Dear Chris,
I have found that -n 15 is for our 0.7x0.7x0.7mm3 data not enough.
I determined optimal value -n 30, empirically, by looking at the shape of inflated surface with various number of iterations. Over -n 30 there was almost no further progression in inflation.
I suppose that better more than less. But maybe experts can correct me or provide better suggestion.
Antonin
Hi all,
If I'm reading this < https://surfer.nmr.mgh.harvard.edu/fswiki/SubmillimeterRecon%3E correctly, the current best practice for `-hires` is to include an expert file containing "mris_inflate -n 15", and that this should work for all voxel sizes (0.75mm)^3 - (1mm)^3? Or do we need to empirically determine the best value for a given voxel size, and if so, what should be the criteria for making this determination?Thanks, Chris Markiewicz
Dear Chris and Antonin,
I found in some archived message or in the wiki that the default used to be 50 iterations at some time in previous releases of FreeSurfer for standard recon-all. Therefore, I changed it to 50 as default for every resolution in the recent release. This works fine for example for up to 0.5x0.5x0.5mm3 data.
I'd also say, more is better and I have not experienced any drawbacks. Processing time doesn't seem to increase noticeably, too.
Best, Falk
________________________________ Von: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu]" im Auftrag von "Antonin Skoch [ansk@ikem.cz] Gesendet: Donnerstag, 9. Februar 2017 16:20 An: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] Expert file for recon-all -hires
Dear Chris,
I have found that -n 15 is for our 0.7x0.7x0.7mm3 data not enough.
I determined optimal value -n 30, empirically, by looking at the shape of inflated surface with various number of iterations. Over -n 30 there was almost no further progression in inflation.
I suppose that better more than less. But maybe experts can correct me or provide better suggestion.
Antonin
Hi all,
If I'm reading this < https://surfer.nmr.mgh.harvard.edu/fswiki/SubmillimeterRecon%3E correctly, the current best practice for `-hires` is to include an expert file containing "mris_inflate -n 15", and that this should work for all voxel sizes (0.75mm)^3 - (1mm)^3? Or do we need to empirically determine the best value for a given voxel size, and if so, what should be the criteria for making this determination?
Thanks, Chris Markiewicz
Hello Falk Chris and Antonin, The default is 55 https://surfer.nmr.mgh.harvard.edu/fswiki/mris_inflate. Best, Paul
On Thu, Feb 9, 2017 at 10:42 AM, Falk Lüsebrink falk.luesebrink@ovgu.de wrote:
Dear Chris and Antonin,
I found in some archived message or in the wiki that the default used to be 50 iterations at some time in previous releases of FreeSurfer for standard recon-all. Therefore, I changed it to 50 as default for every resolution in the recent release. This works fine for example for up to 0.5x0.5x0.5mm3 data.
I'd also say, more is better and I have not experienced any drawbacks. Processing time doesn't seem to increase noticeably, too.
Best, Falk
*Von:* freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh. harvard.edu]" im Auftrag von "Antonin Skoch [ansk@ikem.cz] *Gesendet:* Donnerstag, 9. Februar 2017 16:20 *An:* freesurfer@nmr.mgh.harvard.edu *Betreff:* Re: [Freesurfer] Expert file for recon-all -hires
Dear Chris,
I have found that -n 15 is for our 0.7x0.7x0.7mm3 data not enough.
I determined optimal value -n 30, empirically, by looking at the shape of inflated surface with various number of iterations. Over -n 30 there was almost no further progression in inflation.
I suppose that better more than less. But maybe experts can correct me or provide better suggestion.
Antonin
Hi all,
If I'm reading this https://surfer.nmr.mgh.harvard.edu/fswiki/SubmillimeterRecon correctly, the current best practice for `-hires` is to include an expert file containing "mris_inflate -n 15", and that this should work for all voxel sizes (0.75mm)^3 - (1mm)^3? Or do we need to empirically determine the best value for a given voxel size, and if so, what should be the criteria for making this determination?
Thanks, Chris Markiewicz
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