Re: [Freesurfer] recommendation for T1 and T2-based sequences use with FreeSurfer

I think the HCP CCF protocol is a good start: http://protocols.humanconnectome.org/ Peace, Matt. From: on behalf of Colm Connolly Reply-To: Freesurfer support list Date: Tuesday, February 6, 2018

Re: [Freesurfer] bbregister error -- Human Connectome Project Data

Lana Ruck, M.A. Associate Instructor, Department of Anthropology Graduate Scholars Fellow, Cognitive Science Program Indiana University, Bloomington Student Building 166 lr...@umail.iu.edu On Wed, Dec 27, 2017 at 7:02 PM, Matt Glasser <m...@ma-tea.com> wrote: > I wouldn¹t trus

Re: [Freesurfer] bbregister error -- Human Connectome Project Data

pology Graduate Scholars Fellow, Cognitive Science Program Indiana University, Bloomington Student Building 166 lr...@umail.iu.edu On Wed, Dec 27, 2017 at 6:26 PM, Matt Glasser <m...@ma-tea.com> wrote: > You would be better off resampling the existing CIFTI data to the fsaverage4 > surfac

Re: [Freesurfer] bbregister error -- Human Connectome Project Data

You would be better off resampling the existing CIFTI data to the fsaverage4 surface rather than redoing the projection and smoothing in the volume. Instructions for getting to fsaverage are available here: https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFA

Re: [Freesurfer] asking for literature

Also we used T2w scans in the HCP Pipelines Paper and have Figure 14 showing the effects of using T2w scan vs not using one. Peace, Matt. On 10/20/17, 10:00 AM, "Bruce Fischl" wrote: >Hi Jiook > >this paper: >

Re: [Freesurfer] volume vs surface-based and surface smoothing

thing Thanks Matt! Does rawfunc2surf-sess create the surface and smooth? From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Matt Glasser <m...@ma-tea.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Date: Thursday, October 12, 2017 at 1:39

Re: [Freesurfer] volume vs surface-based and surface smoothing

Volume-based registration is fine with subject as you have the same brain that you are registering (ideally such registrations are 6 DOF rigid registrations and any image distortions are corrected for). Surface-based registration is better when comparing across subjects due to the variability in

Re: [Freesurfer] Transformation between spaces

ce 2017-10-09 22:28 GMT-04:00 Matt Glasser <m...@ma-tea.com>: > The latest version of melodic is compatible with CIFTI data (e.g. From the > HCP). > > Peace, > > Matt. > > From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Florence Campana > &l

Re: [Freesurfer] Transformation between spaces

try it, thank you again! Florence Le lundi 9 octobre 2017, Matt Glasser <m...@ma-tea.com <javascript:_e(%7B%7D,'cvml','m...@ma-tea.com');> > a écrit : > I¹d note that you can run the group ICA on surface data in surface space > pretty easily using melodic, which would avoi

Re: [Freesurfer] Transformation between spaces

I¹d note that you can run the group ICA on surface data in surface space pretty easily using melodic, which would avoid the issue that Doug mentions. Peace, Matt. From: on behalf of Douglas Greve Reply-To: Freesurfer support

Re: [Freesurfer] Brodmann areas - exvivo labels

I would use the versions where the group size approximately matched the individual size. Peace, Matt. From: on behalf of Trisanna Sprung-Much Reply-To: Freesurfer support list

Re: [Freesurfer] Need Urgent Help!! Regarding FreeSurfer Installation

No. From: on behalf of "Tabassum, Ruchira" Reply-To: Freesurfer support list Date: Saturday, August 5, 2017 at 12:22 PM To: "freesurfer@nmr.mgh.harvard.edu"

Re: [Freesurfer] smoothing data

Smoothing in the volume is the single worst thing that is traditionally done to brain imaging data as far as precision of spatial localization goes. Peace, Matt. On 7/12/17, 5:46 PM, "Douglas N Greve" wrote: >you

