Dear Doug and All,
I want to register the individual subject surface into the fsaverage surface. I
used mdi_surf2surf command. But one error occurred. Could you please help me
with this. Here are the scripts:
—
[root@localhost sub001]#
Greetings,
The aim of this mail is about some problems that I am facing using the
standalone copy (that is becouse I am using v5.1) of the LNE Matlab Tool
provided on the FreeSurfer Wiki (
http://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels).
Currently, I am carrying out a
Dear all
I am segmenting data of 2 year olds and as freesurfer fails on segmneting
inferior parts of the temporal lobe, I try to edit this manually using tkmedit
(protocol from fswiki: WhiteMatterEdits_tktools, PialEdits_tktools,
ControlPoints_tktools).
I first add control points, with
Sure, thanks!
tcsh
shalim-ubunut:/media/Shared_Data/freesurfer setenv FREESURFER_HOME
/media/Shared_Data/freesurfer
shalim-ubunut:/media/Shared_Data/freesurfer source
$FREESURFER_HOME/SetUpFreeSurfer.csh
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Setting up environment
Dear Bruce Matt,
thank you for your help.
@Bruce: I would be happy to send you the data, just let me know by
e-mail which files you would need.
@Matt: Could you please specify the commands for the flags
-nsigma_above and -nsigma_below and how you would rerun the pipeline?
Also what values
Hi Mark
if you upload a subject that failed and the gca I'll take a look
Bruce
On Mon, 12
May 2014, Mark Plantz wrote:
Yes, I created my own atlas for use with 1-2 year olds. It seems to be
happening for all of
the subjects. I am wondering if changing the recon-all code to load the manual
I see. Then measure the thickness normally, then see how it changes in
those directions. You could average the thickness along each A/P coordinate
- that wouldn't be a problem. You just don't want to measure it that way
cheers
Bruce
On Mon, 12 May 2014,
pfot...@nmr.mgh.harvard.edu wrote:
Hi Qiongmin
try making the output format .mgz (or maybe .nii) and see if that fixes the
problem
cheers
Bruce
On Tue, 13 May 2014, Caka wrote:
Dear Doug and All,
I want to register the individual subject surface into the fsaverage surface. I
used mdi_surf2surf command. But one error
can you send us the recon-all.log?
On Tue, 13 May 2014, Mayer Kristina
wrote:
Dear Bruce,
I was running:
recon-all -autorecon2-cp, after adding control points.
When I then look at the surfaces using tkmedit -surfs or inflated surfaces
using tksurfer, everything seems to fit and I can open
Hi Emil
I would need the entire subject dir plus the T2-space volume
cheers
Bruce
On Tue, 13 May
2014, Emil H.J. Nijhuis wrote:
Dear Bruce Matt,
thank you for your help.
@Bruce: I would be happy to send you the data, just let me know by e-mail which
files you wo
uld need.
@Matt: Could
Hi Kristina
are you running:
recon-all -autorecon2-cp -autorecon3 ...
after adding control points and editing the wm?
Bruce
On Tue, 13 May 2014, Mayer
Kristina
wrote:
Dear all
I am segmenting data of 2 year olds and as freesurfer fails on segmneting
inferior parts of the temporal lobe,
Hi Victor
As explained in the wikifs_read_surf.m andfs_read_Y.m depend on Freesurfer's
scripts so you need to have installed
Freesurfer software package and included the Freesurfer's matlab
subdirectory in your Matlab's search path.
Best
-Jorge
El Martes 13 de Mayo de 2014 4:40, Victor
Hi Bruce,
Just to clarify, when you say average the thickness along each A/P
coordinate do you mean by looking up at the average cortical thickness of
each parcellation and then calculating their average from P-A, or is
there another way to find the average thickness of each slice and then see
Dear Doug,
I am trying to run mris_preproc as you indicated, but it fails with the
following error:
MRISread($SUBJECTS_DIR/fsaverage/surf/lh.fsaverage_sym.sphere.reg): could
not open file.
Why is target file searched in the fsaverage folder? I was expecting it is
searched in the fsaverage_sym
Hi everyone
Just wanted to point
out that all the technology required to implement the statistical
methods used in our last paper:
Event time analysis
of longitudinal neuroimage data. Neuroimage. doi:
10.1016/j.neuroimage.2014.04.015.
is available on
github:
https://github.com/NeuroStats
I
I don’t know if recon-all will pass those flags in or not. Probably best
to let Bruce take a look.
Peace,
Matt.
