Hi Stephane,
I am afraid I cannot really say what might have gone wrong from this
info. Could you please go into one of the directories where it failed
and then cut and paste the fnirt command from the pertinent log-file
into a terminal window and then add --verbose at the end of the
command, i.e.
/usr/local/fsl4.1.0/bin/fnirt --in=highres_head --
aff=highres2standard.mat --cout=highres2standard_warp --
iout=highres2standard --jout=highres2standard_jac --
config=T1_2_MNI152_2mm --ref=standard_head --refmask=standard_mask --
warpres=10,10,10 --verbose
If it fails again (I hope it does) could you then send me all the
output that was written to the screen?
Jesper
On 12 Sep 2008, at 18:01, Stephane Jacobs wrote:
> Hello FSL!
>
> I'm trying to run the latest version of FSL, including FNIRT, and
> have some
> strange problems with it: on some data sets it runs just fine, but
> with
> others, it doesn't complete but doesn't throw any error message.
> The error
> comes up only when slicer tries to use the output that FNIRT never
> created.
>
> When I look at the log, it varies: either I only have the FNIRT
> command
> without the usual "Setting subsampling, Setting reg mode, Setting
> lambda",
> or just a few iterations of those, or it can even look OK, but the
> output is
> consistently missing in all cases!
>
> I have attached 3 different logs illustrating this. Any help would
> as always
> be greatly appreciated.
>
> Thanks,
>
> Stephane
>
> --
> :::::::::::::::::::::::::::::::::::::::::::::::::::
> Stephane Jacobs
>
> Postdoctoral Research Associate
> Human Neuroimaging and Transcranial Stimulation Lab
> Department of Psychology
> 1227 University of Oregon
> Eugene, OR 97403 - USA
>
> Email: [log in to unmask]
> Tel: (1) 541-346-4184
> :::::::::::::::::::::::::::::::::::::::::::::::::::
>
> <report_logs.zip>
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