nope, we don't have anything to segment thalamic nuclei yet. It's one of
the things we are interested in pursuing, but haven't gotten to it yet
On
Thu, 7 Jul 2016, Dorsa Haji Ghaffari wrote:
> Hi,
> I am trying to segment the thalamus into its nuclei such as VLA , VLP and
> VIM. I see those labe
Hi XJ
this is a known problem but we haven't gotten to fixing it yet. Do you
need it to complete that step? It is pretty close to the end so it may be
that the error doesn't effect you
cheers
Bruce
On Thu, 7 Jul 2016, Kang, XJ wrote:
Hi,
I am trying to inflate right hemisphere only using t
I'm not sure I totally understand. What kind of continuity do you
require? That every voxel has at least one adjacent voxel with the same
label?
On Thu, 7 Jul 2016, Douglas N Greve wrote:
> Sorry, I can't think of an easy way to do this. It is possible for two
> adjacent vertices to be in two v
u for your explanations. I will wait for the future corrections on
the problem.
On 7/7/2016 11:11 AM, Bruce Fischl wrote:
Hi XJ
this is a known problem but we haven't gotten to fixing it yet.
Do you need it to complete that step? It is pretty close to the
end so it may be
Hi Hari
if you include the -f flag to mri_cc it will include the fornix in the cc
segmentation. We haven't tested it a ton so I'm not sure how well it will
work on your data, but give it a try
cheers
Bruce
On Thu, 7 Jul 2016, Hari Guragain wrote:
Dear Freesurfer Experts,
I am interested t
no, sorry, we have some things we have messed around with but nothing
ready for prime time
Bruce
On Fri, 8 Jul 2016, Dorsa Haji Ghaffari wrote:
> Hi,
> I want to refine the surface of my segmented subcortical structures such as
> thalamus. I know -fix is used for refining the cortex surface, but
Hi Erik
you could map your data to one of the lower res fsaverage subjects.
Probably fsaverage 5 or so (which is a 5th order icodahedron with about
10K vertices). Or you could use mris_make_face_parcellation. There also are
some decimation tools around which you could use, maybe someone else
r
no, the extension should be fine. Can you include the entire correspondence
in your email as well as the command and the output of it?
thanks
Bruce
On Sat, 9 Jul 2016, Dulce Maria Magdaleno Arroyo wrote:
Thank you for replied me! :)
Oh, sorry!
but even If a remove the back slash in the fil
Hi Sampada
can you elaborate a bit? What are you trying to achieve? Do you want an
average hippocampus? Average maps of subfields? What hypothesis are you
trying to test? The individual subject data is not resampled to a common
coordinate system, so just averaging them as is won't produce anyth
On 01 Jul 2016, at 15:40, Bruce Fischl
wrote:
Hi Hinke
we need more details if you want us to help you. Images, exact
command lines and outputs, etc
cheers
Bruce
On Fri, 1 Jul 2016, Halbertsma, HN (ohk) wrote:
I’m having issues with the conversion of labels
no, sorry, we don't have that data. If you ask the authors for it we
would be happy to distribute it with FS if they are willing.
cheers
Bruce
On Mon, 11 Jul
2016, Francesca Strappini wrote:
Wang, Mruczek, Arcaro, Kastner (2014).
Probabilistic Maps of Visual Topography in Human Cortex.
Cere
Hi Anders
thanks. Seems like you can just get the data from them and are all set.
Bruce
On Mon, 11 Jul 2016, Anders Hougaard wrote:
Excellent, thank you.The link to the ROI files is this:
http://www.princeton.edu/~napl/vtpm.htm
Best,
Anders
2016-07-11 12:26 GMT+02:00 Francesca Strappini
:
from here. How do I run the glm_fit between eod and lod patients? Secondly,
after running glm_fit how do I calculate the significance from sig.mgh?
Appreciate all your help.
Thanks and regards,
Sampada
On Sun, Jul 10, 2016 at 7:15 PM, Bruce Fischl
wrote:
Hi Sampada
can you elaborate
adding the individual ROIs should work and will ignore non-cortical
regions so be more accurate than measuing the surface area of ?h.pial
cheers
Bruce
On Wed, 13 Jul
2016, Mihaela Stefan wrote:
> Hello Freesurfers,
>
> We would like to know how to calculate the total pial surface area for eac
Hi Gabor
how would that be different from just looking at the aseg?
cheers
Bruce
On Thu, 14 Jul 2016, Gabor Perlaki wrote:
> Dear all,
>
> Is it possible somehow to visually inspect the segmentations of the
> individual subjects used for the RB_all_2008-03-26.gca atlas? I can extract
> the me
Hi Vasudev
no, there is no alternative. Computing resources are cheap these days.