On 5/13/14, 7:36 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:
Hi Emil
I would need the entire subject dir plus the T2-space volume
cheers
Bruce
On Tue, 13 May
2014, Emil
Hi Panos
I would make an average thickness map in fsaverage space, then in matlab
divvy up the a-p direction into bins (say 100 of them) and compute the
average in each bin based on the a/p coordinate
cheers
Bruce
On Tue, 13 May 2014,
pfot...@nmr.mgh.harvard.edu wrote:
Hi Bruce,
Just to
Dear Freesurfer
I want to use surf2vol to get volume files of gray
thickness.And the --volreg Contains the matrix that maps XYZ in the
reference anatomical to XYZ in the functional volume. So I use
bbregister.Why I need not invert the BBR registration matrix with
surf2vol?I mean ,
Hi Bruce,
I see, that's really helpful, thank you!
Best,
Panos
Hi Panos
I would make an average thickness map in fsaverage space, then in matlab
divvy up the a-p direction into bins (say 100 of them) and compute the
average in each bin based on the a/p coordinate
cheers
Bruce
On Tue,
Hello,
I am using the intensity contour tool for defining a white/gray matter border
of my ROI.
I can adjust my ROI according to this contour and save it. However, the contour
itself is not saved (to the same layer as the ROI) and will not be loaded when
opening the ROI layer again later.
Is
Hi doug
Thanks doug.
My mask and input mgh file are all fsaverage space.
I try the mri_segstats, and I cannot get what you mean clearly. So I read the
help of mri_segstats, but neither do I get the information. Then I have to try
to run this:
mri_segstats --i ./rh.36sb.10.mgh --mask
Hi Sarah
what tool are you using to draw the contour?
Bruce
On Tue, 13 May 2014, Burke,
Sarah wrote:
Hello,
I am using the intensity contour tool for defining a white/gray matter
border of my ROI.
I can adjust my ROI according to this contour and save it. However, the
contour itself is
Hi Bruce,
in Freeview, I am using the voxel edit tool called Contour.
Sarah
Van: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] namens Bruce Fischl
[fis...@nmr.mgh.harvard.edu]
Verzonden: dinsdag 13 mei 2014 17:29
Aan:
Dear Freesurfer
I want to use surf2vol to get volume files of gray
thickness.And the --volreg Contains the matrix that maps XYZ in the reference
anatomical to XYZ in the functional volume. So I use bbregister.Why I need
not invert the BBR registration matrix with
Hi Bruce,
Sorry, I had a last follow up question. I just realized that the resulting
bins will be in the fsaverage space, and hence I wouldn't be able to use
mris_anatomical_stats to calculate the average thickness of the bins,
since the fsaverage subject does not have a wm.mgz file. Did you have
Hi Panos
no, mris_anatomical_stats won't do it. I would map the average thickness
to fsaverage coords, then load that into matlab and go from there using
the [xyz] coords of fsaverage for the binning, which is pretty much
MNI305
cheers
Bruce
On Tue, 13 May 2014, pfot...@nmr.mgh.harvard.edu
Hi Bruce,
I was having issues with the part after that, that is how to calculate the
average thickness of those bins, after I create them. Thanks again
Best,
Panos
Hi Panos
no, mris_anatomical_stats won't do it. I would map the average thickness
to fsaverage coords, then load that into
Just to follow up, it looks like mris_thickness needs to be run, but
mris_curvature is unchanged by changes to the pial surface. Thanks again
for the help!
stephen
*stephen v. shepherd phd*
The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA
// 212.327.7620
On Sun,
Just use mri_binarize
doug
On 05/07/2014 05:08 PM, pfot...@nmr.mgh.harvard.edu wrote:
Hi Doug,
That sounds great! I'll go ahead and do that. I would just be interested
in coming up with the binary maps of the lobes, not their associated
stats. Should I still go ahead and use mri_segstats or
surf2vol understands which direction the registration goes and applies
it appropriately. Use --outvol thicknessvolume.nii to get a single nifti
file output
On 05/07/2014 10:22 PM, 刘东博 wrote:
Dear Greve
Thank you for your reply
I want to use surf2vol to get volume files of gray
This is a very vague request. What kind of connectivity analysis? fMRI
or DTI? What software are you using?
On 05/08/2014 05:43 AM, Jutta Ernst wrote:
Dear Freesurfer's
I draw a roi to extract the cortical thickness for my two groups and
that worked fine.
