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] 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] 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] 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

[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] 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

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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] (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] 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] 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] 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] 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] 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] 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] 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] 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] 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] tracula pub

Hi Greg, I think the tracula folks might have gotten their original code from Saad Jbabdi, but then the code-bases have probably diverged. (My apologizes if this is not correct!). Here is Saad's publication on global tractography: http://www.ncbi.nlm.nih.gov/pubmed/17543543/ Peace, Matt.

Re: [Freesurfer] PySurfer - A package for visualizing surfaces

Hi Michael, Out of curiosity, does this also support the GIFTI format? If so, one could use it to view surface data from a wide variety of software packages. Thanks, Matt. -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu]

Re: [Freesurfer] Question about if there is constant number of vertexes across different brains

There are different numbers of vertices in subjects surfaces. It is possible to resample subjects' surfaces to a common mesh after registration, but the FreeSurfer folks don't prefer this approach. They prefer to simply resample the quantitative data. Peace, Matt. -Original Message-

Re: [Freesurfer] label value 0 in annot file

Zero probably means no label. Peace, Matt. _ From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Forrest Sheng Bao Sent: Sunday, July 31, 2011 3:00 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] label value 0

Re: [Freesurfer] Label2label on fsaverage

So I thought the issue had been solved, but perhaps not. Bruce, we (i.e. David) think the problem with Rouhi's data is that FreeSurfer did not detect that the original images were tipped forward 90 degrees and as a result the surface registration failed intermittently (i.e. in some subjects it

[Freesurfer] Viewing Control Points

Hi, Is it possible to view control points (in control.dat), that you already created? If so, how do you do it? Thanks, Matt. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Viewing Control Points

Hi Bruce, That didn't happen, but perhaps because I loaded the volume with -f instead of the more standard way. I'll try it again. Thanks, Matt. -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Thursday, October 27, 2011 12:53 PM To: Matt Glasser Cc

Re: [Freesurfer] anterior temporal lobe problems

Hi Michael, It might have something to do with low myelin content there in general (will make grey matter harder to tell from CSF) and late myelination (at least part of the anterior temporal cortex has its white matter myelinate quite late in development), which would reduce grey/white contrast.

[Freesurfer] Affine Matrix Conversions

Hi, I am wondering what tools FreeSurfer has to convert between different affine matrix formats. For example, if I had a talairach.xfm that did a better job than talairach.lta, is there a way to convert from one to the other? What about FSL FLIRT matricies? Can these be interconverted

Re: [Freesurfer] Affine Matrix Conversions

on a specific case. doug Matt Glasser wrote: Hi, I am wondering what tools FreeSurfer has to convert between different affine matrix formats. For example, if I had a talairach.xfm that did a better job than talairach.lta, is there a way to convert from one to the other? What about

Re: [Freesurfer] Question about ?h.sulc and ?h.curv

I think Bruce meant: the ?h.sulc is the integrated dot product of the movement vector with the surface normal during inflation. Peace, Matt. -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent:

Re: [Freesurfer] dimension mismatch in fieldsign-sess

Greg, I assume you are using the same surfaces as those that I gave you, right? Thanks, Matt. -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Greg Burgess Sent: Thursday, March 08, 2012 2:28 PM To: Douglas N

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

I'm dredging this 2 year old post up for the benefit of Google and anyone else who wonders about the cause of this. It is a non-fatal error (for FreeSurfer, but perhaps not other things) that is caused by having set the variable: POSIXLY_CORRECT=1 It causes bc (on Debian/Ubuntu) systems to fail

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

[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] 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

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] 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

[Freesurfer] Talairach on Non-human Primates

I am wondering if it is necessary to perform the taltransform (or care about the results when it fails) to get good surfaces of non-human primate brains? I know I can go in and manually edit it to get it right, but I would rather not do this if it isn't critical for surface generation. Is it okay

Re: [Freesurfer] Talairach on Non-human Primates

PM To: Matt Glasser Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Talairach on Non-human Primates Hi Matt, it shouldn't be needed for non-human primates, and in fact will probably mess things up. I thought the -monkey switch disabled it, but I could be wrong. cheers Bruce On Thu

Re: [Freesurfer] Talairach on Non-human Primates

. Peace, Matt. -Original Message- From: Nick Schmansky [mailto:ni...@nmr.mgh.harvard.edu] Sent: Friday, December 25, 2009 10:20 AM To: Bruce Fischl Cc: Matt Glasser; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Talairach on Non-human Primates i'm not familiar with the monkey

[Freesurfer] Application of Default Surface Based Registration to Surfaces Other than the Sphere

Hi, I am wondering if there is a way to apply the default surface based registration that is done during recon-all to surfaces other than the sphere so that the nodes are all lined up? I am wanting to have registered white matter surfaces that I can map data from the volume to the surface to

Re: [Freesurfer] Application of Default Surface Based Registration to Surfaces Other than the Sphere

is registered across subjects, it is sufficient to register the wm surfaces. doug Matt Glasser wrote: Hi, I am wondering if there is a way to apply the default surface based registration that is done during recon-all to surfaces other than the sphere so that the nodes are all lined up? I am

