It looks like just wrong window/level setting in freeview. Have you
tried adjust it? You can do it semi-automatically by drawing a ROI with
Ctrl + middle mouse button on the slice.
On 09/20/2017 12:12 PM, Linnea Marie Dramdal Borg wrote:
Hi,
My apologies, freeview_T207_dtifit_FA.nii.gz.png was not compressed
properly. You will find it attached this time.
The issue appears to stem from FreeView, as the intensity in the FA
picture is somehow reversed there, but not when opened in Fslview.
The representation in FreeView is fine, while the visualization goes
wrong. FreeView also manages to do the path reconstructions in TRACULA
even though the intensity appears inversed (see tractsOK.png). Why is
this only happening to some of the files? The scanner settings were
the same, and they are fine when opened in other viewer softwares.
Thank you,
Linnea Marie
------------------------------------------------------------------------
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Ruopeng Wang
<rpw...@nmr.mgh.harvard.edu>
*Sent:* Tuesday, September 19, 2017 5:39:22 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] Strange looking dtifit_FA.nii.gz in FreeView
Hi Linnea,
I don't see any issue in the screenshots you sent. I couldn't find
freeview_T207_dtifit_FA.nii.gz.png in the attachment, either. Also
your second screenshot is comparing FA image with a b0 image, which
will look somewhat inversed.
Best,
Ruopeng
On 09/19/2017 09:17 AM, Linnea Marie Dramdal Borg wrote:
Hi,
We have run TRACULA on a couple hundred subjects and the quality
control shows that most of them are OK, but in a few subjects the
dtifit_FA.nii.gz images look strange in FreeView. The image
intensities appear reversed in FreeView (see
freeview_T207_dtifit_FA.nii.gz.png) but look normal in Fslview (see
Fslview_T207_dtifit_FA.nii.gz.png). T205 is an example of a subject
that looks normal also in FreeView (see
fslview-freeview_T205_dtifit_FA.nii.gz.png), as most of our
subjects' dtifit_FA images do.
207's dwi_orig image looks fine in FreeView (see
freeview_T207_dwi_orig.nii.gz.png) as do all its L1,L2,L3,V1,V2,V3
etc. images.
I'm puzzled as to what has happened here. Since the image looks fine
in Fslview I'm inclined to think this is a FreeView issue?
Thank you,
Linnea Marie
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