Dear All,
I am looking for a postdoc to work on brain image analysis, e.g.,
dynamic functional connectivity. See more information below.
Regards,
Thomas
Job Title: Postdoctoral Fellow in Brain Image Analysis
Project: Develop novel image analysis and machine learning tools for
brain image analy
Hi Alan - If you're using a standard MGH diffusion sequence and you have a
Martinos account, look for the appropriate gradient table in this
directory:
$FREESURFER_HOME/diffusion/mgh-dti-seqpack/
You'll have to find out how many gradient directions are in your data
(that's the number
When you loaded the lowb into freeview and it looked registered with the
anatomical, did you load the lowb with the registration file? If not,
then the registration may be wrong. Things may look almost right when
you don't specify a registration file because you probably collected the
dti and
Hi Gerit - There's no difference in tracula between 5.2 and 5.3.
a.y
On Mon, 17 Feb 2014, Gerit Pfuhl wrote:
> Dear Freesurfer experts,
> we are curious whether we can run trac-all -qa in 5.3. and use it as
> regressors with our results from tracula 5.2.
> I.e. is it advisable or shall we run t
The lesion_vol2vol volume is still not correctly overlapping the DTI.
The only command that didn't give me registration issue is mri_convert
where I did not put any registration file but I was not completely happy
with the interpolation resampling. (nearest missed some lesions, maybe
interpolate a
what does it look like if you run
tkmedit -f lowb.nii.gz -ov lesion_WM_vol2vol.nii.gz -fminmax .5 1
On 2/17/14 10:00 PM, Celine Louapre wrote:
> No problem, sorry!
> So when I am loading my lesion mask on freeview on brainmask.mgz and on
> DTI_fit_FA.nii, the lesions are correctly registered
No problem, sorry!
So when I am loading my lesion mask on freeview on brainmask.mgz and on
DTI_fit_FA.nii, the lesions are correctly registered on both DTI and T1.
The only thing I would like to do is to resample the lesion mask that has
a resolution of 0.3*0.3*1 on the resolution of the DTI that h
oops, sorry! That command looks like it is correct. Can you say more
about what is going wrong? How are you determining that something is
going wrong?
doug
On 2/17/14 9:30 PM, Celine Louapre wrote:
> Hi Doug
> I don't know if you had the chance to read my email below to resample a
> lesion m
btw, if I had to guess, I'd say it is an "endianness" problem.
On 2/17/14 5:41 PM, Dave Frank wrote:
Hello,
I'm trying to use anatomical regions of a subject labeled by
freesurfer as an fMRI mask in brainvoy
I've never used BV, so I can't help you. You might want to contact
the BV folks as they may have more experience in this.
best
doug
On 2/17/14 5:41 PM, Dave Frank wrote:
Hello,
I'm try
Hello,
I'm trying to use anatomical regions of a subject labeled by freesurfer as
an fMRI mask in brainvoyager. I'm using mri_convert to change
aparc+aseg.mgz to a nifti, and then changing that into a brainvoyager vmr
file.
However, the vmr file in brainvoyager looks wrong (see attached screensho
Sorry, no. You can use mri_mask from the command-line though
doug
On 2/14/14 11:19 AM, Joerg Pfannmoeller wrote:
> Hello,
>
> I am using tkmedit to display functional data as an overlay on anatomical
> data. I am asking myself if there is a feature in tkmedit which allows to
> apply a mask to t
Hi Greg, use the defect-seg script to create segmentations and labels.
See the help for more info.
doug
On 2/17/14 1:42 PM, Bruce Fischl wrote:
> Hi Greg
>
> there is a ?h.defect_labels file that gets created in curvature format I
> believe that you can overlay (the overlay is the defect numbe
Hi Goi, please remember to post to the freesurfer list. Thanks! The max
psd depends upon how long it takes for the HRF to return to baseline
(and do not related to the TR). This is usually something like 20 sec +
the duration of your stimulus.
doug
On 2/17/14 1:31 PM, Goi Khia Eng wrote:
Hi Linn,
I have never done that, so I am not sure, but since it is likely
affecting the surface, I think you need to do it in the base, to get
good initial surfaces. You may have to do it again in the long stage.
Start with the base.
Best, Martin
On 02/10/2014 10:49 AM, Linn Christin Bonaven
Hi Anastasia:
Yes I am using a standard MGH diffusion sequence.
thanks,
Alan
On Fri, Feb 14, 2014 at 10:20 PM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:
>
> Hi Alan - The gradient table is not saved in the nifti header. Are you
> using a standard MGH diffusion sequence?
>
> a.y
Hi Greg
there is a ?h.defect_labels file that gets created in curvature format I
believe that you can overlay (the overlay is the defect number of each
connected component). I think Doug might have something even better, but I
can't remember
cheers
Bruce
On Mon, 17 Feb 2014,
Gregory Kirk wro
im trying something novel with a veryb young brain, i ran freesurfer standard
stream
and got decent results and then did some manual editing to fix a skull struip
problem
and reran and now it is detecting a large defect, is there a way i can look at
the data to see what topological defect it is
Dear Freesurfer experts,
we are curious whether we can run trac-all -qa in 5.3. and use it as
regressors with our results from tracula 5.2.
I.e. is it advisable or shall we run the complete analysis?
Thanks,
Gerit Pfuhl
___
Freesurfer mailing list
Frees
Thanks a lot.
Best regards,
Amirhossein Manzouri
On Mon, Feb 17, 2014 at 4:54 PM, Bruce Fischl wrote:
> they are automatically detected, but sometimes they can be too permissive
> (or restrictive) in some regions in some acquisitions. If you look through
> the recon-all.log file in your subj
yes, where "stronger" means greater in magnitude ignoring the sign
doug
On 2/17/14 10:41 AM, Yang, Daniel wrote:
I see. You are saying that the interpretation can be made in two ways:
blue/cyan =
the cortical thinning effect of Age is stronger in patients (vs.
controls)
Or, the cortical th
they are automatically detected, but sometimes they can be too permissive
(or restrictive) in some regions in some acquisitions. If you look
through the recon-all.log file in your subject's scripts dir you can see
what they are set to (search for mris_make_surfaces), then look at where
the surf
Thanks Bruce for the prompt reply. Would you please explain how can I
control mris_make_surfaces parameters, is this a part of recon-all process?
Best regards,
Amirhossein Manzouri
On Mon, Feb 17, 2014 at 3:35 PM, Bruce Fischl wrote:
> Hi Amirhossein
>
> it's hard to tell without looking at
Yes, you should see cyan. Note that you would see cyan if group1 slope
is 0 and group 2 slope is positive. Probably not a problem with age, but
it is just something to think about.
doug
On 2/17/14 1:38 AM, Yang, Daniel wrote:
Dear FreeSurfer developers and experts,
If I have a binary fac
Hi Amirhossein
it's hard to tell without looking at the data, but you could try using
the expert options to change the allowable intensity ranges for the
different surfaces (e.g. if the white is too far out, don't allow
mris_make_surfaces to put the gray/white border at intensities that are
t
yes, it certainly looks like a library problem. You should talk to your
sysadmin, or perhaps Zeke or Nick can comment
cheers
Bruce
On Mon, 17 Feb 2014, Durai
Arasan wrote:
Hi Freesurfer experts,
so I got this error when I ran recon-all on my cluster. I am really hoping
this is just a case o
Hi all,
There is incorrect pial surface lines (red and yellow) in the right
hemisphere of some of my subjects. The white matter and grey matter are
very close regarding intensity and this can be seen in just a few slices
and then it gets correct. I tried control points but regarding the low
intensi
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