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.renner@cshs.orgmailto:brian.renner@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.orghttps://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.
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-bounces@nmr.mgh.harvard.edu on behalf of "Renner, Brian" Brian.Renner@cshs.org Reply-To: FS Help freesurfer@nmr.mgh.harvard.edu Date: Monday, April 13, 2020 at 8:54 PM To: FS Help 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.renner@cshs.orgmailto:brian.renner@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.orghttps://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.
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:
[cid:92febe9e-1d8d-4f32-a346-0c18bce748c1] Fig 1. This is the flair file compared side by side (fv --trilinear vs. fsleyes, respectively).
[cid:76948cc8-abd1-4df9-b913-9e66b80f1988] 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.
[cid:05e3fa5e-d936-41f5-a257-9d1f5ccdc1c2] 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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Hoopes, Andrew AHOOPES@mgh.harvard.edu Sent: Tuesday, April 14, 2020 9:25:08 AM To: Freesurfer support list 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-bounces@nmr.mgh.harvard.edu on behalf of "Renner, Brian" Brian.Renner@cshs.org Reply-To: FS Help freesurfer@nmr.mgh.harvard.edu Date: Monday, April 13, 2020 at 8:54 PM To: FS Help 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.renner@cshs.orgmailto:brian.renner@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.orghttps://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.
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.Renner@cshs.org wrote:
External Email - Use CautionHey 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-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Hoopes, Andrew <AHOOPES@mgh.harvard.edu mailto:AHOOPES@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-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Renner, Brian" <Brian.Renner@cshs.org mailto:Brian.Renner@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 CautionHello 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.renner@cshs.org mailto:brian.renner@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
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.
[cid:93440aa9-0b9a-4b2e-9507-ae14dde3adca] fig 1
[cid:21a18522-d823-4f67-a866-982fe6ea6bc2] 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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Ruopeng Wang rpwang@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.Renner@cshs.orgmailto:Brian.Renner@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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Hoopes, Andrew <AHOOPES@mgh.harvard.edumailto:AHOOPES@mgh.harvard.edu> Sent: Tuesday, April 14, 2020 9:25:08 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Renner, Brian" <Brian.Renner@cshs.orgmailto:Brian.Renner@cshs.org> Reply-To: FS Help <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, April 13, 2020 at 8:54 PM To: FS Help <freesurfer@nmr.mgh.harvard.edumailto: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.renner@cshs.orgmailto:brian.renner@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.orghttps://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.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.Renner@cshs.org wrote:
External Email - Use CautionHi 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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Ruopeng Wang rpwang@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.Renner@cshs.org mailto:Brian.Renner@cshs.org> wrote:
External Email - Use CautionHey 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-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Hoopes, Andrew <AHOOPES@mgh.harvard.edu mailto:AHOOPES@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-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Renner, Brian" <Brian.Renner@cshs.org mailto:Brian.Renner@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 CautionHello 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.renner@cshs.org mailto:brian.renner@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
I could not tell a difference either.
On 4/14/2020 4:59 PM, Ruopeng Wang wrote:
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.Renner@cshs.org mailto:Brian.Renner@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-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Ruopeng Wang <rpwang@nmr.mgh.harvard.edu mailto:rpwang@nmr.mgh.harvard.edu> *Sent:*Tuesday, April 14, 2020 11:10 AM *To:*Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto: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.Renner@cshs.org mailto:Brian.Renner@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-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu<freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Hoopes, Andrew <AHOOPES@mgh.harvard.edu mailto:AHOOPES@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-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Renner, Brian" <Brian.Renner@cshs.org mailto:Brian.Renner@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.renner@cshs.org mailto:brian.renner@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
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External Email - Use Caution
Thanks all; I've added --trilinear --smoothing and --contrast so the images run with them natively. I agree with some calibration they actually do look similar. A question: is there some basis for which level/window values are loaded? The initial image comes up very saturated, though is corrected by raising both of these levels significantly.
I will update if I hear more from my side. Thank you, both!
BR ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Sent: Tuesday, April 14, 2020 2:09 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [External] Re: Freesurfer display resolution very low compared to other viewers
I could not tell a difference either.
On 4/14/2020 4:59 PM, Ruopeng Wang wrote: 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.Renner@cshs.orgmailto:Brian.Renner@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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Ruopeng Wang <rpwang@nmr.mgh.harvard.edumailto:rpwang@nmr.mgh.harvard.edu> Sent: Tuesday, April 14, 2020 11:10 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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.Renner@cshs.orgmailto:Brian.Renner@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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Hoopes, Andrew <AHOOPES@mgh.harvard.edumailto:AHOOPES@mgh.harvard.edu> Sent: Tuesday, April 14, 2020 9:25:08 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Renner, Brian" <Brian.Renner@cshs.orgmailto:Brian.Renner@cshs.org> Reply-To: FS Help <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Monday, April 13, 2020 at 8:54 PM To: FS Help <freesurfer@nmr.mgh.harvard.edumailto: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.renner@cshs.orgmailto:brian.renner@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.orghttps://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.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Douglas N. Greve -
Hoopes, Andrew -
Renner, Brian -
Ruopeng Wang