Paul,
No, not that I noticed. We're starting it by double-clicking the
FSLeyes.app folder. Do you want us to try to start it from a
Terminal?
-- bennet
On Thu, Jan 30, 2020 at 5:46 AM paul mccarthy <[log in to unmask]> wrote:
>
> Hi Bennet,
>
> This is a bug - is anything printed to the terminal when the error occurs?
>
> Paul
>
> On Jan 29 2020, at 11:42 pm, Bennet Fauber <[log in to unmask]> wrote:
>
> I have a user who downloaded and installed FSLeyes 0.32.0 for Mac,
> .zip file. She is in a workshop, and they are working with the
> standard ds102 dataset from OpenfMRI.org (OpenNeuro).
>
> She uses FSL to create from sub-08_T1w.nii.gz using bet the mask file,
> sub-08_T1w_brain.nii.gz.
>
> When she uses FSLeyes 0.32.0 to open first the T1w file, that works,
> but when she tries to add the mask as an overlay she gets the error
> window attached, which says, basically, that the mask file isn't
> proper BIDS. In case the screen shot does not pass the listserver,
> the text is roughly,
>
> Error loading overlay
> An error occurred loading the image /path/to/sub-08_T1w_brain.nii.gz
> Details: Does not look like a BIDS file: /path/to/mask
>
> This error does not occur with FSLeyes 0.31.2+build0. Can checking
> BIDS format be suppressed via an option? I looked, as did several
> others here, and we aren't finding this settable.
>
> It doesn't seem like an image viewer/manipulator should really care
> what the format of the image filenames is.
>
> This situation surprised many of us here, and I am able to replicate easily.
>
> We can make the error stop by removing all .json files from the root
> of the BIDS directory, and effectively de-BIDSifying it.
>
> It also appears to work if the image is removed entirely from the BIDS
> directory, but I think that would not be obvious, nor in agreement
> with current, standard practice according to FSL tutorials, which I
> think suggest creating the mask in the same directory.
>
> Assuming that the directory that contains the subject's anatomical
> image is username/ds102/sub-08/anat, then what directory location and
> filename will FSLeyes accept according to its BIDS validation rules?
>
> I tried creating inside the derivatives directory a directory for FSL,
> adding a dataset_description.json per the description at
>
> https://bids-specification.readthedocs.io/en/derivatives/05-derivatives/01-introduction.html
>
> and putting the mask file into
> derivatives/fsl/sub-08/anat/sub-08_T1w_brain.nii.gz and that did not
> help.
>
> I see from the Changelog at
> https://github.com/pauldmccarthy/fsleyes/blob/master/CHANGELOG.rst
> that
>
> Metadata from JSON sidecar files (e.g. in BIDS data sets) is now
> displayed in the overlay information panel.
>
> Anyway, if you would, please let us know where FSLeyes expects to see
> the brain masks generated by bet/bet2, which JSON files might need to
> be written, and what information might be required in them.
> Presumably, this will also be a problem when using FSLeyes to look at
> images directories created by feat, if they are in the same BIDS
> folder?
>
> Thanks in advance for your guidance, -- bennet
>
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