Hi Alan,
Thanks; there seems to be an issue either in FSLeyes, or in the
voxelwise confound EV files that were generated by PNM - I'll
investigate and will get back to you.
Cheers,
Paul
On 09/04/2019, Alan Seifert <[log in to unmask]> wrote:
> Hi Paul,
>
> Thanks for taking another look at this. I just uploaded the feat directory
> archive. I've also included below the errors that result when I enter FEAT
> mode and try to plot the EV1 fit.
>
> -Alan
>
> WARNING idle.pyc 146: wrapper - Task "getData"
> crashed
> Traceback (most recent call last):
> File "fsl/utils/idle.pyc", line 139, in wrapper
> File "fsleyes/views/plotpanel.pyc", line 609, in getData
> File "fsleyes/views/timeseriespanel.pyc", line 374, in prepareDataSeries
> File "fsleyes/plotting/timeseries.pyc", line 775, in getData
> File "fsl/data/featimage.pyc", line 323, in fit
> File "fsl/data/featimage.pyc", line 158, in getDesign
> File "fsl/data/featdesign.pyc", line 217, in getDesign
> File "fsl/data/image.pyc", line 1361, in __getitem__
> File "fsl/data/imagewrapper.pyc", line 632, in __getitem__
> File "fsl/data/imagewrapper.pyc", line 779, in canonicalSliceObj
> File
> "/usr/local/fsl/bin/FSLeyes.app/Contents/Resources/lib/python3.5/nibabel/fileslice.py",
> line 131, in canonical_slicers
> ValueError: Integer index 84 to large
> WARNING idle.pyc 146: wrapper - Task "getData"
> crashed
> Traceback (most recent call last):
> File "fsl/utils/idle.pyc", line 139, in wrapper
> File "fsleyes/views/plotpanel.pyc", line 609, in getData
> File "fsleyes/views/timeseriespanel.pyc", line 374, in prepareDataSeries
> File "fsleyes/plotting/timeseries.pyc", line 775, in getData
> File "fsl/data/featimage.pyc", line 323, in fit
> File "fsl/data/featimage.pyc", line 158, in getDesign
> File "fsl/data/featdesign.pyc", line 217, in getDesign
> File "fsl/data/image.pyc", line 1361, in __getitem__
> File "fsl/data/imagewrapper.pyc", line 632, in __getitem__
> File "fsl/data/imagewrapper.pyc", line 779, in canonicalSliceObj
> File
> "/usr/local/fsl/bin/FSLeyes.app/Contents/Resources/lib/python3.5/nibabel/fileslice.py",
> line 131, in canonical_slicers
> ValueError: Integer index 87 to large
> WARNING idle.pyc 146: wrapper - Task "getData"
> crashed
> Traceback (most recent call last):
> File "fsl/utils/idle.pyc", line 139, in wrapper
> File "fsleyes/views/plotpanel.pyc", line 609, in getData
> File "fsleyes/views/timeseriespanel.pyc", line 374, in prepareDataSeries
> File "fsleyes/plotting/timeseries.pyc", line 775, in getData
> File "fsl/data/featimage.pyc", line 323, in fit
> File "fsl/data/featimage.pyc", line 158, in getDesign
> File "fsl/data/featdesign.pyc", line 217, in getDesign
> File "fsl/data/image.pyc", line 1361, in __getitem__
> File "fsl/data/imagewrapper.pyc", line 632, in __getitem__
> File "fsl/data/imagewrapper.pyc", line 779, in canonicalSliceObj
> File
> "/usr/local/fsl/bin/FSLeyes.app/Contents/Resources/lib/python3.5/nibabel/fileslice.py",
> line 131, in canonical_slicers
> ValueError: Integer index 87 to large
> WARNING idle.pyc 146: wrapper - Task "getData"
> crashed
> Traceback (most recent call last):
> File "fsl/utils/idle.pyc", line 139, in wrapper
> File "fsleyes/views/plotpanel.pyc", line 609, in getData
> File "fsleyes/views/timeseriespanel.pyc", line 374, in prepareDataSeries
> File "fsleyes/plotting/timeseries.pyc", line 775, in getData
> File "fsl/data/featimage.pyc", line 323, in fit
> File "fsl/data/featimage.pyc", line 158, in getDesign
> File "fsl/data/featdesign.pyc", line 217, in getDesign
> File "fsl/data/image.pyc", line 1361, in __getitem__
> File "fsl/data/imagewrapper.pyc", line 632, in __getitem__
> File "fsl/data/imagewrapper.pyc", line 779, in canonicalSliceObj
