(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
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" wrote:
>sorry, I think this may be
provide further help.
Peace,
Matt.
On 8/13/15, 12:12 PM, "Bruce Fischl"
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
>Aug 2015, Jan Will
You cannot have spaces in the file name unless you enclose it with quotes.
Peace,
Matt.
From: on behalf of Hugh Pemberton
Reply-To: Freesurfer support list
Date: Sunday, August 16, 2015 at 1:34 PM
To: "Freesurfer@nmr.mgh.harvard.edu"
Subject: [Freesurfer] Basic error
Hi freesurfer team
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: on behalf of Fernando
Pasquini Santos
al Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
> On 9 Jun 2016, at 19:31, Matt Glasser wrote:
>
> I would be interested to know how well 0.7mm isotropic resolution data
> performs at hippocampal segmentation. It would be better if folk
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: on behalf of "Alexopoulos,
Dimitrios"
s.com
http://cmictig.cs.ucl.ac.uk/
> On 10 Jun 2016, at 17:04, Matt Glasser wrote:
>
> 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 usin
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: on behalf of Trisanna
Sprung-Much
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 list
Subject: [Freesurfer] modifying files on older versions of FS
I have successfully processed da
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
doesn
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
brain
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 p
: [Freesurfer] Support for surface data on NeuroVault.org
On Sat, Aug 20, 2016 at 10:39 AM, Matt Glasser wrote:
> 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 t
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 designs are wrong. There
>are ways to try to compensate for it, which is what PALM is
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 dura. It is still a beta version though as
>we don't have a ton of experience with
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:
Subject: [Freesurfer] Optimal combination of MRI-sequences
Dear Freesufer experts,
We are in the process of starti
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
Reply-To: Freesurfer support list
Date: Sunda
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: on behalf of Antonin Skoch
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" wrote:
>Hi Michael
>
>that looks pretty bad! What is the resolution of the T2? The T1 that you
>overlay on al
Someone sent me a different kind of T2w image and it didn't work so well,
so we need to know what kind of image this is.
Peace,
Matt.
On 9/27/13 1:33 PM, "Bruce Fischl" wrote:
>nope, pretty much only with T2-space with and without a flair pulse
>On Fri,
>27 Sep
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
Date: Friday, September 27, 2013 2:20 PM
To: Matt Glasser
Cc: Bruce Fischl ,
"Freesurfer@nmr.mgh.harvard.edu"
Subject: Re: [Fr
Date: Friday, September 27, 2013 10:06 PM
To: Matt Glasser
Cc: Bruce Fischl ,
"Freesurfer@nmr.mgh.harvard.edu"
Subject: Re: [Freesurfer] Major problems with T2-based pial removal
Hmm, Ok. Thanks Matt.
I still think it's weird that the T2 didn't seem to ever get registered to
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
Date: Friday, November 1, 2013 2:55 AM
To: Matt Glasser
Cc: free surfer
Subje
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
Date: Thursday, November 14, 2013 8:13 AM
To: freesurfer
Cc: Veronica Popescu , Hugo Vrenken
Subject: [Freesurfer] T2pial/FLAI
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 Steenwi
We
>preserve all the RAS information when we "conform", so the info should be
>there for flirt
>
>cheers
>Bruce
>
>
>On Thu, 14 Nov 2013, Matt Glasser wrote:
>
>> I think you can do it with mri_convert ?rl. I don't think it makes
>>sense to
>>
Higher than 1mm resolution helps a lot. We use 0.7mm isotropic in the HCP.
Peace,
Matt.
From: "Megha K."
Date: Monday, December 9, 2013 10:23 PM
To:
Subject: [Freesurfer] Occipital cortex segmentation
Dear Sir/Madam,
I am using freesurfer for 3T MRI analysis of visual cortical thickness
Newer versions also have the ability to run some stages on multiple CPU
cores (with the -openmp 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,
Matt.
On
Some pictures would probably be helpful to know what the issue is.
Peace,
Matt.
From: Christine Smith
Date: Thursday, January 23, 2014 1:05 PM
To:
Subject: [Freesurfer] poor grey/white distinction in superior part of scan
Hello,
I am emailing to inquire about whether poor grey/white cont
From: Christine Smith
Date: Thursday, January 23, 2014 3:58 PM
To: Matt Glasser
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 picture. Please find attached a
If you are compiling with clang openmp might not work.
Peace,
Matt.