Now I'm trying to export the
Sorry, I was going through old emails and did not see this had already
been addressed. Please ignore, which I'm sure most of you were doing
anyway :-)
On 05/13/2014 01:37 PM, Douglas N Greve wrote:
This is a very vague request. What kind of connectivity analysis? fMRI
or DTI? What software
the pial curvatures will change, but you probably don't use them anyway
cheers
Bruce
On Tue, 13 May 2014, S.V.Shepherd [work] wrote:
Just to follow up, it looks like mris_thickness needs to be run, but
mris_curvature is unchanged by changes to the pial surface. Thanks again
for the help!
The partial volume correction is done based on the intensity and label
of the surrounding voxels. By using aparc+aseg you change the label of
the surrounding structures and it changes the PV correction. Use
aseg.mgz and not aparc+aseg
doug
On 05/09/2014 05:27 AM, Schreiber, Stefanie wrote:
You can't use analyze for this. mgh format will work. nii might work
On 05/13/2014 04:37 AM, Caka wrote:
Dear Doug and All,
I want to register the individual subject surface into the fsaverage surface.
I used mdi_surf2surf command. But one error occurred. Could you please help
me with
Sorry, I've totally lost the thread on this one. Can you send the
command line, the terminal output, and the log file again?
doug
On 05/12/2014 04:11 PM, Sherryse Corrow wrote:
Hi Douglas,
I don’t receive any emails from anyone, I only receive the the digest
which is what I “reply” to.
Hi Jodie,
are you familiar with mixed effects models? If not I would recommend you
include a biostatistician.
What I mean (and you can do this in the matlab code, no need to include
it in the qdec file) is to use a piecewise linear model.
So for a subject with visits at 0, 0.4 and 0.9 years
Not exactly sure why your getting a permission denied error. Can you
please try the following and provide us with the relevant output?
1) What is the output of the following:
ls -ld $FREESURFER_HOME/bin
2) After sourcing FreeSurfer, what happens when you type:
tkmedit -f
During the Spring Freesurfer workshop the newest version of Freeview was
used as the primary viewing tool. Are there compatibility issues with
using the newest version of Freeview while running analyses in an older
version of Freesurfer (v5.1.0)? That is, if you run recon-all through
v5.1.0, can
Sorry, in both of those mris_preproc commands add
--target fsaverage_sym
doug
On 05/13/2014 09:48 AM, Paola Valsasina wrote:
Dear Doug,
I am trying to run mris_preproc as you indicated, but it fails with the
following error:
There are a lot of things that I don't understand about your command
line. Why are you passing the thickness as the segmentation? The mask
only limits the computations to be inside the mask. What precisely are
you trying to do?
On 05/13/2014 11:27 AM, charujing123 wrote:
Hi doug
Thanks
You can use the new version of freeview with older versions of FS.
doug
On 05/13/2014 03:10 PM, Sarah Blankenship wrote:
During the Spring Freesurfer workshop the newest version of Freeview
was used as the primary viewing tool. Are there compatibility issues
with using the newest version of
Hi Christopher --
Indeed, you can use 'mris_pmake' to calculate the shortest distance
along the surface between arbitrary mesh points.
Given a valid FreeSurfer environment, $SUBJECTS_DIR, etc:
$mris_pmake --subj 101 --hemi lh --surface smoothwm --mpmProg pathFind
--mpmArgs
Hello-
We’re having a problem with our Freesurfer 5.3 install: freeview exits with a
Segmentation fault. No windows open, and there is no other other output.
strohm::funcserv1:=freeview
Segmentation fault
All I have been able to find is that it appears to be making an
Hi,
The same result! the last is insula !
Best regards,
Amirhossein Manzouri
On Mon, May 12, 2014 at 5:05 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:
Try this version
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/
greve/aparcstats2table
On 05/12/2014 03:41 AM,
Hi doug,
I read your last e-mail again. After changed my command, it worked.
Thanks doug.
Rujing Zha
2014-05-14
charujing123
发件人：Douglas N Greve gr...@nmr.mgh.harvard.edu
发送时间：2014-05-14 03:14
主题：Re: [Freesurfer] problems about extracting specific vertex thickness value
and getting a
Dear Doug and all,
I have already done two things:
(1) 'recon-all’ to the segmentation for 140 subjects;
(2) surface registration to fsaverage template for 1 subject using:
mri_surf2surf --hemi lh --srcsubject sub001 --srcsurfval thickness --src_type
curv --trgsubject fsaverage --trgsurfval
Hi FS experts and users
I want to change the background color of tksurfer from black to white. However
I cannot find the drop-down list. Is there anyone who can tell me to desolve
this?
Thanks. All the best.
Rujing Zha
2014-05-14
charujing123 ___
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