Most cluster would let you run all your subjects in a single night.
cheers
Bruce
On Thu,
14 Jul 2016, Dev vasu wrote:
Dear Sir / madam,
I have 50 subjects (25 healthy controls and 25 patients with BLVP)
Hi Zach
check out asegstats2table and aparcstats2table and see if they do what
you want
cheers
Bruce
On Thu, 14 Jul 2016, Zachariah Holub wrote:
I have run various batches of freesurfer on our MRI scans. Now I want to
take many of the stats files from all of our subjects and export them to o
Hi Gabor
if you upload a subject and let us know what you think is suboptimal
(including voxel coords of inaccurate locations) we will take a look
cheers
Bruce
On Fri, 15 Jul 2016, Gabor Perlaki wrote:
Dear Bruce,
Some subcortical structures seems to be suboptimally segmented in our
subject
Hi Vasudev
run recon-all -all on each one of them.
cheers
Bruce
On Fri, 15 Jul 2016, Dev vasu wrote:
> Dear sir,
>
> I would like to know how could i possibly generate white and pial surface
> data for pool of 50 subjects ( 25 healthy controls and 2 subjects with BLVP)
> using free surfer.
>
>
Hi Tamara
if you are more interested in things like ventricular volume then the
surfaces aren't so important to check.
cheers
Bruce
On Fri, 15 Jul 2016, Tamara Tavares wrote:
> Hi All,
>
> I was hoping to get some help with understanding the surface and aseg
> volumes. I have some patient's
Hi Mahtab
check out bbregister. It should do the trick.
cheers
Bruce
On Mon, 18 Jul 2016, Mahtab
Farahbakhsh wrote:
> Dear FreeSurfer,
> I am trying to register my SPM activation maps to the structural data of
> each subjects. Except for the commands I could find for the registration, I
> could
Hi Ri
I think you can just run it all as one recon-all command.
cheers
Bruce
On Mon, 18 Jul
2016, Ritobrato Datta wrote:
> Hi All,
>
> We have some subjects who have both wm errors and gm errors.
>
> Is the following workflow possible
>
>
> Step 1) control points for the white matter edits. DON
e: Contents of Freesurfer digest..."
Today's Topics:
1. Re: Checking Surfaces vs. aseg outputs (Bruce Fischl)
--
Message: 1
Date: Sat, 16 Jul 2016 13:35:10 -0400 (EDT)
Fr
nope, I would start with the aseg and only check other things if the
ventricles aren't accurate
On Mon, 18 Jul 2016, Tamara Tavares wrote:
Thank you again Bruce.
Since I am primarily interested in ventricular volume, do you think it is
necessary to check the the brainmask.mgz for bright or dark
Hi Michelle
that's a tough question. We don't have a ton of experience with it one
way or the other, but if I had to pick one I would pick FLAIR as long as
you are getting a 3D FLAIR with around 1mm voxels
cheers
Bruce
On Mon, 18 Jul 2016,
Michelle T Kassel wrote:
Hello,
I am beginnin
Hi Reema
you should visualize it over the norm.mgz. The brainmask and brain will
wash out many low contrast borders (e.g. thalamus, pallidum)
cheers
Bruce
On Mon, 18 Jul
2016, Reema Jayakar wrote:
Hello FS Listserv members,
With regard to checking amygdala segmentation, is it appropriate t
What segmentation do you mean? Where are you getting vtk files? We write the
segmentation into .mgz volumes such as aseg.mgz
Cheers
Bruce
> On Jul 18, 2016, at 1:19 PM, Abbie McNulty wrote:
>
> So we were able to figure out how to segment the different parts of the brain
> using the bert sa
Hi Falk
I think openmp will help with this in V6, but probably not before
Bruce
On Tue, 19
Jul 2016, Falk Lüsebrink wrote:
Hi all,
I’m currently processing a 250 µm MPRAGE with a dev build from mid of May.