Re: [Freesurfer] difference in T1 and T2 resolution

What was the error message? Peace, Matt. From: on behalf of John Anderson Reply-To: Freesurfer support list Date: Sunday, June 11, 2017 at 9:06 AM To:

Re: [Freesurfer] Can we use fressurfer 6 with the Human connectome project's pipeline ?

nces, field strengths and scanners. We visually >inspected dozens of brains multiple times in the process of improving >accuracy and robustness. I can believe that on Wash U HCP data there >could >be some specific issues, but to imply that V6 is generally less accurate >is >simply incorrec

Re: [Freesurfer] Can we use fressurfer 6 with the Human connectome project's pipeline ?

dozens of brains multiple times in the process of improving >accuracy and robustness. I can believe that on Wash U HCP data there >could >be some specific issues, but to imply that V6 is generally less accurate >is >simply incorrect. > >cheers >Bruce > > >On Mon, 1

Re: [Freesurfer] Can we use fressurfer 6 with the Human connectome project's pipeline ?

Not yet. We are hoping FreeSurfer 6.1 will work nicely with the HCP Pipelines. For now version 6.0 has some regressions as far as surface placement goes and there are also some adaptations we need to make to the pipelines. Peace, Matt. From: on

Re: [Freesurfer] issues with -T2pial option in v.5.3

You could try with the HCP Pipelines and see if that helps: https://github.com/Washington-University/Pipelines Peace, Matt. From: on behalf of Petr Bednarik Reply-To: Freesurfer support list Date:

Re: [Freesurfer] -FLAIRpial in v6.0 positions pial surfaces much more externally in comparison to v5.3

Since I believe you said you are using my code, I would recommend to stick with 5.3 at this time. Peace, Matt. From: on behalf of Antonin Skoch Reply-To: Freesurfer support list Date: Tuesday, February

Re: [Freesurfer] license file not working

forced to change to the new format. >It >was not done gratuitously on our part or as a way to get people to >request >new licenses - we had no choice. > >cheers >Bruce > > >On Thu, 2 Feb 2017, Matt Glasser wrote: > >> Like I said, they changed the format a

Re: [Freesurfer] license file not working

again. That may be where the issue is. I'll post if that turns out to be the problem. Thanks! Anthony On 2/2/17 6:28 PM, Matt Glasser wrote: > > Like I said, they changed the format at some point and stopped accepting the > old format with FS 6.0. I have used FreeSurfer for a

Re: [Freesurfer] license file not working

Like I said, they changed the format at some point and stopped accepting the old format with FS 6.0. I have used FreeSurfer for a long time too and found that I had to get a new license file with this version. Peace, Matt. From: on behalf of Anthony

Re: [Freesurfer] license file not working

They updated the format so you have to get another. Peace, Matt. On 2/2/17, 2:13 PM, "Anthony Dick" wrote: >Hello, > >I have been using Freesurfer for a number of years, and just installed >v6.0. I run into this problem: >

Re: [Freesurfer] freesufer v6 beta - T2 pial refinement performance and nsigma_below setting

Hi Antonin, In our experience with FreeSurfer 5.3 we were getting very consistent results. We are going to try some of this locally and work with the FreeSurfer folks to get the T2w stream working robustly in FreeSurfer v6.0+. Thanks for testing this, Matt. From:

Re: [Freesurfer] freesufer v6 beta - T2 pial refinement performance and nsigma_below setting

How does it work if you just use vanilla recon-all v6 beta with the T2 refinement flag and the hires option? We haven¹t yet updated the HCP scripts for FreeSurfer v6, but this is on our to do list. Peace, Matt. From: on behalf of Antonin Skoch

Re: [Freesurfer] Optimal combination of MRI-sequences

What do you mean by ³combining² sequences? Peace, Matt. From: on behalf of Erik Lindberg Reply-To: Freesurfer support list Date: Tuesday, October 18, 2016 at 2:52 PM To:

Re: [Freesurfer] inclusion of both T1 and T2 in a recon-all run

Sure there¹s a publication. See Figure 14: http://www.sciencedirect.com/science/article/pii/S1053811913005053 Peace, Matt. On 8/30/16, 10:21 AM, "Bruce Fischl" wrote: >Hi Don > >the T2 or FLAIR helps us avoid

Re: [Freesurfer] mri_glmfit-sim permutation testing running after 3 days!

