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

External Email - Use Caution Yes, you are right. However, the original HCP runs were based on Freesurfer version 5.3, which is an older version. Recent studies have reported significant differences in Freesurfer outputs across versions, especially in the case of cortical thickne

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] Skull stripping with external brainmask

Pass your mask to recon-all with -xmask On 1/30/2023 1:13 AM, Boa Sorte Silva, Narlon wrote: External Email - Use Caution Hi there, I just wanted to follow-up on this. Thanks! Nárlon Cássio *Nárlon Cássio Boa Sorte Silva* PhD (He, Him, His) CIHR and MSHR BC/PARF Postdoctoral Resear

Re: [Freesurfer] Skull stripping with external brainmask

port list mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Monday, January 30, 2023 at 01:14 To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] Skull stripping with external brainmask External Email - Use Caution Hi there, I just wante

Re: [Freesurfer] Skull stripping with external brainmask

t;Boa Sorte Silva, Narlon" Reply-To: Freesurfer support list Date: Monday, January 30, 2023 at 01:14 To: Freesurfer support list Subject: Re: [Freesurfer] Skull stripping with external brainmask External Email - Use Caution Hi there, I just wanted to follow-up on this. Thanks! Nár

Re: [Freesurfer] Skull stripping with external brainmask

External Email - Use Caution Hi there, I just wanted to follow-up on this. Thanks! Nárlon Cássio Nárlon Cássio Boa Sorte Silva PhD (He, Him, His) CIHR and MSHR BC/PARF Postdoctoral Research Fellow Aging, Mobility, and Cognitive Health Lab Djavad Mowafaghian Centre for Brain Heal

Re: [Freesurfer] Skull stripping with T2

It looks like you are running a T2 through recon-all, which won't work. recon-all only takes T1-weighted. You can run it through samseg, eg, samseg --i T2_age_reg_bias.nii.gz --o samseg You can then binarize the seg.mgz to get everything inside the skull On 4/7/2021 2:17 PM, Rohan Bareja wrote:

Re: [Freesurfer] Skull stripping quality assessment

Hi Adam the most common metric would involve doing a manual stripping, usually of a T2. Note that in FS we designed it using a risk-minimization approach that weighs removing brain as much more costly (~10x I think) then leaving around skull. cheers Bruce On Mon, 17 Feb 2020, Adam Rytina wr

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

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

Dear John, you can prepare expert options file with the entry: mri_gcut -T and run recon-all -skullstrip -clean-bm -gcut -subjid -expert expert_opts_file.txt The mri_gcut help page reads: -T set threshold to value (%) of WM intensity, the value should be >0

Re: [Freesurfer] skull stripping and white matter labelling

ckBerry 10 smartphone.   Original Message   From: Bruce Fischl Sent: Friday, October 21, 2016 1:19 PM To: Freesurfer support list Reply To: Freesurfer support list Subject: Re: [Freesurfer] skull stripping and white matter labelling Hi Paul no, I don't think so. If you use our voxel-labeling

Re: [Freesurfer] skull stripping and white matter labelling

Thanks Bruce. Where can I find them? Sent from my BlackBerry 10 smartphone.   Original Message   From: Bruce Fischl Sent: Friday, October 21, 2016 1:19 PM To: Freesurfer support list Reply To: Freesurfer support list Subject: Re: [Freesurfer] skull stripping and white matter labelling Hi Paul

Re: [Freesurfer] skull stripping and white matter labelling

Hi Paul no, I don't think so. If you use our voxel-labeling conventions you should just be able to copy them in to the mri dir cheers Bruce On Fri, 21 Oct 2016, miracle ozzoude wrote: Hello experts, I did my skull stripping  and white matter labelling using an lesion explorer and I want t

Re: [Freesurfer] Skull-Stripping Atlas Usage

it does use an atlas. Check out the help in mri_watershed - there is a switch that turns off the atlas usage. cheers Bruce On Fri, 27 Jun 2014, Teo Gelles wrote: Hi Everyone, I am trying to skullstrip an mri image without using an atlas.  Does the following command use an atlas at any point

Re: [Freesurfer] Skull-Stripping Atlas Usage

Hi Teo, Yes it does, but you can use the -no-wsgcaatlas flag. You can also try using gcut which doesn't use an atlas (almost certain). Link with skullstripping info: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix_freeview -Louis On Fri, 27 Jun 2014, Teo Gelles wrote: Hi