Running recon-all with default parameters ran flawlessly. Afterwards I added
the
Hi Bart
1M is really not enough for you? How many would you need? I'll try to find
the time to make it dynamically allocated and configurable one of these
days
Bruce
On Tue, 19 Jul 2016, Ferguson, B. wrote:
Dear Freesurfer team,
I am running Falk Luesebrinks hires recon, and am running i
Hi Dorsa
are they really that highres? Sometimes people do zero-padding and Fourier
interpolation on the scanner. 1/2mm cubic is pushing the resolution and if
they are really that high res they will be either very noisy or very long
scans (or both)
cheers
Bruce
On Tue, 19 Jul 2016, Dorsa Ha
pload
into matlab. Is there a way to convert this 3D brain piece as an .mgz file?
Thanks
On Mon, Jul 18, 2016 at 5:40 PM, Bruce Fischl
wrote:
What segmentation do you mean? Where are you getting vtk files? We write the
segmentation into .mgz volumes such as aseg.mgz
Cheers
Bruce
On Jul 18,
save as a .vtk file, I am not
converting anything
Abbie
On Tue, Jul 19, 2016 at 10:51 AM, Bruce Fischl
wrote:
Hi Abbie
I'm not sure what page you mean. The segmentations start life as an .mgz
file, so why convert them at all? Just load the aseg.mgz (or whichever
segme
k you
Dorsa
On Tue, Jul 19, 2016 at 1:49 PM, Bruce Fischl
wrote:
Hi Dorsa
are they really that highres? Sometimes people do zero-padding
and Fourier interpolation on the scanner. 1/2mm cubic is pushing
the resolution and if they are really that high res they wi
hmmm, no, that's odd. Did you do anything outside of FS on any of the
volumes? Try running mri_info on aseg.presurf.mgz, brainmask.mgz and
norm.mgz and send us the output
cheers
Bruce
On Tue, 19 Jul 2016, Uquillas, Federico D'Oleire wrote:
Dear fellow Freesurfer users,
I have 4 jobs that
ue, 19 Jul 2016, Abbie McNulty
wrote:
So say I load aseg.mgz into matlab and I want to extract the brainstem in
matlab to plot its own volumetric mesh vs. the entire brain, how would I extract
the brainstem in matlab?
On Tue, Jul 19, 2016 at 11:00 AM, Bruce Fischl
wrote:
but why not jus
sorry, perhaps someone else can help you with this. I haven't used
plotmesh.
cheers
Bruce
On Tue, 19 Jul 2016, Abbie McNulty wrote:
Perfect. now if I wanted to use plotmesh with this, what would the variables
be for x and y: plotmesh('x,y')
On Tue, Jul 19, 2016 at 11:40 A
hear
any comments about the thalamus size.
Thank you
Dorsa
On Tue, Jul 19, 2016 at 2:08 PM, Bruce Fischl
wrote:
Hi Dorsa
why not give the original 1mm scans to freesurfer, then upsample
the segmented images? And no, I wouldn't venture a guess without
seein
00 1. -0. 135.1890
0. 0. 0. 1.
Best,
Fred
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
[fis...@nmr.mgh.harvard.edu]
Sent: Tuesday
contrast medium. I have played with the intensities in Analyze and this
> is the best I could get. Do you have any suggestions for getting better
> contrast?
>
> Thank you
>
> Dorsa
>
> On Tue, Jul 19, 2016 at 4:29 PM, Bruce Fischl
> wrote:
> also,
works best with 1mm^3
voxel size?
Thank you!
On Tue, Jul 19, 2016 at 4:06 PM, Bruce Fischl
wrote:
Hi Dorsa
without the norm.mgz I have no way to evaluate the accuracy of
the aseg.
cheers
Bruce
On Tue, 19 Jul 2016, Dorsa Haji Ghaffari wrote:
Yes
MRIs and will let you know when I hear back. I also wanted to ask if you know a
good way to refine the thalamus and fill out the missing parts within the
volume?
Thank you
Dorsa
On Tue, Jul 19, 2016 at 5:10 PM, Bruce Fischl
wrote:
what is a "3TS" image? Do you mean it was acqui
Haji Ghaffari wrote:
I mean the holes in the thalamus and also some parts that are labeled as
thalamus
but not attached to the rest of thalamus volume.
On Wed, Jul 20, 2016 at 10:49 AM, Bruce Fischl
wrote:
what missing parts do you mean? The segmentation seemed pretty
reasonable, bu
Hi Younghoon
what structure are you talking about? In general it doesn't make sense to
flatten volumetric structures. We flatten the cortex, which is a folded
2D sheet. What would you do with the interior of the volume?
cheers
Bruce
On Wed, 20 Jul
2016, Younghoon Kim wrote:
Hello,
We hav
Hi Fred
that just means that you need to change the window levels.
