External Email - Use Caution
We have data acquired at 0.8mm isotropic and would like to maintain this resolution in the processing stream rather than FS resampling to 1mm. Is the command to do this 'recon-all -hires -all'?
Are there any drawback to doing this?
Jim
________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
better to use a patch I created for the HCP, see https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/hcp/readm...
On 10/15/19 12:13 PM, Alexopoulos, Dimitrios wrote:
External Email - Use Caution
We have data acquired at 0.8mm isotropic and would like to maintain this resolution in the processing stream rather than FS resampling to 1mm.
Is the command to do this ‘recon-all -hires -all’?
Are there any drawback to doing this?
Jim
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Thanks. Will give it a try.
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Greve, Douglas N.,Ph.D. Sent: Tuesday, October 15, 2019 11:54 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all at native resolution
better to use a patch I created for the HCP, see https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/hcp/readm...
On 10/15/19 12:13 PM, Alexopoulos, Dimitrios wrote:
External Email - Use CautionWe have data acquired at 0.8mm isotropic and would like to maintain this resolution in the processing stream rather than FS resampling to 1mm.
Is the command to do this 'recon-all -hires -all'?
Are there any drawback to doing this?
Jim
--
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
External Email - Use Caution
Doug,
I copied over files and ran using the -conf2hires flag, however, the orig.mgz/brainmask.mgz are resampled to 1mm isotropic not the native 0.8mm.
Using the -hires flag maintains the orig.mgz/brainmask.mgz at native 0.8mm resolution.
Is this expected when running -conf2hires?
Jim
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Greve, Douglas N.,Ph.D. Sent: Tuesday, October 15, 2019 11:54 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all at native resolution
better to use a patch I created for the HCP, see https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/hcp/readm...
On 10/15/19 12:13 PM, Alexopoulos, Dimitrios wrote:
External Email - Use CautionWe have data acquired at 0.8mm isotropic and would like to maintain this resolution in the processing stream rather than FS resampling to 1mm.
Is the command to do this 'recon-all -hires -all'?
Are there any drawback to doing this?
Jim
--
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
oh, sorry, yes it is. The surfaces are placed on the high res volumes, but the aseg will be at 1mm. If you need the aseg at highres, then you will need to use the -hires flag (but the surfaces will suffer)
On 10/24/19 2:55 PM, Alexopoulos, Dimitrios wrote:
External Email - Use CautionDoug,
I copied over files and ran using the -conf2hires flag, however, the orig.mgz/brainmask.mgz are resampled to 1mm isotropic not the native 0.8mm.
Using the -hires flag maintains the orig.mgz/brainmask.mgz at native 0.8mm resolution.
Is this expected when running -conf2hires?
Jim
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Greve, Douglas N.,Ph.D. Sent: Tuesday, October 15, 2019 11:54 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all at native resolution
better to use a patch I created for the HCP, see https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/hcp/readm...
On 10/15/19 12:13 PM, Alexopoulos, Dimitrios wrote:
External Email - Use CautionWe have data acquired at 0.8mm isotropic and would like to maintain this resolution in the processing stream rather than FS resampling to 1mm.
Is the command to do this 'recon-all -hires -all'?
Are there any drawback to doing this?
Jim
--
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
The cortical parcellations in the aseg and aparc+seg have some issues in the orbital prefrontal regions and we're were hoping that the higher resolution images would help. The surfaces look fine.
We should use the -hires flag instead in this scenario?
Thx.
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Greve, Douglas N.,Ph.D. Sent: Thursday, October 24, 2019 5:06 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all at native resolution
oh, sorry, yes it is. The surfaces are placed on the high res volumes, but the aseg will be at 1mm. If you need the aseg at highres, then you will need to use the -hires flag (but the surfaces will suffer)
On 10/24/19 2:55 PM, Alexopoulos, Dimitrios wrote:
External Email - Use CautionDoug,
I copied over files and ran using the -conf2hires flag, however, the orig.mgz/brainmask.mgz are resampled to 1mm isotropic not the native 0.8mm.
Using the -hires flag maintains the orig.mgz/brainmask.mgz at native 0.8mm resolution.
Is this expected when running -conf2hires?
Jim
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Greve, Douglas N.,Ph.D. Sent: Tuesday, October 15, 2019 11:54 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all at native resolution
better to use a patch I created for the HCP, see https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/hcp /readme
On 10/15/19 12:13 PM, Alexopoulos, Dimitrios wrote:
External Email - Use CautionWe have data acquired at 0.8mm isotropic and would like to maintain this resolution in the processing stream rather than FS resampling to 1mm.
Is the command to do this 'recon-all -hires -all'?
Are there any drawback to doing this?
Jim
--
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
You mean the surfaces using -hires look fine? If so, then continue to use -hires
On 10/24/19 6:32 PM, Alexopoulos, Dimitrios wrote:
External Email - Use CautionThe cortical parcellations in the aseg and aparc+seg have some issues in the orbital prefrontal regions and we're were hoping that the higher resolution images would help. The surfaces look fine.
We should use the -hires flag instead in this scenario?
Thx.
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Greve, Douglas N.,Ph.D. Sent: Thursday, October 24, 2019 5:06 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all at native resolution
oh, sorry, yes it is. The surfaces are placed on the high res volumes, but the aseg will be at 1mm. If you need the aseg at highres, then you will need to use the -hires flag (but the surfaces will suffer)
On 10/24/19 2:55 PM, Alexopoulos, Dimitrios wrote:
External Email - Use CautionDoug,
I copied over files and ran using the -conf2hires flag, however, the orig.mgz/brainmask.mgz are resampled to 1mm isotropic not the native 0.8mm.
Using the -hires flag maintains the orig.mgz/brainmask.mgz at native 0.8mm resolution.
Is this expected when running -conf2hires?
Jim
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Greve, Douglas N.,Ph.D. Sent: Tuesday, October 15, 2019 11:54 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all at native resolution
better to use a patch I created for the HCP, see https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/hcp /readme
On 10/15/19 12:13 PM, Alexopoulos, Dimitrios wrote:
External Email - Use CautionWe have data acquired at 0.8mm isotropic and would like to maintain this resolution in the processing stream rather than FS resampling to 1mm.
Is the command to do this 'recon-all -hires -all'?
Are there any drawback to doing this?
Jim
--
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
I apologize for the confusion. Whether I use the -hires or -conf2hires flag the subcortical segmentations look good.
The cortical segmentations have some issues in the ventral medial area (see snapshot below), which is likely caused by difficulty in FS delineating WM superior to the gyrus rectus. I'm not sure how to correct this so I was thinking the higher resolution data may lead to a better WM segmentation?
Is my thinking correct? If so, which flag is best?
Jim
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Greve, Douglas N.,Ph.D. Sent: Thursday, October 24, 2019 5:37 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all at native resolution
You mean the surfaces using -hires look fine? If so, then continue to use -hires
On 10/24/19 6:32 PM, Alexopoulos, Dimitrios wrote:
External Email - Use CautionThe cortical parcellations in the aseg and aparc+seg have some issues in the orbital prefrontal regions and we're were hoping that the higher resolution images would help. The surfaces look fine.
We should use the -hires flag instead in this scenario?
Thx.
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Greve, Douglas N.,Ph.D. Sent: Thursday, October 24, 2019 5:06 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all at native resolution
oh, sorry, yes it is. The surfaces are placed on the high res volumes, but the aseg will be at 1mm. If you need the aseg at highres, then you will need to use the -hires flag (but the surfaces will suffer)
On 10/24/19 2:55 PM, Alexopoulos, Dimitrios wrote:
External Email - Use CautionDoug,
I copied over files and ran using the -conf2hires flag, however, the orig.mgz/brainmask.mgz are resampled to 1mm isotropic not the native 0.8mm.
Using the -hires flag maintains the orig.mgz/brainmask.mgz at native 0.8mm resolution.
Is this expected when running -conf2hires?
Jim
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Greve, Douglas N.,Ph.D. Sent: Tuesday, October 15, 2019 11:54 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all at native resolution
better to use a patch I created for the HCP, see https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/hc p /readme
On 10/15/19 12:13 PM, Alexopoulos, Dimitrios wrote:
External Email - Use CautionWe have data acquired at 0.8mm isotropic and would like to maintain this resolution in the processing stream rather than FS resampling to 1mm.
