External Email - Use Caution Ok. Looks like the updated -hires might be the better option overall. Anecdotally, wouldn't you expect better segs using high res input (in our case 0.8mm^3)?
Get Outlook for Android<https://aka.ms/ghei36> ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas Greve <dgr...@mgh.harvard.edu> Sent: Wednesday, September 9, 2020, 9:48 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] -hires vs -conf2hires in 7.1.1. * External Email - Caution * In both cases, the surfaces are placed on the high-resolution images. I'm not sure whether volume segmentation (ie, aseg) of highres images is better than at 1mm. On 9/9/20 10:30 AM, Alexopoulos, Dimitrios wrote: External Email - Use Caution Falk and Doug, thx for clarifying. Before we begin processing a new cohort using 7.1, I want to make sure I have a good grasp of the options/output. We want good volumes and surfaces, for potential cortical surface expansion analysis, thickness, etc. So, if you want better aseg segmentations/volumes use -hires, however, -conf2hires will give better surfaces (since they are placed on the hi res image) and thus more accurate cortical thickness and aparc measures. Jim Get Outlook for Android<https://aka.ms/ghei36> ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu> Sent: Wednesday, September 9, 2020, 9:11 AM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] -hires vs -conf2hires in 7.1.1. * External Email - Caution * Hi Jim, and thanks for jumping in Falk. This description is almost all correct. The one inaccuracy is that the -hires option will downsample the surface to a number of vertices equal to the number that would have resulted if recon-all had been run at 1mm. The main difference is that you will get volume segmentations at the higher resolution with -hires where as you will get them at 1mm with -conf2hires. On 9/9/2020 3:13 AM, falk.luesebr...@med.ovgu.de<mailto:falk.luesebr...@med.ovgu.de> wrote: External Email - Use Caution Hi Jim, The -hires will conform the data to the highest resolution of your input data, instead of 1mm^3. In case it was an isotropic resolution, it will stay at native resolution. If it is anisotropic, e.g. 0.3x0.3x0.7, it will be resampled to 0.3mm^3 – which is not really recommended. The segmentation and surface placement will take place at that resolution. The -conf2hires flag will conform your input data to 1mm^3. Segmentation and initial surface placement will be handled at conformed (1mm) resolution. Then the initial surface placement is used at native resolution to refine the surface placement. With -hires the number of vertices per hemisphere depends on your input resolution being roughly at 300k at 0.7mm and 500k at 0.5 mm. With -conf2hires the number of vertices will be around 140k per hemisphere and, therefore, processing (especially the topologic correction) will be much faster compared to -hires. The principle behind -conf2hires was used in the processing pipeline of the HCP (https://doi.org/10.1016/j.neuroimage.2013.04.127) and has been shown to improve the segmentation in highly myelinated areas, e.g. around the visual cortex or central sulcus. Natalia Zaretskaya and Jon Polimeni (https://doi.org/10.1016/j.neuroimage.2017.09.060) and I (https://doi.org/10.1016/j.neuroimage.2012.12.016) could show that the principles behind the -hires flag yield different results than downsampling high resolution input data or using 1mm data to being with. It is hypothesized that using high resolution data with the -hires flag leads to better surface placement and, therefore, more accurate cortical thickness measures. However, missing ground truth always makes it complicated to proof. To answer your question which is recommended: In the release notes of FreeSurfer it is written with regards to conf2hires “This was originally programmed for the HCP. The now-standard hi-res stream should work just as well, but we kept conf2hires for backwards compatibility.” I don’t think someone published a comparison between -hires and -conf2hires, yet. However, I would use the -hires flag instead of -conf2hires. I assume the surface placement to be equally good, with potential benefits towards -hires due to the higher number of vertices. The drawbacks of -hires (e.g. longer processing time) should be compensated to some extent by the new denoising feature prior to the intial surface placement. Personally, I haven’t had much time to test v7 intensively, though. Hope this helps. Best, Falk Von: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu> Im Auftrag von Alexopoulos, Dimitrios Gesendet: Mittwoch, 9. September 2020 05:27 An: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Betreff: [Freesurfer] -hires vs -conf2hires in 7.1.1. External Email - Use Caution Does the hires flag still generate segs at the native hi resolution and place surfaces on the 1mm volumes, whereas conf2hires generates volumes at 1mm but places surfaces on the hires images? Which option is recommended and why? Jim Get Outlook for Android<https://aka.ms/ghei36> ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. 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