Note that we have deprecated the use of tksurfer and tkmedit and don't
really support them any longer
cheers
Bruce
On Wed, 20 Jul
2016, Uquillas, Federico D'Oleire wrote:
> Hi fellow FreeSurfer users,
>
> I just did a gcut pro
Lab
Wellman Center, Massachusetts General Hospital
Bouma’s Lab
--
younghoon.h@gmail.com
aktivh...@kaist.ac.kr
On July 20, 2016 at 5:00:55 PM, Bruce Fischl (fis...@nmr.mgh.harvard.edu) wrote:
Hi Younghoon
what structure are you talking about? In
oon.h@gmail.com
aktivh...@kaist.ac.kr
On July 20, 2016 at 5:12:59 PM, Bruce Fischl (fis...@nmr.mgh.harvard.edu) wrote:
HI Younghoon
I guess that could work. You will need to introduce at least one cut if not
more if you surface has substantial Gaussian curvature
cheers
Bruce
On Wed,
20 Jul
I don't assume
any faster processing.
Best,
Falk
-Ursprüngliche Nachricht-
Von: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl
Gesendet: Dienstag, 19. Juli 2016 15:37
An: Freesurfer support list
Betreff: Re: [Frees
Hi Subin
it looks more likely that you just don't have write access to your
SUBJECTS_DIR. Can you check that with ls -l? Or maybe you just haven't set
it and it still points to the one we distribute? Typically you want to set
the SUBJECTS_DIR env variable to some other directory where you will
Hi Tobias
yes, mris_calc should do it. If you give the output extension .mgz it will
save in that format instead of curv I believe (and will work fine as an
overlay)
cheers
Bruce
On Thu, 21 Jul 2016, Granberg, Erik Tobias wrote:
Hi,
Is there a way to subtract one surface overlay from ano
Hi Varsha
try using mri_aparc2aseg
cheers
Bruce
On Thu, 21 Jul 2016, vars...@cns.iisc.ernet.in
wrote:
>
> Hi,
>
> I've been working on getting a finer parcellation of the Desikan-Killiany
> atlas using mris_divide_parcellation. I was able to generate two
> annotation files; one each for the lef
Best,
Falk
Von: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Gesendet: Donnerstag, 21. Juli 2016 15:30
An: Falk Lüsebrink
Cc: Freesurfer support list
Betreff: Re: AW: [Freesurfer] mri_ca_label with high resolution data
Hi Falk
the dev version of mri_ca_label does use openmp, so
p. of Bio and Brain Engineering, KAIST
OMICS Lab
Wellman Center, Massachusetts General Hospital
Bouma’s Lab
--
younghoon.h@gmail.com
aktivh...@kaist.ac.kr
On July 20, 2016 at 5:29:24 PM, Bruce Fischl (fis...@nmr.mgh.harvard.edu) wrote:
If you h
Hi Falk
yes, it's an active area of devlopment for us
cheers
Bruce
On Thu, 21 Jul 2016, Falk
Lüsebrink wrote:
Hi Bruce,
I thought so. Are there any other means to accelerate this procedure (in the
future)?
Best,
Falk
-Ursprüngliche Nachricht-
Von: Bruce Fischl [mailt
using different imaging
methods)
Our machine has 16GB RAM.
Thanks,
Younghoon Kim
--
Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST
OMICS Lab
--
younghoon.h@gmail.com
aktivh...@kaist.ac.kr
On July 21, 2016 at 10:35:18 AM, Bruce Fischl
Hi Jinsong
you can either copy those labels out into their own volume using
mri_extract_label, or use matlab to find the other labels and zero them out
cheers
Bruce
On Thu, 21 Jul 2016, Jinsong Tang wrote:
Hello freesurfers,
I want to select the subcortical structures (thalamus, pallidum,
yes, that should work also
On Thu, 21 Jul 2016, Koubiyr, Ismail wrote:
> I think you can use mri_binarize and set the match values as you like.
> Hope it can help.