PALM handles GIFTI and CIFTI data. Peace, Matt. On 8/29/16, 6:21 PM, "Douglas N Greve" wrote: >Does PALM do surface-based? Also, there is no way to appropriately >handle this. For permutation, non-orthogonal

Re: [Freesurfer] Support for surface data on NeuroVault.org

<freesurfer@nmr.mgh.harvard.edu> Date: Saturday, August 20, 2016 at 1:51 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Support for surface data on NeuroVault.org On Sat, Aug 20, 2016 at 10:39 AM, Matt Glasser <m...@ma-tea.com> wrote: > Wh

Re: [Freesurfer] Support for surface data on NeuroVault.org

Hi Chris, Why not focus on distributing GIFTI files that are viewable both by FreeSurfer and many other applications instead of FreeSurfer¹s native format? For the same reason that it is helpful to provide NIFTI files because of their strong, cross-platform adoption, it would be more helpful to

Re: [Freesurfer] T2 vs. T2-FLAIR update

And I would say if you want to do T1w/T2w myelin mapping the T2w scan will give you more contrast for that, as the fluid inversion does seem to reduce your contrast for myelin some (though it may increase your contrast for CSF). FLAIR can be useful for other things (like seeing some kinds of

Re: [Freesurfer] FreesurferNHP

We haven¹t yet released our NHP pipeline yet, mainly because the software support requirements are a bit higher and so it has made more sense to work with people as a part of collaborations. This is more of a question for the HCP Users list or an off-list inquiry because the FreeSurfer group

Re: [Freesurfer] modifying files on older versions of FS

Why would you want to do that? Peace, Matt. From: on behalf of "Alexopoulos, Dimitrios" Reply-To: Freesurfer support list Date: Thursday, June 16, 2016 at 4:06 PM To: Freesurfer support

Re: [Freesurfer] Fwd: concerting surface format

Look at mris_convert. If that doesn¹t help would also see if BrainVisa allows conversion to a third format that mris_convert works with. Finally, does BrainVisa not support GIFTI (the standard, cross-neuroimaging software surface format)? Peace, Matt. From:

Re: [Freesurfer] using both T1/T2 and resolutions

r T1. We are working on a solution. Cheers, Eugenio Juan Eugenio Iglesias Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ > On 10 Jun 2016, at 17:04, Matt Glasser <m...@ma-tea.com> wrote: > > Hi Jim, > > I would ju

Re: [Freesurfer] using both T1/T2 and resolutions

Hi Jim, I would just use the HCP Pipelines for that: https://github.com/Washington-University/Pipelines, as they take care of all of those things re FreeSurfer. I would set to using the 0.8mm templates so that nothing is down sampled. Peace, Matt. From:

Re: [Freesurfer] Hippocampal subfields segmentation - what is the voxel size of the input?

mentation - what is the voxel size of the input? Hi Matt, you can use strategy 3 of my previous email ;-) Cheers, Eugenio Juan Eugenio Iglesias Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ > On 9 Jun 2016, at 19:31, Matt Glasser

Re: [Freesurfer] Hippocampal subfields segmentation - what is the voxel size of the input?

I would be interested to know how well 0.7mm isotropic resolution data performs at hippocampal segmentation. It would be better if folks could do this then needing to acquire specialized anisotropic scans for hippocampal segmentation. Peace, Matt. From:

Re: [Freesurfer] axial or sagittal?

