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		FSL April 2019
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Subject:
Re: Cannot See Model Fit in FSLEyes FEAT Mode
From:
paul mccarthy <[log in to unmask]>
Reply-To:
FSL - FMRIB's Software Library <[log in to unmask]>
Date:
Tue, 16 Apr 2019 12:23:48 +0100
Content-Type:
text/plain
Parts/Attachments:
text/plain (654 lines)
Hi Alan,

It sounds like there are now two problems:

 - FEAT may be generating outputs with unset orientation. This is most worrying.
 - FSLeyes is behaving differently when you fix the orientation on the
FEAT outputs. This makes no sense, as FSLeyes does not use the
orientation information when calculating model fits.

Would you be able to again share your data so I can try and reproduce
both of these problems - if you could upload both the unprocessed fMRI
input data, and the problematic .feat directory (ideally before any
modifications using fslcpgeom) to:

 https://oxfile.ox.ac.uk/oxfile/work/extBox?id=716491DA74F8A36D00

Cheers,

Pau

On 16/04/2019, Alan Seifert <[log in to unmask]> wrote:
> Hi Paul,
>
> The FEAT outputs were produced using FSL 6.0.1, and the FEAT log says that
> the FEAT version was 6.0.0.
>
> Before using fslcpgeom, FSLEyes was able to display the model fits in FEAT
> mode, but the images produced by FEAT (filtered_func_data, mean_func,
> zstat1, etc.) were not oriented correctly (they were not in radiological
> coordinates, i.e., the outputs were flipped left-to-right with respect to
> the input data), and were not co-registered with the input 4D data.  I was
> at least able to use the -no option in FSLEyes to make the image
> orientation consistent with the input data.
>
> I then used fslcpgeom, with the input 4D data as the source, to copy the
> orientation information to the FEAT outputs.  First, I applied this only to
> the FEAT output images that I opened and displayed in FSLEyes
> (filtered_func_data, mean_func, zstat1), The images were then displayed
> correctly in FSLEyes, but when attempting to view the model fits in
> FSLEyes' FEAT mode, the model fits took very long to process, and then the
> result for each explanatory variable was just a flat line.  I then went
> back and used fslcpgeom to copy the orientation information onto every
> *.nii.gz in the FEAT output directory, including the stats subdirectory.
> This did not change the result.  The model fits were still just flat lines.
>
> -Alan
>
> On Tue, Apr 16, 2019 at 4:55 AM paul mccarthy <[log in to unmask]>
> wrote:
>
>> Hi Alan,
>>
>> > I used FSL 6.0.1 for this.  I did try using fslcpgeom to copy the
>> orientation info from the input image to every NIFTI file in the feat
>> directory, but after doing that, FSLEyes was no longer able to calculate
>> the model fits.
>>
>> Can you elaborate on this?
>>
>> Paul
>>
>> On 15/04/2019, Alan Seifert <[log in to unmask]> wrote:
>> > Hi Paul,
>> >
>> > I used FSL 6.0.1 for this.  I did try using fslcpgeom to copy the
>> > orientation info from the input image to every NIFTI file in the feat
>> > directory, but after doing that, FSLEyes was no longer able to
>> > calculate
>> > the model fits.
>> >
>> > My interim solution is to use the -no option in FSLEyes, which causes
>> > the
>> > images in the feat directory to be displayed in radiological
>> > coordinates,
>> > but doesn't solve the misregistration issue.
>> >
>> > -Alan
>> >
>> > On Mon, Apr 15, 2019 at 3:43 PM paul mccarthy <[log in to unmask]>
>> > wrote:
>> >
>> >> Hi Alan,
>> >>
>> >> FSLView aligns images based on voxel dimensions, and only uses the
>> >> s/qform affines to calculate the anatomical labels.  FSLeyes uses the
>> >> s/qform affines to align images in the display. If FSLView cannot
>> >> determine the anatomical orientation, or FSLeyes cannot display the
>> >> images in register, this indicates a problem with the data.
>> >>
>> >> The problem, as you discovered, is that your filtered_func_data,
>> >> zstat1, etc images have unset sform/qform codes.
>> >>
>> >> I'm not sure why the FEAT outputs would have unset s/qform codes -
>> >> what version of FSL are you using? This may be due to a bug in an
>> >> older FSL version - it is worth upgrading to the latest version of
>> >> FSL, as this should not normally happen.
>> >>
>> >> An interim solution is to use fslcpgeom to copy the orientation
>> >> information from your original unprocessed data set to the FEAT
>> >> outputs.
>> >>
>> >> Cheers,
>> >>
>> >> Paul
>> >>
>> >>
>> >>
>> >> On 15/04/2019, Alan Seifert <[log in to unmask]> wrote:
>> >> > Hi Paul,
>> >> >
>> >> > I can see the FEAT model fits now!  Thank you for fixing this.
>> >> >
>> >> > Now I've noticed another difference between FSLView and FSLEyes: in
>> >> > FSLView, when I open the filtered_func_data and stats/zstat1, the
>> >> > images
>> >> > are displayed in radiological coordinates, but if I open the same
>> >> > dataset
>> >> > in FSLEyes, they display in neurological coordinates (flipped in X).
>> >> >
>> >> > If I also open the original functional dataset's temporal mean image
>> in
>> >> > FSLEyes, then the filtered_func_data and stats/zstat1 are out of
>> >> > register
>> >> > with (rotated and translated away from) the temporal mean image.  It
>> >> > appears that filtered_func_data and stats/zstat1 have sform_code = 0
>> >> > and
>> >> > qform_code = 0, and the sform and qform matrices are different.  If
>> >> > I
>> >> open
>> >> > the same set of images in FSLView, then they are in register and
>> >> displayed
>> >> > in radiological coordinates, as expected, but the A/P L/R S/I labels
>> >> > are
>> >> > not present.
>> >> >
>> >> > Do you have any suggestions on how to force all the images to be
>> >> displayed
>> >> > consistently in register and in radiological coordinates?  My first
>> >> thought
>> >> > was to use fslcpgeom, but the fact that this wasn't necessary in
>> >> > FSLView
>> >> > and isn't automatically done by FEAT made me hesitate.  Or is this a
>> >> > bug?
>> >> >
>> >> > Thanks,
>> >> >
>> >> > -Alan
>> >> >
>> >> > On Sun, Apr 14, 2019 at 2:24 PM paul mccarthy <
>> [log in to unmask]>
>> >> > wrote:
>> >> >
>> >> >> 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
>> >> >> >>> >> >> >
>> >> >> >>> >> >> >
>> >> >> >>> >>
>> >> >>
>> ########################################################################
>> >> >> >>> >> >> >
>> >> >> >>> >> >> > To unsubscribe from the FSL list, click the following
>> >> >> >>> >> >> > link:
>> >> >> >>> >> >> >
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
>> >> >> >>> >> >> >
>> >> >> >>> >> >>
>> >> >> >>> >> >>
>> >> >> >>>
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