>
> Best,
>
> Ismail
>
>> On Jul 21, 2016, at 2:13 PM, Jinsong Tang wrote:
>>
>> Hello freesurfers,
>>
>> I want to select the subcor
try using the -rl switch in mri_convert. It will "reslice
like" the you give. Give it the 512 volume as
cheers
Bruce
On Thu,
21 Jul 2016, Dorsa Haji Ghaffari wrote:
> Hi,
> I have segmented 288 slices of 512x512 dicom MRIs but when I create a mask of
> the
> left thalamus I get 256 slices o
t;> Message: 17
>> Date: Thu, 21 Jul 2016 09:31:57 -0400 (EDT)
>> From: Bruce Fischl
>> Subject: Re: [Freesurfer] Combined parcellation of the left and right
>> hemispheres
>> To: Freesurfer support list
>> Message-ID:
>>
>> Content-Type: tex
dded to them. I created a look-up table
> with the right indices and it worked fine. Thank you.
>
> Regards,
> Varsha
>>
>>
>>
>>> Message: 17
>>> Date: Thu, 21 Jul 2016 09:31:57 -0400 (EDT)
>>> From: Bruce Fischl
>>> Subject: Re: [F
Hi Jinsong
if you use rawavg.mgz as the template ("--temp rawavg.mgz") the output
will be resliced into that voxel space. Try using orig.mgz instead.
As for saving in int from matlab, I'm not sure we have anything to do so.
You can always convert it using mri_convert
cheers
Bruce
On Sat,
Hi Dorsa
you need to give us more details. What was your reslicing command line?
And the screen output?
Bruce
On Mon, 25 Jul 2016, Dorsa Haji Ghaffari wrote:
Hi,
I re-sliced my left thalamus so that the size and number of slices correspond
with the original MRI, but when I open it in free
> -fthresh 0.5
>
> mri_surf2surf --s ${subj_number} --trgsubject ${subj_number} --hemi lh --sval
> lh.thickness --tval lh.thickness.fsaverage.mgh --reshape
>
> mri_segstats --seg lh.${subj_number}.ACG.mgh --in
> ${subj_number}/surf/lh.thickness.fsaverage.mgh --sum
> segstats-
u!
On Mon, Jul 25, 2016 at 12:41 PM, Bruce Fischl
wrote:
Hi Dorsa
you need to give us more details. What was your reslicing
command line? And the screen output?
Bruce
On Mon, 25 Jul 2016, Dorsa Haji Ghaffari wrote:
Hi,
I re-sliced my left t
f the thalamus corresponds to the
original mri.
Thank you!
Dorsa
On Mon, Jul 25, 2016 at 3:29 PM, Bruce Fischl
wrote:
Hi Dorsa
did you create the aseg.mgz from 1mm data (using the standard
"conform" process), or higher res? The file you sent is higher:
,
Younghoon Kim
--
Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST
OMICS Lab
Wellman Center, Massachusetts General Hospital
Bouma’s Lab
--
younghoon.h@gmail.com
aktivh...@kaist.ac.kr
On July 21, 2016 at 11:15:43 AM, Bruce Fischl (fis
Hi Elisabetta
FS 6 is not available yet. We are hoping to have a beta in a couple of
weeks and are actively working on getting it out
cheers
Bruce
On Thu, 28 Jul 2016,
elisabetta_de...@hms.harvard.edu wrote:
Dear FreeSurfer team,
we are trying to find a downloadable version of FS6.0 to
Hi Tom
it's tough for us to tell without some images or the data. If you upload
the entire subject dir of a subject that failed we will take a look. You
can't just change which peak is the WM - lots of things downstream would
fail
cheers
Bruce
On Fri, 29 Jul 2016, tvg[fs] wrote:
> Dear comm
FYI
---
The Neuroradiology Section at the University of California, San Francisco
(UCSF) is seeking an exceptional postdoctoral candidate in multimodal
imaging of neuropsychiatric and neurodegenerative disorders.