Re: [Freesurfer] Application of Default Surface Based Registration to Surfaces Other than the Sphere

. When the sphere.reg is registered across subjects, it is sufficient to register the wm surfaces. doug Matt Glasser wrote: Hi, I am wondering if there is a way to apply the default surface based registration that is done during recon-all to surfaces other than the sphere so

Re: [Freesurfer] Application of Default Surface Based Registration to Surfaces Other than the Sphere

. I think you need the surfaces for your tractography stuff. But if all you need is average metric data on average40, then I doubt you need the individual surfaces on a standard mesh. Donna On 03/02/2010 12:58 PM, Matt Glasser wrote: Hi Doug and Bruce, I am somewhat surprised by your responses

Re: [Freesurfer] How to get deformation maps in surface-basedregistrations

It is possible to do this sort of thing in Caret (using the FreeSurfer registration); one can create a deformation map between sphere and sphere.reg. What do you need the deformation map for? Peace, Matt. -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu

Re: [Freesurfer] shared library error

I have /usr/lib64/libtiff.so.3 linked to /usr/lib64/libtiff.so.4 which is linked to /usr/lib64/libtiff.so.4.3.2 in my Lucid 64bit install. See if libtiff.so.4.3.2 exists on your system in /usr/lib64 and if so: sudo ln -s /usr/lib64/libtiff.so.4.3.2 /usr/lib64/libtiff.so.3 If not, find

Re: [Freesurfer] Which version should I download?

The CentOS 4 download works with Ubuntu. Just make sure to get the correct 32 or 64 bit version that matches your operating system. Use uname -m to tell. Peace, Matt. _ From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of

Re: [Freesurfer] FreeSurfer ROI masks for DTI tractograpy

FSL's tools don't use an FA threshold for tractography. So long as there is a consistent direction(s) to follow it will track through a voxel. Peace, Matt. -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of

Re: [Freesurfer] --fsl flag in bbregister

Hi Doug, It appears in FreeSurfer 5.0 the flag the bbregister script is looking for is --fslmat but in the docs it says it is --fsl. Peace, Matt. -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N

[Freesurfer] Convert transforms from xfm to lta

Is it possible to convert an .xfm to an .lta or alternatively to initialize mri_em_register with an .xfm that one has manually generated? It is not doing a very good job for me. Thanks, Matt. ___ Freesurfer mailing list

Re: [Freesurfer] conversion

MRICron's dcm2nii does a good job with par and rec files. Peace, Matt. -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Wednesday, August 12, 2009 5:28 PM To: Lindsay Nagamatsu Cc:

[Freesurfer] Conversion of wmparc.mgz to Original Volume Space without Resampling

I am curious about how to use mri_convert to convert wmparc.mgz back to the space that the original nii.gz volume that I gave FreeSurfer was in without resampling for further analysis with FSL. The volume I imported was 176x208x176, and oriented xorient: Left to Right, yorient: Posterior to

Re: [Freesurfer] Conversion of wmparc.mgz to Original Volume Space without Resampling

Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Sunday, August 23, 2009 5:47 PM To: Matt Glasser Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Conversion of wmparc.mgz to Original Volume Space without Resampling Hi Matt, you can give a -rl volume name switch to reslice like a template

Re: [Freesurfer] Conversion of wmparc.mgz to Original Volume Space without Resampling

Subject: Re: [Freesurfer] Conversion of wmparc.mgz to Original Volume Space without Resampling It depends on the resolution. On Aug 23, 2009, at 6:53 PM, Matt Glasser m...@ma-tea.com wrote: Hi Bruce, Presumably all that was done to the volume when it was imported was that some zero

Re: [Freesurfer] installing on ubuntu

Just do it before you try to run any of the FreeSurfer programs. What issues are you having? I have FreeSurfer installed on a number of Ubuntu machines. Peace, Matt. _ From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of

Re: [Freesurfer] installing on ubuntu

I assume you meant sudo ln -s /usr/lib/libtiff.so.4 /usr/lib/libtiff.so.3 -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Rudolph Pienaar Sent: Monday, August 24, 2009 10:04 AM To: Ahmed, F, Me fah...@sun.ac.za

Re: [Freesurfer] Input/Output to specific atlas space/dimensions?

mri_convert, I want to specifically return to the same 111 volume size and space and I provided as accurately as possible (hopefully using the inverse of the total transform applied to the image during processing). I know Matt Glasser has worked out a way to convert (and apparently re-register

Re: [Freesurfer] reslicing question

That looks correct to me. Peace, Matt. _ From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Mehul Sampat Sent: Thursday, November 05, 2009 3:38 PM To: Freesurfer Mailing List Subject: [Freesurfer] reslicing question Hi

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] 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] 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] 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] 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] 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] 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] 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] 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?

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] 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] 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] 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] 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

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] 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

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

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