Dear Doug,
I used bblabel for making coronal cut.
The definition is given below.
bblabel
Applies a bounding box to a label. The bounding box is specified by
six coordinates (xmin,xmax,ymin,ymax,zmin,zmax). Only those label
points within this box are copied to the output. If a min is not
specified
Hi Nicolas
The "common random effects design matrix" expression
means that all subjects in your prospective study are expected in
advance to have the same random effects design matrix (Zi). If you
assume a linear trajectory over time and a two-year study with repeated
measurements every six
Hi Marco, the aparc+aseg.mgz is probably going to be the best one (it is
what I use:). When you binarize it, you can dilate it by a voxel as well
with:
mri_binarize --i aparc+aseg.mgz --min 0.5 --dilate 1 --o yourmask.mgz
doug
On 04/11/2013 03:31 PM, Marco Loggia, PhD wrote:
> Dear all,
>
> w
yes, I agree. Two surfaces could be extremely close and have 0 dice. I
don't think it would be as informative as Hausdorff or RMS as Mike
suggests
Bruce
On Thu, 11 Apr 2013, Michael Harms wrote:
Try:
mri_surf2vol --surf pial --mkmask --hemi lh --identity --template
/mri/norm.mgz --o
/mri/p
Hi Doug
I can motion correct the briks with 3dvolreg
Jon
- Original Message -
From: "Douglas N Greve"
To: "Jon Wieser"
Cc: "freesurfer"
Sent: Thursday, April 11, 2013 11:22:13 AM
Subject: Re: [Freesurfer] merging dti data
That might work. I think "motion" correction is going to be your
Try:
mri_surf2vol --surf pial --mkmask --hemi lh --identity --template
/mri/norm.mgz --o /mri/pial_in_vol.mgz
FWIW, I'm not sure if sampling two surfaces to the volume, and then
computing a dice coefficient is really the best way to "compare" two
surfaces. I would instead compare the two surfac
Hi,
I did the command:
mri_surf2vol --surfval $SUBJECTS_DIR/Patient1/surf/rh.pial --hemi rh --identity
Patient1.
ERROR: cannot recognize the type of
/home/lucille/Freesurfer/freesurfer/subjects/Patient1/surf/rh.pial
The name of my subject is ' Patient1'.
Did I do a wrong entery at the --surf
Dear all,
what is the 'best' skull stripped file produced by freesurfer? From what I see,
it would seem to be 'brainmask'. However this file -if I understand correctly-
is produced in the very first stages of recon-all, and therefore does not take
advantage of the detailed reconstruction of the
Thanks Nick! I have uploaded the relevant files to you.
Thanks,
Daniel
--
Yung-Jui "Daniel" Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454
On 4/10/13 1:19 PM, "Nick Schmansky" wrote:
>Daniel,
>
>We're repeating our paired-analysis of thickness meas
Hi,
I am new to Freesurfer and the Linear Mixed Effects (LME) Models packages.
And I would like to compute sample size from volumetric measures for 2
groups.
I followed the longitudinal example provided in the wiki (
http://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels#a.29Univariate)
Hi PPJ and all,
I found that the 5.2 – 5.1 difference is primarily seen in the cortical
thickness, and much less so in the aseg.volume.
Here, I picked right-amygdala volume as an example of aseg.volume and
rh_bankssts_thickness as an example of rh.aparc.thickness.
While the correlation between
That is a good value, so the regis not the problem. If you upload your
dt_recon folder as well as your recon-all folder for that subject I'll
take a look.
doug
On 04/11/2013 10:02 AM, Rotem Saar wrote:
> Hi Douge,
>
> In your last reply to my email (that contained questions regarding
> some rea
Hi Lucile, don't use autoreg-sess (that is an old program and was for
fMRI). Use mri_surf2vol with --identity subjectname instead of --reg
doug
On 04/11/2013 11:45 AM, Lucille Deroche wrote:
> Hi Bruce,
>
> In fact, have 2 differents surfaces of pial surface. I would like
> to save my surfac
Hi,
I am doing a longitudinal analysis using the LME toolbox, and I would
like to perform a clusterwise correction for multiple comparisons.
Would it be correct to use mri_surfcluster on the resulting maps, or do
you suggest any alternative otherwise ? I can only find functions
implementing FDR
Hi Paul, try using this color table, something like
tkmedit HS_001 orig.mgz -seg aug_aparc+aseg.mgz paul.ctab
doug
On 04/08/2013 10:02 AM, Paul Beach wrote:
Hi Freesurfers,
I'm currently trying to take manually made ROIs (label files) that
have been incorporated into new annotation files (
That might work. I think "motion" correction is going to be your biggest
problem since the slabs were acquired at different times.