Combining neuroimaging, genetics, and computational methods, our group is
interest
Hi > Domenico
I think the problem is that you have a forward slash in your subject
name, as well as your SUBJECTS_DIR and FREESURFER_HOME. Did you perhaps but
them inside double quotes or something? Usually the forward slash \ let's
you extend command over multiple lines, but in this case it a
which error? The mri_normalize problem? If so, then yes I believe that is
now fixed
On Mon, 1 Aug 2016, Liu, Daniel wrote:
> Hi,
>
>
> I wanted to follow up on the error that came up in the freesurfer dev version
> this past week. Has it been fixed yet? If so, has the link to the download
> p
Hi Fengji
we have frozen the code and are going through various tests now so are
hoping sometime in the next few weeks, but of course it's impossible to say
as it depends on how well the tests turn out.
cheers
Bruce
On Mon, 1
Aug 2016, Fengji Geng wrote:
Hi fs developers,
I am wonderin
Hi Caroline
the colortables are in $FREESURFER_HOME. Usually we use
$FREESURFER_HOME/FreeSurferColorLUT.txt
cheers
Bruce
On Mon, 1 Aug 2016, Caroline Beelen wrote:
Dear FS,
Sorry to bother again, but I’m currently in need for some quick help.
Today, I also ran into another problem. I
Hi Fred
what version are you running? I think we fixed this bug a long time ago.
cheers
Bruce
On
Thu, 4 Aug 2016, Fred Dick wrote:
Dear Doug et al
I was doing some cross-subject label morphing over a bunch of subjects (a
big continuous patch of vertices) and was having problems with quite a
it might be fixed in 5.3, no? What version are you using Fred?
On Thu, 4 Aug 2016, Douglas Greve wrote:
Hi Fred, I think there are problems with trying to use v6 binaries without
the v6 distribution. Zeke may have more of an idea.
doug
On 8/4/16 4:32 AM, Fred Dick wrote:
Dear Doug et
Hi Sam
usually this means that the cerebellum is too far from isocenter and hence
has low SNR/more distortion. If you can place your subjects higher in the
scanner that might help.
For existing data try putting some control points in cerebellar wm or
brainstem. That might help
cheers
Bruce
HI Jasmin
we use the definition from various papers from the Center for
Morphometric Analysis (CMA) such as:
Filipek, P.A., Richelme, C., Kennedy, D.N., and Caviness, V.S., Jr.
(1994). The young adult human brain: an MRI-based morphometric
analysis. Cereb. Cortex 4, 344–360
You can find the
FYI
The Neurobiology Research Unit (NRU) at Copenhagen University Hospital,
Rigshospitalet has an opening for a MRI physicist position. The position
entails design, development, implementation and evaluation of novel
multimodal MRI acquisition protocols and image analysis techniques in
relation t
Hi Vasudev
those areas are definied in the aseg.mgz (and the wmparc.mgz), so you
should be able to get them from either of those volumes.
cheers
Bruce
On Thu, 25 Aug
2016, Dev vasu wrote:
Dear all,
After running through recon-all ,I have obtained wmparc parcellation file (see
the at
do you mean the ones that are between the two surfaces? You could use
mris_fill to fill the interior of the white then use it as a mask in
mri_mask
cheers
Bruce
On Sun, 28 Aug 2016, Fire Tech wrote:
Dear all
I am searching for a solution to remove wm.mgz voxels which are enclosed by
pial
Hi Woo-Suk
why not just do the surface analysis that they are requesting? I'm not
sure what you are asking, but certainly volume = surface area * thickness
in general, and so a volumetric effect can be driven by one or both of
surface area and thickness
cheers
Bruce
On
Sat, 27 Aug 2016, Wo
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 it, and no, there is no reference
for it yet (or maybe ever) :)
Bruce
On Tue, 30 Aug 2016, Krieger, Donald N. wrote:
Dear list:
What are the advantages of including
Hi Vasudev
probably not. What resolution are they? They are likely to be too low
resolution to be useful and also quite significantly distorted w.r.t. the
T1s. You can try it if you like, but my guess is it will hurt more than it
helps
sorry
Bruce
On Tue, 30 Aug 2016, Dev vasu wrote:
Dea
Hi Eelco
we've made a bunch of improvements in the T2/FLAIR stream since 5.3 so you
might check them out. Unfortunately I don't think they will be officially
supported in 6.0 as we just don't have the resources to include it in our
unit/system/regression test cycle.
cheers
Bruce
On Tue, 3
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 it, and no, there
n Tue, 30 Aug 2016, Bruce Fischl wrote:
Hi Matt
I don't think that counts as a methods paper for the T2-based deformation.
There is no validation or comparison with other methods in it, and really not
enough detail to replicate what we did.
cheers
Bruce
On Tue, 30 Aug 2016, Matt Gla
glad to hear it
Bruce
On Wed, 31 Aug 2016, Eelco Van Duinkerken wrote:
Thanks for the suggestion Bruce!That totally solved the problem! Good to
know that with the upcoming version this is solved.