> File
> "/usr/local/fsl/bin/FSLeyes.app/Contents/Resources/lib/python3.5/nibabel/fileslice.py",
> line 131, in canonical_slicers
> ValueError: Integer index 87 to large
> WARNING idle.pyc 146: wrapper - Task "getData"
> crashed
> Traceback (most recent call last):
> File "fsl/utils/idle.pyc", line 139, in wrapper
> File "fsleyes/views/plotpanel.pyc", line 609, in getData
> File "fsleyes/views/timeseriespanel.pyc", line 374, in prepareDataSeries
> File "fsleyes/plotting/timeseries.pyc", line 775, in getData
> File "fsl/data/featimage.pyc", line 323, in fit
> File "fsl/data/featimage.pyc", line 158, in getDesign
> File "fsl/data/featdesign.pyc", line 217, in getDesign
> File "fsl/data/image.pyc", line 1361, in __getitem__
> File "fsl/data/imagewrapper.pyc", line 632, in __getitem__
> File "fsl/data/imagewrapper.pyc", line 779, in canonicalSliceObj
> File
> "/usr/local/fsl/bin/FSLeyes.app/Contents/Resources/lib/python3.5/nibabel/fileslice.py",
> line 131, in canonical_slicers
> ValueError: Integer index 87 to large
> WARNING idle.pyc 146: wrapper - Task "getData"
> crashed
> Traceback (most recent call last):
> File "fsl/utils/idle.pyc", line 139, in wrapper
> File "fsleyes/views/plotpanel.pyc", line 609, in getData
> File "fsleyes/views/timeseriespanel.pyc", line 374, in prepareDataSeries
> File "fsleyes/plotting/timeseries.pyc", line 775, in getData
> File "fsl/data/featimage.pyc", line 323, in fit
> File "fsl/data/featimage.pyc", line 158, in getDesign
> File "fsl/data/featdesign.pyc", line 217, in getDesign
> File "fsl/data/image.pyc", line 1361, in __getitem__
> File "fsl/data/imagewrapper.pyc", line 632, in __getitem__
> File "fsl/data/imagewrapper.pyc", line 779, in canonicalSliceObj
> File
> "/usr/local/fsl/bin/FSLeyes.app/Contents/Resources/lib/python3.5/nibabel/fileslice.py",
> line 131, in canonical_slicers
> ValueError: Integer index 87 to large
>
> On Mon, Apr 8, 2019 at 4:52 PM paul mccarthy <[log in to unmask]>
> wrote:
>
>> Hi Alan,
>>
>> Is there any chance that you could zip up your .feat directory, and
>> upload it to:
>>
>> https://oxfile.ox.ac.uk/oxfile/work/extBox?id=7138027B75CA04FFD0
>>
>> So I can take a look.
>>
>> Cheers,
>>
>> Paul
>>
>> On 08/04/2019, Alan Seifert <[log in to unmask]> wrote:
>> > Hi Paul,
>> >
>> > Sorry for the very delayed response. As of 0.27.3, I still cannot see
>> the
>> > model fit in FSLEyes. The error is slightly different now:
>> >
>> > WARNING idle.pyc 146: wrapper - Task "getData"
>> > crashed
>> > Traceback (most recent call last):
>> > File "fsl/utils/idle.pyc", line 139, in wrapper
>> > File "fsleyes/views/plotpanel.pyc", line 609, in getData
>> > File "fsleyes/views/timeseriespanel.pyc", line 374, in
>> prepareDataSeries
>> > File "fsleyes/plotting/timeseries.pyc", line 775, in getData
>> > File "fsl/data/featimage.pyc", line 323, in fit
>> > File "fsl/data/featimage.pyc", line 158, in getDesign
>> > File "fsl/data/featdesign.pyc", line 217, in getDesign
>> > File "fsl/data/image.pyc", line 1361, in __getitem__
>> > File "fsl/data/imagewrapper.pyc", line 632, in __getitem__
>> > File "fsl/data/imagewrapper.pyc", line 779, in canonicalSliceObj
>> > File
>> >
>> "/usr/local/fsl/bin/FSLeyes.app/Contents/Resources/lib/python3.5/nibabel/fileslice.py",
>> > line 131, in canonical_slicers
>> > ValueError: Integer index 49 to large
>> >
>> > Apart from this error text, nothing from my original message is
>> different.
>> >
>> > Thanks,
>> >
>> > -Alan
>> >
>> > On Tue, Nov 27, 2018 at 11:52 AM paul mccarthy
>> > <[log in to unmask]>
>> > wrote:
>> >
>> >> Hi Alan,
>> >>
>> >> These problems should be resolved in the latest version of FSLeyes
>> >> (0.26.6). Let me know if you are still having issues.