On 5/2/14, 2:13 PM, "Bruce Fischl" 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,
>lukas.sch...@ukb.u
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"
Reply-To: Fre
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" 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,
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 measures in 500+ subjects from HCP
>data -- wm-anat-snr, pctsurfcon, G/W cnr
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 Adamson
Reply-To: Freesurfer support li
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:
http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n
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:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Matt Glasser
>Sent: Wednesday,
>Mohamad
>
>
>-Original Message-
>From: freesurfer-boun...@nmr.mgh.harvard.edu
>[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Matt Glasser
>Sent: Wednesday, March 23, 2016 8:49 PM
>To: Freesurfer support list
>Subject: Re: [Freesurfer] Surface based an
er
>integrity.
>
>Yes I am looking for an optimal measure to evaluate tissue damage.
>
>Mohamad
>
>From: freesurfer-boun...@nmr.mgh.harvard.edu
>[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Matt Glasser
>[m...@ma-tea.
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"
wrote:
>Hi Gamaliel
>
>many things will change whe
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:
http://brainvis.wustl.edu/wiki/index.php/Ca
he image with
skull for the initial registration step, and then you can use mri_watershed
on the original image..."
How can this be implemented practically? Are the HCP protocols / pipelines
you mentioned later available for the research community?
Many thanks in advance,
Luke
Matt Glasser
This is available online now:
http://authors.elsevier.com/sd/article/S1053811913005053
On 5/7/13 3:10 PM, "Bruce Fischl" 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 in Andre'
;- Why are you using partial fourier in the read direction? You're
>throwing away 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 wrote:
>
>> This is ava
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"
wrote:
>Hi!
>I am failing to get a proper pial surface in orbitofrontal cortex.
>See attached screenshot.
>This is NHP d
al voxel size
>>>> 0.5x0.5x0.5 mm).
>>>> Thanks, Caspar
>>>>
>>>> 2013/5/16 Bruce Fischl :
>>>>>
>>>>> Hi Caspar
>>>>>
>>>>> if it's primate I don't think I'm going to be able to
gt;>>> The pial surface in the rest of the brain is ok, it is only the
>>>>> orbitofrontal/piriform cortex that is problematic. I now wanted to
>>>>>add
>>>>> -p 0.7.
>>>>>
>>>>> Caspar
>>>>>
>>
k we had any tools for doing that, and said so much on the
>>>FSL
>>> mailbase. 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.
>>>
>>&g
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" wrote:
>Hi Anupa
>
>it means that for some acquisition types the pial surfaces in 5.2 had
>substantial errors. We recommend rerunning with 5.3. Note that this
>sh
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, July
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 subje
Are you using a 32-channel coil? It looks like B1- receive field
inhomogeneity to me.
Peace,
Matt.
From: youngmin huh
Date: Monday, November 12, 2012 10:22 PM
To: Bruce Fischl ,
Subject: Re: [Freesurfer] bad acquisition and noise problem.
Hi,
3D SPGR sequences were used. (TR=22, TE=4, th
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" wrote:
>Yes, def
e
contrast.
Also I'm not sure how a FLAIR would be better than a T2-SPACE.
Peace,
Matt.
From: Satrajit Ghosh
Date: Tuesday, November 20, 2012 5:51 PM
To: Matt Glasser
Cc: "Watson, Christopher" ,
"Winter, Warren" ,
"freesurfer@nmr.mgh.harvard.edu"
Subject: Re:
fects
>less of a problem. Dura 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
>>
>> wrote:
>> yes, that's probably 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 bur
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
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
Date: Wednesday, February 20, 2013 10:49 AM
To:
Subject: [Freesurfer]
I'd collect highres T1w as well and then refine the 1mm surfaces using that.
Peace,
Matt.
From: SHAHIN NASR
Date: Monday, February 25, 2013 1:39 PM
To: Freesurfer , Bruce Fischl
, Doug Greve
Subject: [Freesurfer] High resolution fMRI and resolution of anatomical
scans
Hi,
We are plann
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 giv
nding all of the inputs needed
and converting them or generating them. I think the main goal here is to
use the longitudinal surface registration.
Matt.
On 3/14/13 8:04 PM, "Bruce Fischl" wrote:
>Hi Kara
>
>I think the answer is yes as there are people at Wash U that do thi
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 correct,
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:
>
>--
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 Dick
Reply-To: Freesurfer support list
D
To:
Subject: Re: [Freesurfer] license file not working
Thanks Matt. I already tried it with a new registration, but it doesn't hurt
to try it 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, Ma
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 at some point and stopped
>>accepting the old format with FS 6.0. I
>> hav
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 7, 2017 at 2:59 PM
To:
Subject: Re: [Freesurfer] -FLAIRpial in v6.0 positions pial su
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: Monday, February 20, 2017 at 12:26 PM
To:
Subject: [Freesurfer] issues with -T2pial optio
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 behalf of CAGNA Bastien
Reply-To: Freesurfe
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, 13 Mar 2017, Matt Glasser wrote:
>
>> Not yet. We are hoping FreeSurfer 6.1
y that V6 is generally less accurate
>is
>simply incorrect.
