Hi - if it's occasionally not finding FSL programs then definitely
it's a problem with your computer system.
Maybe you have a dodgy network file system....
Cheers, Steve.



On 22 Oct 2007, at 19:45, Martin M Monti wrote:

> Dear FSLers,
>
> I seem to have a fairly odd problem. I'm uncertain whether it
> relates to the scripts I run or the system I'm running it on, so I
> thought I'd submit this for thoughts.
> I am running possibly the "standardest" first level FEAT analysis,
> and occasionally I will get a command not found (or similar) error.
>
> For example, out of the log file:
> [...]
> /imaging/local/linux/bin/fsl-3.3.11/bin/avwstats thresh_zstat1 -l
> 0.0001 -R
> 1.645502 9.620274
> /imaging/local/linux/bin/fsl-3.3.11/bin/avwstats thresh_zstat2 -l
> 0.0001 -R
> 1.644912 9.755136
> /imaging/local/linux/bin/fsl-3.3.11/bin/avwstats thresh_zstat3 -l
> 0.0001 -R
> 1.645053 8.413849
> /imaging/local/linux/bin/fsl-3.3.11/bin/avwstats thresh_zstat4 -l
> 0.0001 -R
> sh: line 1: /imaging/local/linux/bin/fsl-3.3.11/bin/avwstats: No
> such file or directory
> /imaging/local/linux/bin/fsl-3.3.11/bin/avwstats thresh_zstat5 -l
> 0.0001 -R
> 1.644964 12.803717
> /imaging/local/linux/bin/fsl-3.3.11/bin/avwstats thresh_zstat6 -l
> 0.0001 -R
> 1.644927 6.907343
> /imaging/local/linux/bin/fsl-3.3.11/bin/avwstats thresh_zstat7 -l
> 0.0001 -R
> 1.645141 5.426872
> /imaging/local/linux/bin/fsl-3.3.11/bin/avwstats thresh_zstat8 -l
> 0.0001 -R
> 1.644897 6.717268
> /imaging/local/linux/bin/fsl-3.3.11/bin/avwstats thresh_zstat9 -l
> 0.0001 -R
> 1.645143 5.004468
> [...]
>
> I ran the same script on another file, and all went well, except I
> got a different error (not got when running it on the file that
> gave the error above...)
>
> [...]
> Spatially smoothing auto corr estimates
> /imaging/local/linux/bin/fsl-3.3.11/bin/susan_smooth stats/
> preSmoothVol 1 stats/postSmoothVol 5 3D 0 1 stats/epivolume 395
> stats/usanSize
> .........This program has not been compiled for this data type
> [...]
>
> On a third occasion, I got yet another error (although at the same
> processing stage):
>
> [...]
> Spatially smoothing auto corr estimates
> /imaging/local/linux/bin/fsl-3.3.11/bin/susan_smooth stats/
> preSmoothVol 1 stats/postSmoothVol 5 3D 0 1 stats/epivolume 395
> stats/usanSize
> sh: line 1: /imaging/local/linux/bin/fsl-3.3.11/bin/
> susan_smooth_16SI: No such file or directory
> ** ERROR: nifti_image_read(stats/postSmoothVol): can't open header
> file
> ** ERROR: nifti_image_open(stats/postSmoothVol): bad header info
> Error: failed to open file stats/postSmoothVol
> Error:: FslGetDim: Null pointer passed for FSLIO
> Error: FILM did not complete - it probably ran out of memory
> [...]
>
> finally, the (almost) same script on a different file ran smoothly
> up to:
>
> [...]
> /imaging/local/linux/bin/fsl-3.3.11/bin/slicer
> rendered_thresh_zstat8 -A 750 rendered_thresh_zstat8.png
> /imaging/local/linux/bin/fsl-3.3.11/bin/overlay 1 0 example_func -a
> thresh_zstat9 1.644865 12.858842 rendered_thresh_zstat9
> /imaging/local/linux/bin/fsl-3.3.11/bin/slicer
> rendered_thresh_zstat9 -A 750 rendered_thresh_zstat9.png
> /imaging/local/linux/bin/fsl-3.3.11/bin/overlay 1 0 example_func -a
> thresh_zstat10 1.644865 12.858842 rendered_thresh_zstat10
> sh: line 1: /imaging/local/linux/bin/fsl-3.3.11/bin/overlay: No
> such file or directory
> /imaging/local/linux/bin/fsl-3.3.11/bin/slicer
> rendered_thresh_zstat10 -A 750 rendered_thresh_zstat10.png
> ** ERROR: nifti_image_read(rendered_thresh_zstat10): can't open
> header file
> ** ERROR: nifti_image_open(rendered_thresh_zstat10): bad header info
> Error: failed to open file rendered_thresh_zstat10
> ERROR: Could not open image rendered_thresh_zstat10
> Image Exception : #22 :: Failed to read volume rendered_thresh_zstat10
> /imaging/local/linux/bin/fsl-3.3.11/bin/overlay 1 0 example_func -a
> thresh_zstat11 1.644865 12.858842 rendered_thresh_zstat11
> /imaging/local/linux/bin/fsl-3.3.11/bin/slicer
> rendered_thresh_zstat11 -A 750 rendered_thresh_zstat11.png
>
> mkdir tsplot
>
> /imaging/local/linux/bin/fsl-3.3.11/bin/tsplot . -f
> filtered_func_data -o tsplot
> sh: /imaging/local/linux/bin/fsl-3.3.11/bin/convert: /bin/sh: bad
> interpreter: No such file or directory
> sh: /imaging/local/linux/bin/fsl-3.3.11/bin/convert: /bin/sh: bad
> interpreter: No such file or directory
> sh: /imaging/local/linux/bin/fsl-3.3.11/bin/convert: /bin/sh: bad
> interpreter: No such file or directory
> sh: /imaging/local/linux/bin/fsl-3.3.11/bin/convert: /bin/sh: bad
> interpreter: No such file or directory
> sh: /imaging/local/linux/bin/fsl-3.3.11/bin/convert: /bin/sh: bad