Re: [Freesurfer] Skull stripping and RAM

the documentation is a bit ahead of the release, so talairach_with_skull_2.lta doesnt exist in a 5.1 run. however, it is the same file as that produced during the -skull-lta stage (so its file date will be newer than talairach.lta), so if it is newer, then you can try rerunning skullstrip and it w

Re: [Freesurfer] Skull stripping and RAM

1. A linear transform isn't always good enough to describe brain/skull variability. It helps more often than it hurts, but sometimes it does worse. 2-3. I'll leave these for Nick except to say I think 3g/recon should be fine and you might be able to get away with a bit less. So 4 would be safe

Re: [Freesurfer] Skull stripping and RAM

Dear Bruce and Freesurfer Experts, Thanks for the quick answer, Bruce, to previous post. As I work my way through all the checks on output I had a couple of other quick questions 1) I noticed by skull-stripping was poor (too aggerssive at the back of the brain with part of the occipital lobe and

Re: [Freesurfer] skull stripping and gcut error

...@nmr.mgh.harvard.edu] Sent: Thursday, August 04, 2011 11:39 AM To: Jacquelynn Nicosia Copeland Cc: Khoa Nguyen; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] skull stripping and gcut error I guess it is detecting the fact that gcuts failed. Nick: is there any way to disable the

Re: [Freesurfer] skull stripping and gcut error

Medical/Clinical Psychology Program > Department of Psychology > University of Alabama at Birmingham > Email:jcopel...@uab.edu > > From: Khoa Nguyen [k...@nmr.mgh.harvard.edu] > Sent: Thursday, August 04, 2011 6:38 AM > To: Jacquelynn Nicosia Cop

Re: [Freesurfer] skull stripping and gcut error

> From: Khoa Nguyen [k...@nmr.mgh.harvard.edu] > Sent: Thursday, August 04, 2011 6:38 AM > To: Jacquelynn Nicosia Copeland > Cc: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] skull stripping and gcut error > > Hi, > > How much dura/skull is left on your su

Re: [Freesurfer] skull stripping and gcut error

rtment of Psychology University of Alabama at Birmingham Email:jcopel...@uab.edu From: Khoa Nguyen [k...@nmr.mgh.harvard.edu] Sent: Thursday, August 04, 2011 6:38 AM To: Jacquelynn Nicosia Copeland Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer]

Re: [Freesurfer] skull stripping and gcut error

Hi, How much dura/skull is left on your subjects that you want to remove? Sometimes gcut takes away more than just dura, especially in the cerebellum region so that might be why it is much smaller. If the surfaces are not including the extra dura/skull, then it is not necessary that you remove

Re: [Freesurfer] skull stripping of IBSR using freesurfer

try without the atlas (-noatlas? Check the help, can't remember) On Sun, 6 Jun 2010, Jinyoung Hwang wrote: > hi bruce, > In fact, I'm trying to test the skull stripping method of freesurfer. > > Other images showed good skull stripped results, but 7_8 data couldn't > be segmented as the previous

Re: [Freesurfer] skull stripping of IBSR using freesurfer

hi bruce, In fact, I'm trying to test the skull stripping method of freesurfer. Other images showed good skull stripped results, but 7_8 data couldn't be segmented as the previous e-mail. I also tested mri_watershed without -T1 option, and I met same error message. How can I treat the error? re

Re: [Freesurfer] skull stripping of IBSR using freesurfer

Hi Jinyoung , those images have labels - why not just zero out everything with a zero label? And make sure you are trying to srip the intensity image, not the label one. You probably don't want to use a -T1 flag unless you used our intensity normalization. cheers Bruce On Sat, 5 Jun 2010, Jiny

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:

Re: [Freesurfer] Skull Stripping extra dura & vasculature

Bruce. Is there anyway to address it in the intensity normalization > > phase? > > > > > > -Original Message- > >> From: Bruce Fischl > >> Sent: Feb 9, 2010 12:29 PM > >> To: Sherri Novis > >> Cc: freesurfer@nmr.mgh.ha

Re: [Freesurfer] Skull Stripping extra dura & vasculature

Is there anyway to address it in the intensity normalization > phase? > > > -Original Message- >> From: Bruce Fischl >> Sent: Feb 9, 2010 12:29 PM >> To: Sherri Novis >> Cc: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] Skull

Re: [Freesurfer] Skull Stripping extra dura & vasculature

Thanks Bruce. Is there anyway to address it in the intensity normalization phase? -Original Message- >From: Bruce Fischl >Sent: Feb 9, 2010 12:29 PM >To: Sherri Novis >Cc: freesurfer@nmr.mgh.harvard.edu >Subject: Re: [Freesurfer] Skull Stripping extra dura & vascu