Is the command to do this 'recon-all -hires -all'?
Are there any drawback to doing this?
Jim
--
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
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_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
There was no snapshot. Can you resend?
On 10/24/2019 7:06 PM, Alexopoulos, Dimitrios wrote:
External Email - Use CautionI apologize for the confusion. Whether I use the -hires or -conf2hires flag the subcortical segmentations look good.
The cortical segmentations have some issues in the ventral medial area (see snapshot below), which is likely caused by difficulty in FS delineating WM superior to the gyrus rectus. I'm not sure how to correct this so I was thinking the higher resolution data may lead to a better WM segmentation?
Is my thinking correct? If so, which flag is best?
Jim
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Greve, Douglas N.,Ph.D. Sent: Thursday, October 24, 2019 5:37 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all at native resolution
You mean the surfaces using -hires look fine? If so, then continue to use -hires
On 10/24/19 6:32 PM, Alexopoulos, Dimitrios wrote:
External Email - Use CautionThe cortical parcellations in the aseg and aparc+seg have some issues in the orbital prefrontal regions and we're were hoping that the higher resolution images would help. The surfaces look fine.
We should use the -hires flag instead in this scenario?
Thx.
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Greve, Douglas N.,Ph.D. Sent: Thursday, October 24, 2019 5:06 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all at native resolution
oh, sorry, yes it is. The surfaces are placed on the high res volumes, but the aseg will be at 1mm. If you need the aseg at highres, then you will need to use the -hires flag (but the surfaces will suffer)
On 10/24/19 2:55 PM, Alexopoulos, Dimitrios wrote:
External Email - Use CautionDoug,
I copied over files and ran using the -conf2hires flag, however, the orig.mgz/brainmask.mgz are resampled to 1mm isotropic not the native 0.8mm.
Using the -hires flag maintains the orig.mgz/brainmask.mgz at native 0.8mm resolution.
Is this expected when running -conf2hires?
Jim
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Greve, Douglas N.,Ph.D. Sent: Tuesday, October 15, 2019 11:54 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all at native resolution
better to use a patch I created for the HCP, see https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/hc p /readme
On 10/15/19 12:13 PM, Alexopoulos, Dimitrios wrote:
External Email - Use CautionWe have data acquired at 0.8mm isotropic and would like to maintain this resolution in the processing stream rather than FS resampling to 1mm.
Is the command to do this 'recon-all -hires -all'?
Are there any drawback to doing this?
Jim
--
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Opps, here are the snapshots. The aseg subcortical look good using either the -hires or -conf2hires flags.
The cortical parcellation is not including some ctx in several regions including the region below.
[cid:image001.png@01D58B27.A63D2C70]
[cid:image002.png@01D58B27.A63D2C70]
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Greve, Douglas N.,Ph.D. Sent: Friday, October 25, 2019 11:17 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all at native resolution
There was no snapshot. Can you resend?
On 10/24/2019 7:06 PM, Alexopoulos, Dimitrios wrote:
External Email - Use Caution
I apologize for the confusion. Whether I use the -hires or -conf2hires flag the subcortical segmentations look good.
The cortical segmentations have some issues in the ventral medial area (see snapshot below), which is likely caused by difficulty in FS delineating WM superior to the gyrus rectus. I'm not sure how to correct this so I was thinking the higher resolution data may lead to a better WM segmentation?
Is my thinking correct? If so, which flag is best?
Jim
-----Original Message-----
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 Greve, Douglas N.,Ph.D.
Sent: Thursday, October 24, 2019 5:37 PM
To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] recon-all at native resolution
You mean the surfaces using -hires look fine? If so, then continue to
use -hires
On 10/24/19 6:32 PM, Alexopoulos, Dimitrios wrote:
External Email - Use Caution
The cortical parcellations in the aseg and aparc+seg have some issues in the orbital prefrontal regions and we're were hoping that the higher resolution images would help. The surfaces look fine.
We should use the -hires flag instead in this scenario?
Thx.
-----Original Message-----
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 Greve, Douglas N.,Ph.D.