> interpreter: No such file or directory
> sh: /imaging/local/linux/bin/fsl-3.3.11/bin/convert: /bin/sh: bad
> interpreter: No such file or directory
> sh: /imaging/local/linux/bin/fsl-3.3.11/bin/convert: /bin/sh: bad
> interpreter: No such file or directory
> sh: /imaging/local/linux/bin/fsl-3.3.11/bin/convert: /bin/sh: bad
> interpreter: No such file or directory
> sh: /imaging/local/linux/bin/fsl-3.3.11/bin/convert: /bin/sh: bad
> interpreter: No such file or directory
> sh: /imaging/local/linux/bin/fsl-3.3.11/bin/convert: /bin/sh: bad
> interpreter: No such file or directory
> sh: /imaging/local/linux/bin/fsl-3.3.11/bin/convert: /bin/sh: bad
> interpreter: No such file or directory
> sh: line 6: /imaging/local/linux/bin/fsl-3.3.11/bin/gnuplot: No
> such file or directory
> convertb: no delegate for this image format (/tmp/magicQoKU7b).
> convertb: Missing an image file name.
> sh: /imaging/local/linux/bin/fsl-3.3.11/bin/convert: /bin/sh: bad
> interpreter: No such file or directory
> sh: /imaging/local/linux/bin/fsl-3.3.11/bin/convert: /bin/sh: bad
> interpreter: No such file or directory
> sh: /imaging/local/linux/bin/fsl-3.3.11/bin/convert: /bin/sh: bad
> interpreter: No such file or directory
> sh: /imaging/local/linux/bin/fsl-3.3.11/bin/convert: /bin/sh: bad
> interpreter: No such file or directory
> sh: line 6: /imaging/local/linux/bin/fsl-3.3.11/bin/gnuplot: No
> such file or directory
> convertb: no delegate for this image format (/tmp/magickL3uNY).
> convertb: Missing an image file name.
> sh: /imaging/local/linux/bin/fsl-3.3.11/bin/convert: /bin/sh: bad
> interpreter: No such file or directory
> sh: /imaging/local/linux/bin/fsl-3.3.11/bin/convert: /bin/sh: bad
> interpreter: No such file or directory
> sh: /imaging/local/linux/bin/fsl-3.3.11/bin/convert: /bin/sh: bad
> interpreter: No such file or directory
> sh: /imaging/local/linux/bin/fsl-3.3.11/bin/convert: /bin/sh: bad
> interpreter: No such file or directory
> sh: /imaging/local/linux/bin/fsl-3.3.11/bin/convert: /bin/sh: bad
> interpreter: No such file or directory
> sh: /imaging/local/linux/bin/fsl-3.3.11/bin/convert: /bin/sh: bad
> interpreter: No such file or directory
> sh: /imaging/local/linux/bin/fsl-3.3.11/bin/convert: /bin/sh: bad
> interpreter: No such file or directory
> sh: /imaging/local/linux/bin/fsl-3.3.11/bin/convert: /bin/sh: bad
> interpreter: No such file or directory
> sh: /imaging/local/linux/bin/fsl-3.3.11/bin/convert: /bin/sh: bad
> interpreter: No such file or directory
> sh: /imaging/local/linux/bin/fsl-3.3.11/bin/convert: /bin/sh: bad
> interpreter: No such file or directory
> sh: /imaging/local/linux/bin/fsl-3.3.11/bin/convert: /bin/sh: bad
> interpreter: No such file or directory
> sh: /imaging/local/linux/bin/fsl-3.3.11/bin/convert: /bin/sh: bad
> interpreter: No such file or directory
> sh: /imaging/local/linux/bin/fsl-3.3.11/bin/convert: /bin/sh: bad
> interpreter: No such file or directory
> sh: /imaging/local/linux/bin/fsl-3.3.11/bin/convert: /bin/sh: bad
> interpreter: No such file or directory
> sh: /imaging/local/linux/bin/fsl-3.3.11/bin/convert: /bin/sh: bad
> interpreter: No such file or directory
> sh: line 6: /imaging/local/linux/bin/fsl-3.3.11/bin/convert: No
> such file or directory
> sh: /imaging/local/linux/bin/fsl-3.3.11/bin/convert: /bin/sh: bad
> interpreter: No such file or directory
>
> /bin/mkdir reg
> [...]
>
> Now, my main issue is to at least sort out if this is me being
> "buggy" when creating the .fsf files or whether there may be
> something wrong with the machines that I am running on.
>
> Two things suggest (to me) that it may be the latter: first the
> apparently inconsistent timing of the errors.
> Second, I ran the command that crashed the avwstats in the first
> example above (on that very same thresh_zstat4 file) using repeat:
>
> repeat 10000 avwstats thresh_zstat4 -l 0.0001 -R
>
> it almost always runs smoothly. Occasionally -- and seemingly
> randomly -- it will return "avwstats: command not found."
>
> Ok, I think that's enough problems for one day..
>
> all the best
>
> Martin
>
> “Well! I’ve often seen a cat without a grin,” thought Alice, “but a
> grin without a cat! It’s the most curious thing I ever saw in my
> life!” [Lewis Carroll, Alice in Wonderland]
>
> ----------------------------------------
> Martin M Monti, PhD
> MRC Cognition and Brain Sciences Unit
> 15 Chaucer Road
> Cambridge, CB2 7EF
> Off. +44 (0) 1223 273646
> www.webmartin.net
> ----------------------------------------


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---
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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