I¹d add that SNR may also change if you don¹t acquire as much data axially as you did sagittally. Really it¹s better to acquire your 3D T1w/T2w/FLAIR scans sagittally as this is most efficient. Peace, Matt. On 4/8/16, 10:23 AM, "Bruce Fischl"

Re: [Freesurfer] Surface based analysis using FA maps

ccept RD as a marker for >gray matter integrity. We should accept FA a marker for gray matter >integrity. > >Yes I am looking for an optimal measure to evaluate tissue damage. > >Mohamad > >From: freesurfer-boun...@nmr.mgh.harvard.edu >[frees

Re: [Freesurfer] Surface based analysis using FA maps

us in tissues >other than the brain such as liver, lung, heart, joints, etc > >Mohamad > > >-Original Message- >From: freesurfer-boun...@nmr.mgh.harvard.edu >[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Matt Glasser >Sent: Wednesday, M

Re: [Freesurfer] Surface based analysis using FA maps

using PET >maps, why we can't do it using FA maps? > >I will be more than happy if you can suggest me an alternative approach >to study FA on a surface. > > >Best, >Mohamad > >-Original Message- >From: freesurfer-boun...@nmr.mgh.harvard.edu >[mailto:freesur

Re: [Freesurfer] Surface based analysis using FA maps

I too am puzzled as to why you would want to do this. In terms of getting improvement in the alignment across subjects TBSS is one way to approach this. Another would be to use the fiber orientations in the registration like these folks have done:

Re: [Freesurfer] T2pial shrinks pial surface

What FreeSurfer version are you using? Very small changes to the input images (e.g. a different random see for FreeSurfer) may be able to kick mris_make_surfaces out of that bug, though perhaps Bruce has fixed it. Peace, Matt. From: on behalf of Chris

Re: [Freesurfer] MPRAGE SNR

There is also the issue that grey and white matter are not truly a homogeneous single intensity anatomically. Peace, Matt. On 10/19/15, 9:23 AM, "Harms, Michael" wrote: > >Hi, > >FWIW, I've looked at a number of these

Re: [Freesurfer] Basic error

You cannot have spaces in the file name unless you enclose it with quotes. Peace, Matt. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Hugh Pemberton hughpembert...@gmail.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Sunday, August 16, 2015 at 1:34 PM

Re: [Freesurfer] Caret Human_Macaque.PALS_B12 to freesurfer

provide further help. Peace, Matt. On 8/13/15, 12:12 PM, Bruce Fischl freesurfer-boun...@nmr.mgh.harvard.edu on behalf of fis...@nmr.mgh.harvard.edu wrote: Hi Jan have you asked the HCP/Wash U group? I bet that they would know. Maybe Mike Harms or Matt Glasser can chime in? Bruce On Thu, 13

Re: [Freesurfer] mris_convert gifti

Does SUMA support GIFTI and provide a utility to convert between its formats and GIFTI? I was also wondering what a .dset was and how to get it into GIFTI so it could be easily used across software platforms. Thanks, Matt. On 5/5/15, 5:30 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:

[Freesurfer] Brain Imaging, Built Better: The HCP Course in Hawaii

(hcpcou...@humanconnectome.org): http://humanconnectome.org/course-registration/2015/exploring-the-human-con nectome.php Hope to see you in Honolulu, Matt Glasser. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

Re: [Freesurfer] Quality of surface-based alignment

What criteria would you use to determine one alignment was better than another? Peace, Matt. From: Caspar M. Schwiedrzik cschwie...@mail.rockefeller.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Tuesday, November 4, 2014 at 7:17 AM To:

Re: [Freesurfer] Overclocking CPU for Freesurfer

It will just run faster so long as things like memtest86 and prime95 don¹t have errors. Peace, Matt. From: Chiu, Bryan (PHTH) bryan.c...@ubc.ca Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Monday, September 29, 2014 at 4:26 PM To: freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] how to shrink wm surface

Have a look at mris_make_surfaces.c, this is how I learned about most of this stuff as the code is pretty well commented (and Bruce telling me things). Peace, Matt. On 9/12/14, 11:01 PM, Harms, Michael mha...@wustl.edu wrote: Hi Bruce, I was wondering if there is info somewhere about what

Re: [Freesurfer] Left and Right Vessels

Virchow­Robin spaces is another name for those (they are normal in small amounts, not old strokes, and filled with CSF-like fluid). Peace, Matt. On 8/21/14, 9:23 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Mohammed these are dark regions, usually in inferior pallidum/putamen. There