>> >>
>> >> Cheers,
>> >>
>> >> Paul
>> >>
>> >> On 15/11/2018, Alan Seifert <[log in to unmask]> wrote:
>> >> > Hi Paul,
>> >> >
>> >> > Thanks for your help.
>> >> >
>> >> > A bit more information: this happens on both my Mac OS X machines,
>> >> > one
>> >> > running FSL 5.0.11, and one running FSL 6.0.0.
>> >> >
>> >> > I've also seen this error:
>> >> >
>> >> > WARNING idle.pyc 348: _wxIdleLoop - Idle task
>> >> addCluster
>> >> > crashed - AttributeError: 'Cluster' object has no attribute 'p'
>> >> > Traceback (most recent call last):
>> >> > File "fsl/utils/idle.pyc", line 345, in _wxIdleLoop
>> >> > File "fsleyes/controls/clusterpanel.pyc", line 415, in addCluster
>> >> > AttributeError: 'Cluster' object has no attribute 'p'
>> >> >
>> >> > Thanks again,
>> >> >
>> >> > -Alan
>> >> >
>> >> > On Thu, Nov 15, 2018 at 6:09 AM paul mccarthy <
>> [log in to unmask]>
>> >> > wrote:
>> >> >
>> >> >> Hi Alan,
>> >> >>
>> >> >> This is possibly a bug in the latest version of FSLeyes - I will
>> >> >> try
>> >> >> and get a fix out next week.
>> >> >>
>> >> >> Cheers,
>> >> >>
>> >> >> Paul
>> >> >>
>> >> >> On 14/11/2018, Alan Seifert <[log in to unmask]> wrote:
>> >> >> > Hello,
>> >> >> >
>> >> >> > I have not been able to figure out how to display FEAT model fits
>> in
>> >> >> > FSLEyes.
>> >> >> >
>> >> >> > I cd into my feat directory, and execute 'fsleyes
>> >> >> > filtered_func_data',
>> >> >> then
>> >> >> > in the menu, I select View --> Layouts --> FEAT Mode.
>> >> >> >
>> >> >> > At this point, the filtered_func_data timeseries appears, but the
>> >> model
>> >> >> fit
>> >> >> > does not appear, and my terminal window (I'm running Mac OS X)
>> fills
>> >> up
>> >> >> with
>> >> >> > errors like this:
>> >> >> >
>> >> >> > WARNING idle.pyc 146: wrapper - Task
>> >> >> > "getData"
>> >> >> crashed
>> >> >> > Traceback (most recent call last):
>> >> >> > File "fsl/utils/idle.pyc", line 139, in wrapper
>> >> >> > File "fsleyes/views/plotpanel.pyc", line 609, in getData
>> >> >> > File "fsleyes/views/timeseriespanel.pyc", line 374, in
>> >> >> prepareDataSeries
>> >> >> > File "fsleyes/plotting/timeseries.pyc", line 775, in getData
>> >> >> > File "fsl/data/featimage.pyc", line 323, in fit
>> >> >> > File "fsl/data/featimage.pyc", line 158, in getDesign
>> >> >> > File "fsl/data/featdesign.pyc", line 217, in getDesign
>> >> >> > AttributeError: 'VoxelwiseConfoundEV' object has no attribute
>> >> >> > 'image'
>> >> >> >
>> >> >> > In the Time Series Control window, only the residuals show up
>> >> >> > when
>> I
>> >> >> check
>> >> >> > the 'Plot residuals' box; 'Plot full model fit', 'Plot PE# fit',
>> and
>> >> >> 'Plot
>> >> >> > COPE# fit' do not add any more lines to the timeseries plot, they
>> >> >> > only
>> >> >> > produce another error in the terminal window.
>> >> >> >
>> >> >> > On the other hand, if I open the same dataset in FSLView (execute
>> >> >> > 'fslview_deprecated filtered_func_data'), it immediately enters
>> FEAT
>> >> >> > mode
>> >> >> > and I can plot the data, the full model, and any of the
>> >> >> > individual
>> >> >> > PE
>> >> >> fits
>> >> >> > with no problem, so this gives me confidence that this
>> >> >> > information
>> >> does
>> >> >> > exist in my feat directory.
>> >> >> >
>> >> >> > Has anyone encountered (and hopefully solved) this issue?
>> >> >> >
>> >> >> > Thanks,
>> >> >> >
>> >> >> > Alan Seifert
>> >> >> >
>> >> >> >
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>> >> >>
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