Sent: Thursday, October 24, 2019 5:06 PM
To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] recon-all at native resolution
oh, sorry, yes it is. The surfaces are placed on the high res
volumes, but the aseg will be at 1mm. If you need the aseg at
highres, then you will need to use the -hires flag (but the surfaces
will suffer)
On 10/24/19 2:55 PM, Alexopoulos, Dimitrios wrote:
External Email - Use Caution
Doug,
I copied over files and ran using the -conf2hires flag, however, the orig.mgz/brainmask.mgz are resampled to 1mm isotropic not the native 0.8mm.
Using the -hires flag maintains the orig.mgz/brainmask.mgz at native 0.8mm resolution.
Is this expected when running -conf2hires?
Jim
-----Original Message-----
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 Greve, Douglas N.,Ph.D.
Sent: Tuesday, October 15, 2019 11:54 AM
To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] recon-all at native resolution
better to use a patch I created for the HCP, see
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/h
c
p
/readme
On 10/15/19 12:13 PM, Alexopoulos, Dimitrios wrote:
External Email - Use Caution
We have data acquired at 0.8mm isotropic and would like to maintain
this resolution in the processing stream rather than FS resampling to 1mm.
Is the command to do this 'recon-all -hires -all'?
Are there any drawback to doing this?
Jim
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Yes, this is the issue we have with the high res stream in v6. As I said, you can use the patch that I pointed to below to get better surfaces.
On 10/25/19 12:30 PM, Alexopoulos, Dimitrios wrote:
External Email - Use Caution
Opps, here are the snapshots. The aseg subcortical look good using either the –hires or –conf2hires flags.
The cortical parcellation is not including some ctx in several regions including the region below.
[cid:part1.6B18B5A1.452BD44E@mgh.harvard.edu]
[cid:part2.86F8F402.1E6C2D82@mgh.harvard.edu]
-----Original Message----- 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 Greve, Douglas N.,Ph.D. Sent: Friday, October 25, 2019 11:17 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all at native resolution
There was no snapshot. Can you resend?
On 10/24/2019 7:06 PM, Alexopoulos, Dimitrios wrote:
External Email - Use Caution
I apologize for the confusion. Whether I use the -hires or -conf2hires flag the subcortical segmentations look good.
The cortical segmentations have some issues in the ventral medial area (see snapshot below), which is likely caused by difficulty in FS delineating WM superior to the gyrus rectus. I'm not sure how to correct this so I was thinking the higher resolution data may lead to a better WM segmentation?
Is my thinking correct? If so, which flag is best?
Jim
-----Original Message-----
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 Greve, Douglas N.,Ph.D.
Sent: Thursday, October 24, 2019 5:37 PM
To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] recon-all at native resolution
You mean the surfaces using -hires look fine? If so, then continue to
use -hires
On 10/24/19 6:32 PM, Alexopoulos, Dimitrios wrote:
External Email - Use Caution
The cortical parcellations in the aseg and aparc+seg have some issues in the orbital prefrontal regions and we're were hoping that the higher resolution images would help. The surfaces look fine.
We should use the -hires flag instead in this scenario?
Thx.
-----Original Message-----
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 Greve, Douglas N.,Ph.D.
Sent: Thursday, October 24, 2019 5:06 PM
To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] recon-all at native resolution
oh, sorry, yes it is. The surfaces are placed on the high res
volumes, but the aseg will be at 1mm. If you need the aseg at
highres, then you will need to use the -hires flag (but the surfaces
will suffer)
On 10/24/19 2:55 PM, Alexopoulos, Dimitrios wrote:
External Email - Use Caution
Doug,
I copied over files and ran using the -conf2hires flag, however, the orig.mgz/brainmask.mgz are resampled to 1mm isotropic not the native 0.8mm.
Using the -hires flag maintains the orig.mgz/brainmask.mgz at native 0.8mm resolution.
Is this expected when running -conf2hires?
Jim
-----Original Message-----
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 Greve, Douglas N.,Ph.D.
Sent: Tuesday, October 15, 2019 11:54 AM
To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] recon-all at native resolution
better to use a patch I created for the HCP, see
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/h
c
p
/readme
On 10/15/19 12:13 PM, Alexopoulos, Dimitrios wrote:
External Email - Use Caution
We have data acquired at 0.8mm isotropic and would like to maintain
this resolution in the processing stream rather than FS resampling to 1mm.