Re: [Freesurfer] Left and Right Vessels

I believe their function is to carry blood from one place to another. Peace, Matt. From: Mohammed Goryawala mgory...@fiu.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Tuesday, August 19, 2014 at 1:55 PM To: Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] T2-space vs T2-space-FLAIR

Bruce has said the FLAIR might be a little better for FreeSurfer but it¹s worse for myelin maps (has less CNR for the myelin, though you can still see the major areas). Currently, the T2 and FLAIR flags do exactly the same thing, so it doesn¹t even matter what flag you use. I think it depends on

Re: [Freesurfer] T2-space vs T2-space-FLAIR

freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] T2-space vs T2-space-FLAIR thanks matt, would like to be sure that your comments in relation to the T2-space-flair sequence and not the typical clinical TSE-FLAIR. is that the case? cheers, satra On Wed, Jul 30, 2014 at 2:23 PM, Matt

Re: [Freesurfer] Convert label file to STL file‏

It probably thinks the STL file is just a mesh without coloring. Peace, Matt. From: Mat yuki matsuyuki2...@outlook.jp Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Thursday, July 10, 2014 at 7:19 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] mris_convert to GIFTI misaligned in freeview

Yes the HCP pipelines have to take care of this as well so that the surfaces and volume align outside of FreeSurfer. Peace, Matt. On 5/27/14, 8:35 AM, Franz Liem f.l...@psychologie.uzh.ch wrote: Hi Michael, I had a similar problem a while ago. Maybe this might help.

Re: [Freesurfer] problem with pial surface reconstruction using T1 (MPRAGE) and T2 (SPACE) weighted images

send me an example I'll try to find time to take a look Bruce On Fri, 9 May 2014, Matt Glasser wrote: Hi Bruce, For whatever reason, sometimes the T2w surface adjustment will be way off. Adjusting the -nsigma_above # -nsigma_below # even a little bit up and down can get it out

Re: [Freesurfer] problem with pial surface reconstruction using T1 (MPRAGE) and T2 (SPACE) weighted images

Hi Bruce, For whatever reason, sometimes the T2w surface adjustment will be way off. Adjusting the -nsigma_above # -nsigma_below # even a little bit up and down can get it out of the minimum and make it work, so there might be a bug. Peace, Matt. From: Emil H.J. Nijhuis

Re: [Freesurfer] problem with pial surface reconstruction using T1 (MPRAGE) and T2 (SPACE) weighted images

Probably Emil¹s current example would be best because it is failing in your recon-all setup. Matt. On 5/9/14, 9:31 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Matt if you can send me an example I'll try to find time to take a look Bruce On Fri, 9 May 2014, Matt Glasser wrote: Hi

Re: [Freesurfer] using multiple cores

If you are compiling with clang openmp might not work. Peace, Matt. On 5/2/14, 2:13 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Lukas sorry, I'm out of my depth on the mac. Perhaps Zeke knows what's going on? Does OpenMP have to be enabled somehow? Bruce On Fri, 2 May 2014,

Re: [Freesurfer] Time taken by Freesurfer for processing

Newer versions also have the ability to run some stages on multiple CPU cores (with the -openmp cores flag) which speeds certain stages (e.g. in autorecon2) up considerably. I'm also sure Bruce wouldn't turn down more resources to hire the programmers needed to make it faster either! Peace,

Re: [Freesurfer] poor grey/white distinction in superior part of scan

Some pictures would probably be helpful to know what the issue is. Peace, Matt. From: Christine Smith cnsm...@ucsd.edu Date: Thursday, January 23, 2014 1:05 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] poor grey/white distinction in superior part of scan Hello, I am

[Freesurfer] FW: poor grey/white distinction in superior part of scan

From: Christine Smith cnsm...@ucsd.edu Date: Thursday, January 23, 2014 3:58 PM To: Matt Glasser m...@ma-tea.com Subject: Re: [Freesurfer] poor grey/white distinction in superior part of scan Please note that the left and right sides of the brain are flipped for freesurfer vs the dicom

