Hi Alan,
The voxelwise EV files that are generated by PNM are strange, in that
they only contain one voxel for each slice of the input data (i.e.
they have shape (1, 1, nslices, ntimepoints).
I was unaware of this, so the FSLeyes code does not handle this
situation - it assumes that voxelwise EV files have the same shape as
the input data.
I've updated FSLeyes so that it will correctly load these files - you
can download version 0.28.3 from here:
https://users.fmrib.ox.ac.uk/~paulmc/fsleyes/dist/
Cheers,
Paul
On 09/04/2019, paul mccarthy <[log in to unmask]> wrote:
> 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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>>> >> >> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
>>> >> >> >
>>> >> >>
>>> >> >>
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>>> >> >>
>>> >> >
>>> >> >
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>>
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