On 04/11/2013 11:05 AM, Jon Wieser wrote:
> the gradients were the same for each slab. What is the difficulty with
> runnning the merged brain halves in tracula?
>
>
Yes, assuming a shape will give you much more power, at least for the
individual subject.
doug
On 04/11/2013 02:55 AM, SHAHIN NASR wrote:
>
> Sorry that I keep on asking questions but I want to know if using a
> model can significantly increase the chance of getting a significant
> response.
Hi Anastasia,
I'm running tracula on linux ubuntu (mint 14) on a lenovo thinkpad edge. it has
8gb ram and 4 CPUs, i think it's a lot.. I did not run tracula before on this
computer.
Daria
-
Daria Antonenko, Dipl.-Psych.
Charité - Universitätsmedizin B
Hi Bruce,
In fact, have 2 differents surfaces of pial surface. I would like to save my
surfaces in volume to be able to calculate the dice score between the two.
Cheers
Lucille
De : Bruce Fischl
À : Lucille Deroche
Cc : "freesurfer@nmr.mgh.harvard.ed
Hi Lucille
what do you mean by converting a surface to the volume? What do you want
to do with it? What volume would you like to convert it to?
cheers
Bruce
On Thu, 11 Apr
2013, Lucille Deroche wrote:
Hi,
My name is Lucille and I'm really new with Freesurfer : My questions are very
basi
the gradients were the same for each slab. What is the difficulty with runnning
the merged brain halves in tracula?
I have another to do it that I am going to try. I made AFNI Brik's of the two
slabs, and merged them together into one AFNI brik with the AFNI command
3dZcat. I made a nifti f
Hi,
My name is Lucille and I'm really new with Freesurfer : My questions are very
basic, sorry. I just start a project in segmentation of cerebrum.
For converting a surface in volume. I would like to use mri_surf2vol but for
that I need a volume registration file . For creating that file, I
yes, they work for whole brain, but not if you have two brain halves.
You might be able to do something in matlab. I assume the gradient
direction order was the same for both slabs?
doug
On 4/11/13 10:36 AM, Jon Wieser wrote:
> Those commands were given to me by Anastasia. they work fine for
Hi Satra,
I have been trying to do that too. Do you have it as Nipy code?
Thanks.
Shantanu
On Thu, April 11, 2013 10:53 am, Satrajit Ghosh wrote:
> hi dan,
>
> if you use bbregister to match the DTI b0 to freesurfer space, then you
> can
> transform the surface back (no guarantees on the tesselat
Now why would you like to do that?
On Thu, April 11, 2013 9:27 am, Varghese Chikku wrote:
> Hi All,
> Is there any tool,which can convert mgz files to Dicom?
> In Thanks
> chikku
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://
hi dan,
if you use bbregister to match the DTI b0 to freesurfer space, then you can
transform the surface back (no guarantees on the tesselations though i
think). the only additional component here would be a tkr transform that's
based on the conformed space. i might even have some python code lyi
Hi all,
I want to transform the Freesurfer Smoothwm surfaces to DTI B0 space.
I found
http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferTrackVisTransforms but
this describes transforming the B0 to T1 space and then match the surfaces.
I don't want to change the DTI B0 image.
What is the best w
Those commands were given to me by Anastasia. they work fine for merging two
whole brain datasets.
jon
- Original Message -
From: "Douglas Greve"
To: freesurfer@nmr.mgh.harvard.edu
Sent: Wednesday, April 10, 2013 10:13:05 PM
Subject: Re: [Freesurfer] merging dti data
Hi Jon, I don't
Sorry, we don't write dicom usually, just read it
Bruce
On Apr 11, 2013, at 8:27 AM, Varghese Chikku wrote:
> Hi All,
> Is there any tool,which can convert mgz files to Dicom?
> In Thanks
> chikku
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.
Hi Douge,
In your last reply to my email (that contained questions regarding some
really high FA values - see recent emails below), u asked me to write u the
first value in register.dat.mincost -
I'm copying the line I have:
0.280554 140.210312 156.795241 11.152485
Does this takes us one step fu
Hi All,
Is there any tool,which can convert mgz files to Dicom?
In Thanks
chikku
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for
Dear all,
I think my issue is quite related to this one (if not duplicated,
sorry in that case):
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-February/027622.html
As Shani, I used bbregister to coregister diffusion images to anatomical:
> bbregister --s OE0_T1 --mov DTI_b0_brain.ni
32 matches
Mail list logo