Re: [Freesurfer] Occipital cortex segmentation

Higher than 1mm resolution helps a lot. We use 0.7mm isotropic in the HCP. Peace, Matt. From: Megha K. megha...@gmail.com Date: Monday, December 9, 2013 10:23 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Occipital cortex segmentation Dear Sir/Madam, I am using freesurfer

Re: [Freesurfer] T2pial/FLAIRpial processing issues

To fix the second problem, why not reorient the T2w image so the image axes are oriented in the way that FreeSurfer expects? Peace, Matt. From: Martijn Steenwijk martijnsteenw...@gmail.com Date: Thursday, November 14, 2013 8:13 AM To: freesurfer freesurfer@nmr.mgh.harvard.edu Cc: Veronica

Re: [Freesurfer] T2pial/FLAIRpial processing issues

I think you can do it with mri_convert ­rl. I don't think it makes sense to expect FLIRT to get the registration right reliably if the axes are off (in the HCP Pipelines we definitely don't expect this and make sure all images are RPI before processing them). Peace, Matt. From: Martijn

Re: [Freesurfer] ERROR: comparison in expression (FS with SGE)

I think the latest version of FSL has this sorted out (it doesn't change your machine's POSIXLY_CORRECT setting except briefly in the middle of fsl_sub). Peace, Matt. From: chenchunhuichina chenchunhuich...@gmail.com Date: Friday, November 1, 2013 2:55 AM To: Matt Glasser m...@ma-tea.com Cc

Re: [Freesurfer] Major problems with T2-based pial removal

Also, what kind of T2w sequence is this? I think we've mostly tested it with the T2-SPACE (unless Bruce has tested with other things). Peace, Matt. On 9/27/13 12:58 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Michael that looks pretty bad! What is the resolution of the T2? The T1

Re: [Freesurfer] Major problems with T2-based pial removal

, Matt Glasser wrote: Also, what kind of T2w sequence is this? I think we've mostly tested it with the T2-SPACE (unless Bruce has tested with other things). Peace, Matt. On 9/27/13 12:58 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Michael that looks pretty bad! What

Re: [Freesurfer] Major problems with T2-based pial removal

, is it possible for the user to modify the ­nsigma_above and -nsigma_below flags for mris_make_surfaces when using -T2pial? Peace, Matt. From: Michael Waskom mwas...@stanford.edu Date: Friday, September 27, 2013 2:20 PM To: Matt Glasser m...@ma-tea.com Cc: Bruce Fischl fis...@nmr.mgh.harvard.edu

Re: [Freesurfer] Major problems with T2-based pial removal

Date: Friday, September 27, 2013 10:06 PM To: Matt Glasser m...@ma-tea.com Cc: Bruce Fischl fis...@nmr.mgh.harvard.edu, Freesurfer@nmr.mgh.harvard.edu Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Major problems with T2-based pial removal Hmm, Ok. Thanks Matt. I still think it's

Re: [Freesurfer] version 2 FS

Note that this does not apply to HCP-style FreeSurfer runs or the HCP released data. Peace, Matt. On 9/7/13 8:26 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Anupa it means that for some acquisition types the pial surfaces in 5.2 had substantial errors. We recommend rerunning with

[Freesurfer] FW: apply fnirt transformation on a surface

. But apparently the WashU people has something that does just that for you. I think the best person to contact about the details is Matt Glasser. J On 2 Sep 2013, at 15:58, Saad Jbabdi s...@fmrib.ox.ac.uk wrote: Hi In Probtrackx, this is done internally. If you just want to transform

Re: [Freesurfer] issue with pial surface in orbitofrontal cortex

Matt Glasser m...@ma-tea.com: Is the brain extraction removing that part of the brain? Do you know where the OFC ends and olfactory bulb begins? Peace, Matt. On 5/16/13 11:43 AM, Caspar M. Schwiedrzik cschwie...@mail.rockefeller.edu wrote: Hi! I am failing to get a proper pial surface