Eelco
On 30 Aug 2016, at 12:36, Bruce Fischl
wrote:
Hi Eelco
we've made a
Hi rujing
that can be tough. If all your group1 are on one scanner and all group2 are
on the other how can you tell the difference between a group effect and a
site effect? At the very least you should scan some people on both
scanners.
cheers
Bruce
On Wed, 31 Aug 2016, charujing123 wrote
Hi Carol
the bigventricles stuff works much better in the upcoming 6.0 and dev
than it did in 5.3. You might try downloading dev and trying it out
cheers
Bruce
On Wed,
31 Aug 2016, Carol Nguyen wrote:
Hello FreeSurfer Developers,
I am attempting to segment a brain with large ventricles. I
Hi Ben
are the bright points segmented as wm in the wm.mgz? If so, you might try
erasing them and rerunning
cheers
Bruce
On Wed, 31 Aug 2016, Benjamin Baird wrote:
Dear Freesurfer experts,
We are currently working with some scans that were collected on a GE 3T
scanner. The goal is to analyz
Hi Aziz
can you elaborate? What coordinates do you want? What are you trying to do
with them? The .mgz format contains ras2vox matrices that let you go from
voxel indices to RAS coordinates and such.
cheers
Bruce
On Sun, 4 Sep 2016, Aziz Nanthaamornphong wrote:
Dear Freesurfer experts,
H
oordinates of a left
hippocampus volume.
As you mentioned "ras2vox" matrices, hoe can I see or get these
matrices?
Thank you.
Aziz
On Monday, 5 September 2016, Bruce Fischl
wrote:
Hi Aziz
can you elaborate? What coordinates do you want? What are
you trying to do
Hi Ben
sorry, but I don't know how to fix it automatically. You have voxels that
look just like wm in the gm - that's going to be tough to avoid. You could
try messing with some of the mris_make_surfaces options, but I don't have
much confidence that it will help.
Any idea why you are gettin
sorry, no. You pretty much need to do everything
Bruce
On Wed, 7 Sep 2016,
djpet...@u.washington.edu wrote:
> Hi Freesurfer list,
>
> Say I was interested ONLY in extracting the pial surface for the purpose of
> getting a 3D print of a brain. Are there any time-intensive steps that can I
> s
Hi Cong
you could try using expert options to modify the mris_make_surfaces
parameters. It looks like you white surface is too far out. Try
increasing min_border_white and/or increasing max_gray. If you can't get it
working feel free to upload the entire subject dir and we will take a look
c
n the texture mapping file and eventually mapped onto
the vectorized surface.
Thanks,
Younghoon Kim
--
Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST
OMICS Lab
--
younghoon.h@gmail.com
aktivh...@kaist.ac.kr
켜짐 2016년 7월 27일 에서 06:51:01, Bruce F
Hi Alain
I'm pretty sure that this is a bug in 5.3 that is fixed in dev and will
not be an issue in 6.0. You can test this by downloading and trying out
dev if you like.
cheers
Bruce
On Fri, 9 Sep 2016, Alain Imaging wrote:
Hello everybody,
I am gladly starting my freesurfer adventure af
7;MRIread' for input arguments of type 'char'."
Best Regards,
Aziz.
On Mon, Sep 5, 2016 at 6:46 AM, Bruce Fischl
wrote:
yup, or mri_Info called form the command line. If you use
MRIread on the aseg.mgz you can extract e.g. the left
hippocampus using mat
I think that would be ok, but an easy way to test it is to try it on
another subject first with their actual wm.mgz, then with the one from
fsaverage to check that the thickness is the same.
cheers
Bruce
On Sun, 11 Sep 2016,
Arkadiy Maksimovskiy wrote:
> Dear Freesurfer Experts,
>
> I am tryi
Hi Fred
have you checked the transform to see if it actually failed? If not, you
can just turn off the checking. If it did, you can manually correct it
(or run without it)
cheers
Bruce
On Wed, 14 Sep 2016, Uquillas, Federico D'Oleire wrote:
> Dear fellow FreeSurfer users,
>
> I can't get a su
We are experiencing center-wide hardware problems, and it's likely to be down
for a while
> On Sep 15, 2016, at 11:07 PM, Chris Filo Gorgolewski
> wrote:
>
> FYI - there is something wrong with the FTP server:
>
> $ wget
> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-HCP/freesu
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