Hi Mark,
thanks for getting back to us on this.
Please find attached the relevant design.fsf.
This is a standard single-subject analysis with fieldmaps. You will note
that here
# 4D AVW data or FEAT directory (1)
set feat_files(1)
"/home/bartschandreas/li_frontal_tm/032_NCbenennenneu_mb3_69degr_esp0_70msiP
AT2_PA_200"
# Add confound EVs text file
set fmri(confoundevs) 0
the relevant parts on the fieldmap and highres entries are missing (see
below in my original mail).
When I set these in the GUI, they don't get saved. This was not so in the
previous version of Feat.
It does not seem to be a problem of permissions or filenames. Hohum.
So are you saying you can run the Feat GUI at the FMRIB without such a
problem? We have replicated the issue at three different machines.
As I was saying, when we edit the *.fsf files, we can run it from command
line without problem. However, when we load the edited fsf (with the lines
added) and save it from the GUI the relevant lines are missing again.
Thanks again for looking into that.
Hope all is well on your end!
Many regards,
Andreas
Von: Mark Jenkinson <[log in to unmask]>
Antworten an: FSL - FMRIB's Software Library <[log in to unmask]>
Datum: Freitag, 24. Januar 2014 10:02
An: <[log in to unmask]>
Betreff: Re: [FSL] Bug in Feat v6.00 GUI?
Hi Andreas,
Are you saying that you see this when setting up a standard analysis with
fieldmaps?
That's very odd, as people have been doing that here without problems.
Are you setting it up with a single subject or with multple subjects?
And could you send us the fsf?
All the best,
Mark
On 23 Jan 2014, at 17:46, Andreas Bartsch <[log in to unmask]> wrote:
> Hi everyone,
>
> we have encountered what may be a bug in Feat v6.00.
> We have observed this on OSX (10.6.8), CentOS6 and Ubuntu 12.04.4 (LTS).
> When running Feat from the GUI we get fatal errors that go back to:
> Initialisation
>
> /usr/local/fsl/bin/fslmaths
> /home/bartschandreas/li_frontal_hofsaess/032_NCbenennenneu_mb3_69degr_esp0_70m
> siPAT2_PA_200 prefiltered_func_data -odt float
> Total original volumes = 200
>
> /usr/local/fsl/bin/fslroi prefiltered_func_data example_func 100 1
> can't read "highres_files(1)": no such variable
> while executing
> "if { [ catch {
>
>
> When we look at the design.fsf the following lines get deleted:
>
> # B0 unwarp input image for analysis 1
> set unwarp_files(1) "/path/to/fmap_rads"
>
> # B0 unwarp mag input image for analysis 1
> set unwarp_files_mag(1) "/path/to/magn_brain"
>
> # Subject's structural image for analysis 1
> set highres_files(1) "/path/to/HiRes_T1"
>
> This is even though we specified the files correctly in the gui, with no bad
> characters in the pathnames and with proper images files.
> Once we re-insert the lines into the *.fsf file and run feat from command line
> everything finishes fine.
> Maybe you are able to confirm the issue and track it down.
> Cheers,
> Andreas
>
>