Re: [Freesurfer] issue with pial surface in orbitofrontal cortex

using -p, mri_segment reads in the threshold as the input volume. I tried specifying the input with -i (as explained here: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg18826. html), but now it does not recognize the -i flag. Caspar 2013/5/17 Matt Glasser m...@ma-tea.com

Re: [Freesurfer] using T2* weighted scans to assist with dura stripping in a GE scanner?

a lot of SNR at the high spatial frequencies, seems a shame to go to 0.7mm and then do that. Cheers, Souheil On May 12, 2013, at 10:54 PM, Matt Glasser m...@ma-tea.com wrote: This is available online now: http://authors.elsevier.com/sd/article/S1053811913005053 On 5/7/13 3:10 PM, Bruce

Re: [Freesurfer] using T2* weighted scans to assist with dura stripping in a GE scanner?

This is available online now: http://authors.elsevier.com/sd/article/S1053811913005053 On 5/7/13 3:10 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: actually Matt Glasser points out that a brief description is in his paper that is coming out soon, and there is also some description

Re: [Freesurfer] Advice on integrating FSL\'s BET with recon-all

this be implemented practically? Are the HCP protocols / pipelines you mentioned later available for the research community? Many thanks in advance, Luke Matt Glasser http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.eduq=from: %22Matt+Glasser%22 Wed, 06 Mar 2013 16:09:44 -0800 http

Re: [Freesurfer] Incorporating (high resolution) T2- and FLAIR volumes

I find the T2w image works well for removing dura and blood vessels, but I'm not sure FLAIR would work for T1w/T2w myelin mapping because of what would happen to the ratio near the pial surface. Instructions for T1w/T2w myelin mapping are available here:

Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0

Do the surfaces look correct in these regions? You might post some screenshots of subjects who have a big difference between 5.1 and 5.2 with the 5.1 and 5.2 white and pial surfaces on volume slices that highlight the difference. Without this kind of info, its hard to know which was more

Re: [Freesurfer] Caret to Freesurfer

this routinely. Maybe Matt Glasser or someone else can chime in? cheers Bruce On Thu, 14 Mar 2013, Ellspermann, Kara wrote: I am new to Freesurfer, and I am trying to input/process preterm infant brain data (ultimately attempting longitudinal registration). I already have surfaces generated from Caret

Re: [Freesurfer] Advice on integrating FSL's BET with recon-all

I would check the mri_em_register registrations of the step that immediately precedes mri_watershed (and produces talairach_with_skull.lta). We found that most of the variability and failures occurred in this step, and mri_watershed itself is a very robust brain extraction algorithm when it is

Re: [Freesurfer] High resolution fMRI and resolution of anatomical scans

I'd collect highres T1w as well and then refine the 1mm surfaces using that. Peace, Matt. From: SHAHIN NASR sha...@nmr.mgh.harvard.edu Date: Monday, February 25, 2013 1:39 PM To: Freesurfer freesurfer@nmr.mgh.harvard.edu, Bruce Fischl fis...@nmr.mgh.harvard.edu, Doug Greve

Re: [Freesurfer] unusually long running time in autorecon2

I've noticed this at well when something goes wrong before mri_cc. It gets stuck in some kind of infinite loop. You might check that the linear and nonlinear registration worked correctly. Peace, Matt. From: Dawei Liu ldw70...@gmail.com Date: Wednesday, February 20, 2013 10:49 AM To:

Re: [Freesurfer] How can I get 300 dpi resolution or about when saving tiff files in tksurfer?

Perhaps you can maximize the tksurfer window on a large monitor, take a whole screen screenshot, and then in a photo editing program: decrease the physical size of the image (in mm or inches) while not decreasing the matrix size. You can do this in photoshop in Image Image Size And then change

Re: [Freesurfer] Tool for incorporating T2-SPACE data in pial surface recons?