Is the command to do this 'recon-all -hires -all'?
Are there any drawback to doing this?
Jim
--
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Healthcare Information or other information of a sensitive nature.
If you are not the intended recipient, be advised that any
unauthorized use, disclosure, copying or the taking of any action
in reliance on the contents of this information is strictly prohibited.
If you have received this email in error, please immediately notify
the sender via telephone or return mail.
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_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Thanx Doug.
Tried the patch and got similar results to -hires. Must be the data and tissue contrast in that region where WM is difficult to discern. These are 2yo subjects. We also tried baby freesurfer with poorer results.
Jim
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Greve, Douglas N.,Ph.D. Sent: Monday, October 28, 2019 9:22 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all at native resolution
Yes, this is the issue we have with the high res stream in v6. As I said, you can use the patch that I pointed to below to get better surfaces. On 10/25/19 12:30 PM, Alexopoulos, Dimitrios wrote:
External Email - Use Caution
Opps, here are the snapshots. The aseg subcortical look good using either the -hires or -conf2hires flags.
The cortical parcellation is not including some ctx in several regions including the region below.
[cid:image001.png@01D58D7A.58A802F0]
[cid:image002.png@01D58D7A.58A802F0]
-----Original Message----- 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 Greve, Douglas N.,Ph.D. Sent: Friday, October 25, 2019 11:17 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all at native resolution
There was no snapshot. Can you resend?
On 10/24/2019 7:06 PM, Alexopoulos, Dimitrios wrote:
External Email - Use Caution
I apologize for the confusion. Whether I use the -hires or -conf2hires flag the subcortical segmentations look good.
The cortical segmentations have some issues in the ventral medial area (see snapshot below), which is likely caused by difficulty in FS delineating WM superior to the gyrus rectus. I'm not sure how to correct this so I was thinking the higher resolution data may lead to a better WM segmentation?
Is my thinking correct? If so, which flag is best?
Jim
-----Original Message-----
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 Greve, Douglas N.,Ph.D.
Sent: Thursday, October 24, 2019 5:37 PM
To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] recon-all at native resolution
You mean the surfaces using -hires look fine? If so, then continue to
use -hires
On 10/24/19 6:32 PM, Alexopoulos, Dimitrios wrote:
External Email - Use Caution
The cortical parcellations in the aseg and aparc+seg have some issues in the orbital prefrontal regions and we're were hoping that the higher resolution images would help. The surfaces look fine.
We should use the -hires flag instead in this scenario?
Thx.
-----Original Message-----
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 Greve, Douglas N.,Ph.D.
Sent: Thursday, October 24, 2019 5:06 PM
To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] recon-all at native resolution
oh, sorry, yes it is. The surfaces are placed on the high res
volumes, but the aseg will be at 1mm. If you need the aseg at
highres, then you will need to use the -hires flag (but the surfaces
will suffer)
On 10/24/19 2:55 PM, Alexopoulos, Dimitrios wrote:
External Email - Use Caution
Doug,
I copied over files and ran using the -conf2hires flag, however, the orig.mgz/brainmask.mgz are resampled to 1mm isotropic not the native 0.8mm.
Using the -hires flag maintains the orig.mgz/brainmask.mgz at native 0.8mm resolution.
Is this expected when running -conf2hires?
Jim
-----Original Message-----
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 Greve, Douglas N.,Ph.D.
Sent: Tuesday, October 15, 2019 11:54 AM
To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] recon-all at native resolution
better to use a patch I created for the HCP, see
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/h
c
p
/readme
On 10/15/19 12:13 PM, Alexopoulos, Dimitrios wrote:
External Email - Use Caution
We have data acquired at 0.8mm isotropic and would like to maintain
this resolution in the processing stream rather than FS resampling to 1mm.
Is the command to do this 'recon-all -hires -all'?
Are there any drawback to doing this?
Jim
--
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Healthcare Information or other information of a sensitive nature.
If you are not the intended recipient, be advised that any
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If you have received this email in error, please immediately notify
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-
Alexopoulos, Dimitrios -
Greve, Douglas N.,Ph.D.