Re: [Freesurfer] Freesurfer - skull stripping error

kef> Da: freesurfer-boun...@nmr.mgh.harvard.edu per conto di Joshua K Lee Inviato: Sunday, September 29, 2024 5:53:01 PM A: Freesurfer support list Oggetto: Re: [Freesurfer] Freesurfer - skull stripping error External Email - Use Caution I just want

Re: [Freesurfer] Freesurfer - skull stripping error

...@ucdavis.edu From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Fischl, Bruce R.,PHD Sent: Sunday, September 29, 2024 1:20 AM To: Freesurfer support list Subject: Re: [Freesurfer] Freesurfer - skull stripping error You could try synthstrip, it might work

Re: [Freesurfer] Freesurfer - skull stripping error

Outlook per iOS<https://aka.ms/o0ukef> Da: freesurfer-boun...@nmr.mgh.harvard.edu per conto di Fischl, Bruce R.,PHD Inviato: Sunday, September 29, 2024 4:20:00 AM A: Freesurfer support list Oggetto: Re: [Freesurfer] Freesurfer - skull stripping error You

Re: [Freesurfer] Freesurfer - skull stripping error

rd.edu per conto di Fischl, Bruce R.,PHD Inviato: Sunday, September 29, 2024 4:20:00 AM A: Freesurfer support list Oggetto: Re: [Freesurfer] Freesurfer - skull stripping error You could try synthstrip, it might work Cheers Bruce On Sep 29, 2024, at 7:38 AM, William Baare wrote:  Ex

Re: [Freesurfer] Freesurfer - skull stripping error

You could try synthstrip, it might work Cheers Bruce On Sep 29, 2024, at 7:38 AM, William Baare wrote:  External Email - Use Caution Hi Sara, You need to denoise the background. Here are some links that might be of help. Always check the quality of the output :-) https://github.com

Re: [Freesurfer] Freesurfer - skull stripping error

External Email - Use Caution Hi Sara, You need to denoise the background. Here are some links that might be of help. Always check the quality of the output :-) https://secure-web.cisco.com/11TUQn3ZMjB9gy2mI09erMcLASzJWGpSLFMUxf9tT-XFEDmLfZKdF-O_LIYc_Nlr6rt_zg2mZoh6G-ql4JyDGF9_GK

Re: [Freesurfer] skull stripping error

for optimal performance in HCP data. Matt. From: on behalf of yunus soleymani Reply-To: Freesurfer support list Date: Monday, December 4, 2023 at 7:53 AM To: Freesurfer support list Subject: Re: [Freesurfer] skull stripping error External Email - Use Caution Yes, you are right.

Re: [Freesurfer] skull stripping error

as a part of the HCP Pipelines, not run by itself for optimal performance in HCP data.   Matt.   From: on behalf of yunus soleymani Reply-To: Freesurfer support list Date: Monday, December 4, 2023 at 7:53 AM To: Freesurfer support list Subject: Re: [Freesurfer] skull stripping error

Re: [Freesurfer] skull stripping error

Pipelines, not run by itself for optimal performance in HCP data. Matt. From: on behalf of yunus soleymani Reply-To: Freesurfer support list Date: Monday, December 4, 2023 at 7:53 AM To: Freesurfer support list Subject: Re: [Freesurfer] skull stripping error External Email - Use Caution

Re: [Freesurfer] skull stripping error

: Monday, December 4, 2023 at 4:59 AM To: Freesurfer Support List Subject: [Freesurfer] skull stripping error   External Email - Use Caution   Hello Freesurfers,   I recently analyzed about 600 subjects from HCP database using the Freesurfer recon-all algorithm. However, I

Re: [Freesurfer] skull stripping error

: Freesurfer Support List Subject: [Freesurfer] skull stripping error External Email - Use Caution Hello Freesurfers, I recently analyzed about 600 subjects from HCP database using the Freesurfer recon-all algorithm. However, I noticed that in almost one third of the subjects, the software

Re: [Freesurfer] Skull stripping error - too much brain lost - solved {Disarmed}

Doug, your added text would have been enough to keep me out of the weeds. Thanks. Douglas Greve Thu, 22 Mar 2018 13:28:02 -0700

Re: [Freesurfer] Skull stripping error - too much brain lost - solved

I added some text to clarify in that wiki page. See if you think it is sufficient (and suggest some wording if you don't:). On 3/22/18 4:22 PM, Bruce Fischl wrote: Hi Matt it's not that trivial. There are frequently multiple T1-weighted protocols, and the naming is hardly standardized. We wou

Re: [Freesurfer] Skull stripping error - too much brain lost - solved

Hi Matt it's not that trivial. There are frequently multiple T1-weighted protocols, and the naming is hardly standardized. We would need to run some type of MR simulator to decide if something was T1-weighted in the most general sense, and even then it could be mag-trans or with contrast or som

[Freesurfer] Skull stripping error - too much brain lost - solved

Hi guys, The problem was garbage in - garbage out: 1. The issue manifested in the skull stripping step but was caused by bad input 2. I am a data science guy (not neurology), new to freesurfer, and followed the instructions at https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferBeginnersGuide re

[Freesurfer] Skull stripping error dataset

I uploaded the datasets to the ftp site, does anyone have further advice regarding this issue? Both datasets are for the same subject for a longitudinal concussion study and fail for different reasons. matt1 - has "ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 errors" and fails with "CORRECTING DEF

Re: [Freesurfer] Skull stripping error - too much brain lost

Hi Matt no idea what that would happen. If you upload the dataset we will take a look cheers Bruce On Mon, 5 Mar 2018, Matthew Grecsek wrote: Following your advice below, it was clearly apparent that the output from the skull stripping step was missing a lot. I tried adjusting the -wsthresh

Re: [Freesurfer] skull stripping error?

Hi Elisabeth, try running recon-all with -no-wsgcaatlas and see if that fixes your problem. cheers, Bruce On Mon, 19 Apr 2010, Wenger, Elisabeth wrote: Dear freesurfer specialists, we just ran a sample of 91 subjects (with 3 timepoints), and in 5 of them the following problem occured: