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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Ruopeng Wang <rpwang@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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