oxford University FMRIB Centre
> >>
> >> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
> >> +44 (0) 1865 222726 (fax 222717)
> >> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
> >> ---------------------------------------------------------------------
> >> ---
> >> ---
> >>
>
>
> ------------------------------------------------------------------------
> ---
> Stephen M. Smith, Professor of Biomedical Engineering
> Associate Director, Oxford University FMRIB Centre
>
> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
> +44 (0) 1865 222726 (fax 222717)
> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
> ------------------------------------------------------------------------
> ---
>
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