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> 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>
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