If you get an MPRAGE and T2-SPACE you can make myelin maps too. FreeSurfer's final surface placement benefits a lot from high resolution images (less than 1mm) and you can still get good SNR with when you use 32-channel coils. Peace, Matt. On 11/20/12 4:41 PM, Bruce Fischl

Re: [Freesurfer] Tool for incorporating T2-SPACE data in pial surface recons?

. Also I'm not sure how a FLAIR would be better than a T2-SPACE. Peace, Matt. From: Satrajit Ghosh sa...@mit.edu Date: Tuesday, November 20, 2012 5:51 PM To: Matt Glasser m...@ma-tea.com Cc: Watson, Christopher christopher.wat...@childrens.harvard.edu, Winter, Warren warren.win

Re: [Freesurfer] Tool for incorporating T2-SPACE data in pial surface recons?

is also pretty much totally absent from the FLAIR and in the prelim data that we've processed having the FLAIR images lets the surface recover from pretty much all mistakes in which dura is included in the pial surface. cheers Bruce On Tue, 20 Nov 2012, Matt Glasser wrote: If you make a T1 map

Re: [Freesurfer] Tool for incorporating T2-SPACE data in pial surface recons?

true. The FLAIR we use is just a T2-SPACE scan with an inversion pulse to put CSF at the null point, so if you can get T2-space at .7 you should be able to get FLAIR (although you do burn some SNR with the inversion) On Tue, 20 Nov 2012, Matt Glasser wrote: Hi

Re: [Freesurfer] bad acquisition and noise problem.

Are you using a 32-channel coil? It looks like B1- receive field inhomogeneity to me. Peace, Matt. From: youngmin huh ymin1...@gmail.com Date: Monday, November 12, 2012 10:22 PM To: Bruce Fischl fis...@nmr.mgh.harvard.edu, freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] bad

Re: [Freesurfer] (no subject)

What are the units of that measure? Thanks, Matt. _ From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve Sent: Sunday, August 12, 2012 9:25 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] (no

Re: [Freesurfer] Ribbon

Hi Bruce, He just needs the grey matter part of a typical ribbon.mgz volume. He lost some of his recon-all folder. Peace, Matt. -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Sunday,

Re: [Freesurfer] ERROR: comparison in expression (FS with SGE)

Rather one unsets it like this: unset POSIXLY_CORRECT Peace, Matt. -Original Message- From: Matt Glasser [mailto:m...@ma-tea.com] Sent: Friday, May 18, 2012 12:47 PM To: 'freesurfer@nmr.mgh.harvard.edu' Subject: RE: [Freesurfer] ERROR: comparison in expression (FS with SGE) Another

Re: [Freesurfer] ERROR: comparison in expression (FS with SGE)

. Then one gets the best of both worlds. Peace, Matt. -Original Message- From: Matt Glasser [mailto:m...@ma-tea.com] Sent: Thursday, March 22, 2012 5:36 PM To: 'freesurfer@nmr.mgh.harvard.edu' Subject: RE: [Freesurfer] ERROR: comparison in expression (FS with SGE) I'm dredging this 2

Re: [Freesurfer] Freesurfer 1mm Isotropic standard and the Future

used it yet but me I don't think (unless Matt Glasser has gotten his version working, which on second thought he probably has) On Mon, 14 May 2012, Michael Waskom wrote: Hi Bruce, Is there a flag for this on recon-all?  Or do you need to use mri_make_surfaces directly? Best, Michael

[Freesurfer] Edit Aseg with Surfaces

Is there a way to adjust the grey and white matter of the aseg automatically based on the surfaces? Thanks, Matt. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The

Re: [Freesurfer] Freesurfer 1mm Isotropic standard and the Future

I'd be interested to hear how this goes too. Thanks, Matt. -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Monday, May 14, 2012 4:09 PM To: Joshua Lee Cc: FreeSurfer Subject: Re: [Freesurfer]

Re: [Freesurfer] white matter hyper intensities

Hi Greg, I would say there are a variety of possible confounds for cortical thickness (e.g. changes in cortical myelin content, changes in the closeness of opposition between grey matter and the dura from brain atrophy), but that wouldn't be one of the ones I would think of. White matter

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