Re: [Freesurfer] recon-all at native resolution

28 Oct 2019

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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:
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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:
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I apologize for the confusion.  Whether I use the -hires or -conf2hires flag the subcortical segmentations look good.
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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?
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Is my thinking correct? If so, which flag is best?
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Jim
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-----Original Message-----
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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.
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Sent: Thursday, October 24, 2019 5:37 PM
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To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
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Subject: Re: [Freesurfer] recon-all at native resolution
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You mean the surfaces using -hires look fine? If so, then continue to
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use -hires
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On 10/24/19 6:32 PM, Alexopoulos, Dimitrios wrote:
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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.
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We should use the -hires flag instead in this scenario?
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Thx.
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-----Original Message-----
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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.
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Sent: Thursday, October 24, 2019 5:06 PM
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To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
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Subject: Re: [Freesurfer] recon-all at native resolution
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oh, sorry, yes it is. The surfaces are placed on the high res
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volumes, but the aseg will be at 1mm. If you need the aseg at
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highres, then you will need to use the -hires flag (but the surfaces
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will suffer)
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On 10/24/19 2:55 PM, Alexopoulos, Dimitrios wrote:
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Doug,
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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.
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Using the -hires flag maintains the orig.mgz/brainmask.mgz at native 0.8mm resolution.
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Is this expected when running -conf2hires?
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Jim
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-----Original Message-----
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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.
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Sent: Tuesday, October 15, 2019 11:54 AM
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To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
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Subject: Re: [Freesurfer] recon-all at native resolution
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better to use a patch I created for the HCP, see
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https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/h
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/readme
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On 10/15/19 12:13 PM, Alexopoulos, Dimitrios wrote:
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We have data acquired at 0.8mm isotropic and would like to maintain
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this resolution in the processing stream rather than FS resampling to 1mm.
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Is the command to do this 'recon-all -hires -all'?
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Are there any drawback to doing this?
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Jim
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Re: [Freesurfer] recon-all at native resolution