Re: [Freesurfer] skull stripping error

I7Rya_LJ2SYBMhdBLxraGCc--86eTKfh8ceID9Ti_ED7EjmUyMkJOttmGJyGagZPXhH7A3RhFT9P0ctOvvA5OlvuACK5GMWcKuPRjup36Qp0N8MxaSxpm57w2o0Fp-l5RO3T85qrrAMRw1QrAc3seOvh7G0Q/http%3A%2F%2Fwww.yahoo.com> +98 914 526 9298 On Monday, December 4, 2023 at 05:29:41 PM GMT+3:30, Glasser, Matt wrote: Ex

Re: [Freesurfer] skull stripping error

version. We plan to perform the volumetrics using version 7.4.1 of Freesurfer. Then, we will use both our results and the original HCP runs in our modeling, and maybe compare them. bests, Yunus On Monday, December 4, 2023 at 05:00:40 PM GMT+3:30, Glasser, Matt wrote: External

Re: [Freesurfer] skull stripping error

External Email - Use Caution Why are you rerunning FreeSurfer on HCP data? You are unlikely to match the quality of the original FreeSurfer runs. Matt. From: on behalf of yunus soleymani Reply-To: Freesurfer Support List Date: Monday, December 4, 2023 at 4:59 AM To: Freesur

Re: [Freesurfer] FreeSurfer Parcellation Using Glasser's Atlas (HCP-MMP1)

External Email - Use Caution Sorry, missed this one before I got the personal invitation to respond. I believe this would use a FreeSurfer registration of the group parcellation to the individual. That is a folding-based registration and one can do slightly better than that wit

Re: [Freesurfer] using synthsr with HCP Pipeline

External Email - Use Caution That’s not easy to do out of the box, because you would need to run SynthSR before PreFreeSurfer, when normally you do the reverse. Not having T2w scans just means you would need to enable legacy mode options. I have some code that imports a SynthSR

Re: [Freesurfer] EPI Factor generated by dmri_bids_config

External Email - Use Caution That EPI factor is wrong (if it is a single shot EPI sequence the EPI factor should equal the number of phase encoding steps). That said, it should not matter for eddy/topup unless you want correctly scaled field coefficients (these algorithms inter

Re: [Freesurfer] Huge difference between volumes for Freesurfer vs CAT12

External Email - Use Caution Is it possible that CAT12 reports volumes after alignment to MNI space (incorrect)? That is roughly the magnitude of the difference in total brain volume. Matt. From: on behalf of Michael Mc Laughlin Reply-To: Freesurfer support list Date: Frid

Re: [Freesurfer] ACPC alignment and RF/B1 bias correction before processing

External Email - Use Caution FreeSurfer does not need ACPC alignment to be done. It does benefit from on-scanner B1- correction such as “Pre-Scan Normalize” on Siemens scanners. Matt. From: on behalf of Toshiharu Kamishikiryo Reply-To: Freesurfer support list Date: Sunday,

Re: [Freesurfer] Is it possible to add additional T1 scans to improve surfaces/segmentation

External Email - Use Caution I think there are some deep learning approaches out there that try to infer a high-resolution volume from low resolution volumes in multiple planes. I don’t know if they would work with only axial and sagittal images though. Matt. From: on behalf

Re: [Freesurfer] Apply a nonlinear transform to a surface.

a surface. External Email - Use Caution I think that only works for gifti files. I need it in freesurfer coordinates. Thank you for responding. On Fri, Mar 3, 2023, 7:30 PM Glasser, Matt mailto:glass...@wustl.edu>> wrote: External Email - Use Caution You can do thi

Re: [Freesurfer] Apply a nonlinear transform to a surface.

External Email - Use Caution You can do this with wb_command. Dunno if FreeSurfer offers this. Matt. From: on behalf of Aaron Tanenbaum Reply-To: Freesurfer support list Date: Friday, March 3, 2023 at 7:26 PM To: Freesurfer Subject: [Freesurfer] Apply a nonlinear transform

Re: [Freesurfer] MSM error

External Email - Use Caution This seems a better question for the HCP-Users (hcp-us...@humanconnectome.org) list than the FreeSurfer list, given that you are using the HCP Pipelines and MSM is an FSL rather than a FreeSurfer tool. When you

Re: [Freesurfer] High resolution T1

nks. Sang From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Glasser, Matt Sent: Monday, January 30, 2023 1:23 PM To: Freesurfer support list Subject: [EXTERNAL] Re: [Freesurfer] High resolution T1 CAUTION: This email originated from outside the organization. DO NOT CLICK ON LIN

Re: [Freesurfer] High resolution T1

External Email - Use Caution We showed improved data (more accurate surface placement leading to more accurate myelin maps) in prior publications (Glasser et al., 2013; 2014 Neuroimage). It makes a difference for cortical thickness too (e.g., falsely too low cortical thickness

Re: [Freesurfer] High Resolution Freesurfer Error

External Email - Use Caution How about a picture of the problem? At least at one time, some of FreeSurfer was limited to 256^3 voxels and there is a maximum resolution that you can fit a human brain in with that. Matt. From: on behalf of Brooklyn Wright Reply-To: Freesurfer

Re: [Freesurfer] Autorecon-pial with T1w and T2w images

External Email - Use Caution Use the -T2 and -T2pial flags. Matt. From: on behalf of Steve Petersen Reply-To: Freesurfer support list Date: Sunday, December 4, 2022 at 10:01 AM To: "freesurfer@nmr.mgh.harvard.edu" Subject: [Freesurfer] Autorecon-pial with T1w and T2w images

Re: [Freesurfer] Only extract stats information question

External Email - Use Caution No, the stats are generated at the very end of a long process that requires the prior steps. Matt. From: on behalf of 蔡嘉鑫 Reply-To: Freesurfer support list Date: Saturday, November 12, 2022 at 10:16 AM To: "freesurfer@nmr.mgh.harvard.edu" Subjec

Re: [Freesurfer] T1w/T2w ratio maps: acquisition parameters T1w and T2w

External Email - Use Caution Giving cubic volumes of voxels is a bit confusing, but I assume what you meant to say is that you have 1mm T1w images and 0.7mm T2w images. Although you can certainly can register these and take the ratio (and FreeSurfer bbregister is the recommende

[Freesurfer] Van Essen/Glasser Lab Connectome Post-Doc Opportunity

External Email - Use Caution Hi FreeSurfer Users, We have a Connectome-related Post-Doc position available immediately in the Van Essen/Glasser lab. Please see the below posting. Feel free to forward to anyone you know who might be interested. Thanks, Matt. Postdoctoral Re

Re: [Freesurfer] Tissue fraction effects correction

External Email - Use Caution This is not something we have typically done with T1w/T2w myelin mapping. Is there a reason you are especially concerned about these issues? We tend to find that issues with surface placement, which are more prevalent at 1mm isotropic than at highe

Re: [Freesurfer] Using mri_transform with output of bbregister

External Email - Use Caution If you are using high resolution T1w and T2w images with FreeSurfer, you might just run the HCP Pipelines that depend upon such data and take care of all of this. Alternatively, you can see how FreeSurfer is called by the HCP Pipelines: https://secu

Re: [Freesurfer] Subject ID error with bbregister

External Email - Use Caution Hi Dylan, I call bbregister with --s in the same place you have it. Is it possible there is something wrong with $SUBJECTS_DIR when you are calling bbregister? Matt. On 2/21/22, 2:43 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Tisdall