Re: [Freesurfer] Skull Stripping extra dura & vasculature

Hi Sherry, that's pretty tough. The dura is very bright and quite close to the gm. You may need to erase more of the dura Bruce On Tue, 9 Feb 2010, Sherri Novis wrote: > Hello, > > I have a series of datasets with skull stripping issues - namely left over > dura/vasculature in the occipital

Re: [Freesurfer] skull stripping

Hi Laura, the skull stripping only matters to the extent that it messes up the surfaces or segmentation. Try visualizing the white and pial surfaces and the aseg. cheers Bruce On Sat, 16 Jan 2010, laura_dg80 wrote: > Hi! > I have some difficulties in the Skull stripping. > I'm not experience

Re: [Freesurfer] Skull Stripping Free surfer

Using FreeSurfer just for Skull Striping is like killing an ant with an MP5 :) Are you sure you just want to skull strip? 2009/11/3 Ribes Delphine > Dear Users, > > I've just started using FreeSurfer. I would like to use it for > skull-stripping. > > I've created a batch file to process all my

Re: [Freesurfer] Skull Stripping

you'll also need to make sure it's "conformed" (256^3, 1mm iso, 8 bits/voxel) On Thu, 27 Sep 2007, Nick Schmansky wrote: Paul, You can add the -noskullstrip flag to recon-all -autorecon1. Just be sure, when -autorecon1 is complete, to make a symbolic or copy of T1.mgz to brainmask.auto.mgz,

Re: [Freesurfer] Skull Stripping

Paul, You can add the -noskullstrip flag to recon-all -autorecon1. Just be sure, when -autorecon1 is complete, to make a symbolic or copy of T1.mgz to brainmask.auto.mgz, and a link from brainmask.auto.mgz to brainmask.mgz. Also make sure that that brainmask.mgz looks like what is expected of br

RE: [Freesurfer] Skull Stripping Corrections

Hi Jim, You really only need to be concerned about these issues you've shown if they begin to affect your surfaces - that is, if the pial or white surface includes these regions that it shouldn't. If your surfaces are fine, you can leave this alone! Jenni -Original Message- From: [EMAIL

Re: [Freesurfer] skull stripping mistake

Hi Abel, look at the location of the pial surface and see if it is correct. It probably will be, in which case you don't need to edit. Only edit where the pial surface grabs some dura - not the whole thing. Bruce On Tue, 24 Apr 2007, abel cruz vadell wrote: Hi everyone I have found some

Re: [Freesurfer] Skull Stripping

Hi Derin, the subcortical segmentation will fail unless you correct it, as the registration will try and align a model with a cerebellum to a brain without one. sorry. Bruce On Mon, 7 Aug 2006, Derin Cobia wrote: Hello, After having run -autorecon1 on all of my subjects I've noticed skull

RE: [Freesurfer] Skull stripping

10/2005 10:56 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Skull stripping Hi Alex, if the strip removes the cerebellum, then the aseg stuff will fail (if you're using it). If you aren't it doesn't really matter. cheers, B

RE: [Freesurfer] Skull stripping

, but I'd prefer to edit that after the surfaces are created. Thanks again! Alex -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Sat 9/10/2005 10:56 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer]

RE: [Freesurfer] Skull stripping

Hi Alex, Since autorecon2 uses the brain volume as the first input, there is no need to re-run anything after editing the brain volume following autorecon1. Jenni -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Fornito, Alexander Sent: Friday, September

Re: [Freesurfer] Skull stripping

Hi Alex, if the strip removes the cerebellum, then the aseg stuff will fail (if you're using it). If you aren't it doesn't really matter. cheers, Bruce On Sat, 10 Sep 2005, Fornito, Alexander wrote: Hi all, Couple of questions re: failures of skull stripping" - If you edit the brain volume

Re: [Freesurfer] skull stripping

-atlas checks the deformation field against an atlas to see if it's reasonable. If it not (e.g. if the cerebellum is stripped), it tries to fix it. As for BET or mri_watershed, it's completely empirical. Whichever works better for you is fine. cheers, Bruce On Thu, 2 Jun 2005, Fornito, Alexan

Re: [Freesurfer] Skull Stripping Problem

iag iag- you may want to try increasing the preflooding height and use the -more option. i've found the seed points don't work very well, if at all. if all else fails, you may have to manually fix it in tkmedit with the clone tool. open tkmedit with the brain and T1 volumes as main and aux, res