>
>cheers
>Bruce
>
>
>On Mon, 13 Mar 2017, Matt Glasser wrote:
>
>> 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 a
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:
Subject: [Freesurfer] difference in T1 and T2 resolution
Dear Freesurfer experts,
I have T1 and T2 images were unfortunately acquired w
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 should definitely not smooth the volume data. Smoothing should be
>limited to t
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"
Subject: [Freesurfer] Need Urgent Help!! Regarding FreeSurfer Installation
Hi,
I need Freesurfer for my windows OS. Is there any
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
Date: Tuesday, October 3, 2017 at 7:36 PM
To: Freesurfer support list
Subject: [Freesurfer] Brodmann areas -
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 list
Date: Monday, October 9, 2017 at 7:20 PM
To:
Subject: Re:
Hi Matt,
Thank you for your quick input ; I did not try yet to use melodic, it seems
indeed to be the most straightforward solution, I will try it, thank you
again!
Florence
Le lundi 9 octobre 2017, Matt Glasser > a écrit :
> I¹d note that you can run the group ICA on surface data in s
?), notably for the Main Structural Images and the Standard
Space.
I am sorry if this sounds like a naive question.
Thank you very much,
Florence
2017-10-09 22:28 GMT-04:00 Matt Glasser :
> The latest version of melodic is compatible with CIFTI data (e.g. From the
> HCP).
>
> Peac
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 c
Date: Thursday, October 12, 2017 at 12:42 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] volume vs surface-based and surface smoothing
Thanks Matt! Does rawfunc2surf-sess create the surface and smooth?
From: on behalf of Matt Glasser
Reply-To: Freesurfer support list
Date
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:
>
>https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2408694/
>
>discusses the basic algori
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
Q-9.HowdoImapd
@umail.iu.edu
On Wed, Dec 27, 2017 at 6:26 PM, Matt Glasser wrote:
> 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:
>
am
Indiana University, Bloomington
Student Building 166
lr...@umail.iu.edu
On Wed, Dec 27, 2017 at 7:02 PM, Matt Glasser wrote:
> I wouldn¹t trust resting state data that have not been properly denoised. You
> should only need the structural and FIX cleaned packages for what you are
> doi
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 at 10:41 AM
To: "freesurfer@nmr.mgh.harvard.edu"
Subject: [Freesurfer] recommendation for
>> Yours,
>>
>> Emil
>>
>> 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" wrote:
>>
>> >Hi Matt
>&
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" wrote:
>Hi Michael,
>
>I had a similar problem a while ago. Maybe this might help.
>http://www.mail-archive.com/freesurfer%40nmr.m
It probably thinks the STL file is just a mesh without coloring.
Peace,
Matt.
From: Mat yuki
Reply-To: Freesurfer support list
Date: Thursday, July 10, 2014 at 7:19 AM
To: "freesurfer@nmr.mgh.harvard.edu"
Subject: [Freesurfer] Convert label file to STL file
Dear Freesurfer Experts,
I
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
-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 Glasser wrote:
> Bruce has said the FLAIR might be a little better
I believe their function is to carry blood from one place to another.
Peace,
Matt.
From: Mohammed Goryawala
Reply-To: Freesurfer support list
Date: Tuesday, August 19, 2014 at 1:55 PM
To: "Freesurfer@nmr.mgh.harvard.edu"
Subject: [Freesurfer] Left and Right Vessels
Hello Freesurfer expe
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" wrote:
>Hi Mohammed
>
>these are dark regions, usually in inferior pallidum/putamen. There
>intensity is differen
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" wrote:
>
>Hi Bruce,
>I was wondering if there is info somewhere about what each of those 7
It will just run faster so long as things like memtest86 and prime95 don¹t
have errors.
Peace,
Matt.
From: "Chiu, Bryan (PHTH)"
Reply-To: Freesurfer support list
Date: Monday, September 29, 2014 at 4:26 PM
To: "freesurfer@nmr.mgh.harvard.edu"
Subject: [Freesurfer] Overclocking CPU for Fr
What criteria would you use to determine one alignment was better than
another?
Peace,
Matt.
From: "Caspar M. Schwiedrzik"
Reply-To: Freesurfer support list
Date: Tuesday, November 4, 2014 at 7:17 AM
To: "Freesurfer@nmr.mgh.harvard.edu"
Subject: [Freesurfer] Quality of surface-based alig
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] On
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-
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
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 oka
1 - 100 of 136 matches
Mail list logo
