Hi Brian, I honestly can’t tell the difference, even when the high dpi rendering is turned on. The volume is low res to begin with. There is a smooth display check box you can try in freeview. It will remove the pixelation of the rendering.
Best Ruopeng > On Apr 14, 2020, at 4:28 PM, Renner, Brian <brian.ren...@cshs.org> wrote: > > External Email - Use Caution > Hi Rupoeng! > > Attached is a direct flair opening in same without flags, freeview (L) > fsleyes (R), set with 0-168 min-max for each window (fig 1). I did notice a > tick box in fsleyes was set to "render in high DPI" was checked (fig 2), so I > unchecked it for fig 1. > > <Screen Shot 2020-04-14 at 1.27.06 PM.png> > fig 1 > > <Screen Shot 2020-04-14 at 1.23.18 PM.png> > fig 2. > > Perhaps that is the culprit; is there a similar render mode for freeview or > is that the driver not optimized as Andrew previously wrote? > > Much thanks all! > > BR > 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, April 14, 2020 11:10 AM > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] [External] Re: Freesurfer display resolution very > low compared to other viewers > > Hi Brian, > > Can you load a single volume in freeview to compare? Maybe also use similar > window/level? The one in the picture appears smoothed to me (may due to > trilinear sampling if it is not the first loaded volume). > > Best, > Ruopeng > > >> On Apr 14, 2020, at 1:14 PM, Renner, Brian <brian.ren...@cshs.org >> <mailto:brian.ren...@cshs.org>> wrote: >> >> External Email - Use Caution >> Hey Andrew; >> >> Thanks for the response! To answer your questions, yes, We’re all >> respectively on Macbook Pro retina displays. I hadn't compared the >> visualization on a Windows machine, though I ostensibly could in the near >> future. I have loaded up single vs. multiple volumes and noticed what you >> say; would it be best to load the hypothetical highest resolution scan >> first? ie. freeview -v highest.nii lower.nii. lowest.nii. --trilinear? >> >> An example picture of this is shown below, with a standard 1mm^3 t2 flair >> loaded in freeview with a higher resolution t2* as the first loaded scan, >> ie. on the left freeview -v t2*file flair --trilinear vs. fsleyes t2*file >> flair on the right: >> >> <Screen Shot 2020-04-14 at 9.40.57 AM.png> >> Fig 1. This is the flair file compared side by side (fv --trilinear vs. >> fsleyes, respectively). >> >> <Screen Shot 2020-04-14 at 9.43.58 AM.png> >> Fig 2. This is the t2*file (0.65mm voxel width), which has both noticeable >> quality drop and a different baseline intensity threshold at baseline >> between freeview and fsleyes. >> >> <Screen Shot 2020-04-14 at 10.00.10 AM.png> >> Fig 3. This is the flair --trilinear vs. flair (noflags) vs. fsleyes flair, >> respectively. >> >> Let me know what you think, and again thank you for the response! >> >> BR >> >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> >> <freesurfer-boun...@nmr.mgh.harvard.edu >> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Hoopes, Andrew >> <ahoo...@mgh.harvard.edu <mailto:ahoo...@mgh.harvard.edu>> >> Sent: Tuesday, April 14, 2020 9:25:08 AM >> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu >> <mailto:freesurfer@nmr.mgh.harvard.edu>> >> Subject: [External] Re: [Freesurfer] Freesurfer display resolution very low >> compared to other viewers >> >> Hi Brian, >> >> A couple questions - are you visualizing on a mac retina screen? If so, >> there will be a slight decrease from the standard resolution because the >> underlying rendering library that we use unfortunately does not support >> retina capabilities at this time. Also, are you loading single or multiple >> volumes? Freeview uses the first volume loaded as the base image geometry, >> and all the following volumes are resampled (if necessary) into this base >> geometry using nearest neighbor interpolation. So if you’re working with >> different-resolution images, it might help to enable linear interpolation as >> the default resampling method by using the `--trilinear` freeview flag. If >> that’s not the case, it’d be helpful to see a couple screenshots of the >> issue. >> >> Hope that helps, >> Andrew >> >> From: <freesurfer-boun...@nmr.mgh.harvard.edu >> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of "Renner, >> Brian" <brian.ren...@cshs.org <mailto:brian.ren...@cshs.org>> >> Reply-To: FS Help <freesurfer@nmr.mgh.harvard.edu >> <mailto:freesurfer@nmr.mgh.harvard.edu>> >> Date: Monday, April 13, 2020 at 8:54 PM >> To: FS Help <freesurfer@nmr.mgh.harvard.edu >> <mailto:freesurfer@nmr.mgh.harvard.edu>> >> Subject: [Freesurfer] Freesurfer display resolution very low compared to >> other viewers >> >> External Email - Use Caution >> Hello all! >> >> Inaugural message to the list; I will attempt to be brief with the project >> description. >> >> The setup is consistent between both versions 6.0.0 and 7.0.0-beta, run on a >> high performance cluster, accessed through macOS terminal + Xquartz, most >> recent versions all. >> >> As it stands, our group is attempting to do subfield analysis of hippocampal >> analysis and lesion measurement in MS subjects. We have noticed that there >> is a major discrepancy of resolutions between files, which has irked some of >> our physicians undertaking the lesion measurement. We need to resolve the >> lesions down to 3mm and have noticed the quality between freeview and >> fsleyes of the same nifti files will yield much lower display resolution. >> This is true for most scans, though it has been compared using 1mm T2 FLAIR >> sequences as well as T2* sequences with 0.65mm voxel space. I have been >> attempting to find a workaround as the current solution for the physicians >> is to look at the files in fsleyes and then measure them with the ruler tool >> in freeview. I can send supporting pictures as necessary. >> >> Thank you in advance for any thoughts you may have! >> >> BR >> >> -- >> Brian Renner, MD >> Research Associate, Neurology >> brian.ren...@cshs.org <mailto:brian.ren...@cshs.org> >> >> Cedars-Sinai >> 127 S. San Vicente Blvd, Suite A6600 : Los Angeles CA 90048 >> office 310-423-1589 : mobile 310-658-3492 : cedars-sinai.org >> <https://www.cedars-sinai.org/> >> >> >> >> IMPORTANT WARNING: This message is intended for the use of the person or >> entity to which it is addressed and may contain information that is >> privileged and confidential, the disclosure of which is governed by >> applicable law. If the reader of this message is not the intended recipient, >> or the employee or agent responsible for delivering it to the intended >> recipient, you are hereby notified that any dissemination, distribution or >> copying of this information is strictly prohibited. Thank you for your >> cooperation. >> <Screen Shot 2020-04-14 at 9.40.57 >> AM.png>_______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
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