In that case, you just need to mri_convert aparc+aseg.mgz aparc+aseg.nii
On 10/19/15 3:24 PM, Bruce Fischl wrote:
> Hi Boris
>
> the aparc*aseg.mgz files are probably want you want. They are the surface
> parcellations sampled into the volume. Of course you lose resolution when
> you sample a con
Hi Boris
the aparc*aseg.mgz files are probably want you want. They are the surface
parcellations sampled into the volume. Of course you lose resolution when
you sample a continuous surface into a discrete volume though.
cheers
Bruce
On Mon, 19 Oct 2015, Boris Shabash wrote:
> Hello FreeSurfe
Try mri_surf2vol. Run it with --help to get more docs
On 10/19/15 3:09 PM, Boris Shabash wrote:
> Hello FreeSurfer group
>
> How are you?
>
> I have currently started working with FS and would like to visualize some of
> the volume results. I have no issue visualizing the .mgz volumes produced
>
Hello FreeSurfer group
How are you?
I have currently started working with FS and would like to visualize some of
the volume results. I have no issue visualizing the .mgz volumes produced since
I can use mri_convert to convert them to .nii format and then visualize them
using my software. Howev
Hello All
Several years ago Freesurfer 5.1 was patched to resolve some issues. I
just remember the patch resolved issues plaguing 5.1 and earlier. how does
one get the patch version. no where on the FTP server i can see patched
versions and instruction on performing a patch.
Aaron Tanenbaum
__
My experience, which appears to be consistent with Doug's, is that there is no substitute for reviewing the images and FS results manually. Ultimately, it is a bit of a judgement call, and interacts with the goals/purposes of your study.
--
Michael Harms, Ph.D.
---
Thanks MH,
Let's say that we have 100 MPRAGEs and we want to include them in a cross sectional analysis.
Depending on your experience, do you recommend any criterion to (include/ exclude) these images in the analysis? As I see visualizing the images alone is not enough to say that the quality of
At best that would probably be harmless (if you have a decent number of subjects), but unless SNR, CNR actually relates to those measures in some fashion, you aren't really accomplishing anything by including it as a covariate. You certainly wouldn't
be able to claim that including SNR as a
I think you would just be wasting your power
Bruce
On Mon, 19 Oct 2015, John
Anderson wrote:
Hi All,
Thank you very much for your comments!
Is it advisable to include SNR as a covariate when we use Qdec to run the
final statistics on volumetrics, surfaces and cortical thickness?
Does it make
Hi Seth
do you really want to include the capsule within the brain mask? You can
always view it and find its coordinate by visualizing the orig.mgz. If you
really want it in the brainmask.mgz you can clone it back in using freeview
or tkmedit
cheers
Bruce
On Mon, 19 Oct 2015, Hutton, Seth w
Why not just open the T1.mgz and load the FreeSurfer surfaces? Is there
a more specific goal?
hth
d
On 10/19/15 10:56 AM, Hutton, Seth wrote:
> Dear users,
>
> I have been using FreeSurfer for a while now, but am working in a new
> lab and their goals fall outside of my realm of experience.
> We
Hi All,
Thank you very much for your comments!
Is it advisable to include SNR as a covariate when we use Qdec to run the final statistics on volumetrics, surfaces and cortical thickness?
Does it make sence ?
Bests,
John Anderson
Senior Research Associate
Psychological and Brain Sciences
In theory that should work. I say "in theory" because there might be
something unique to each area in terms of the distribution of the
vertices across space. But I'm betting it will be safe to do. But why
not run both simulations?
On 10/19/15 11:03 AM, Joost Janssen wrote:
Hi,
A question abo
This has been my experience as well. Not much seems to predict which
scans will need to be edited.
On 10/19/15 10:23 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, G/CSF cnr -- to see how th
Hi Pablo,
maybe your file is not clean and contains strange symbols to separate
coumns and rows?
Make sure columns are all separated by spaces.
You could load the table into exel or openoffice spreadsheet and then
export as CSV with space (or you could also try tab) for the separation
and no
It might just work to give recon-all skull stripped brains. I've done it
before
On 10/19/15 8:38 AM, Bruce Fischl wrote:
Hi John
I guess you could run recon-all through to the skull stripping, then
copy your skull-stripped volume to brainmask.mgz in the subject's mri
dir, then restart recon-
Dear Martin and FS experts.I am having difficulty in loading my qdec.table.dat
to Matlab.When I use the [command: Qdec = fReadQdec('qdec.table.dat'); ] Matlab
only recognises a matrix of 140x1 cell, whereas instead it should recognise a
140x4.I tried to import the table as 'table' from the gui i
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
Hi,
A question about building your own Monte Carlo.
here: https://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo
it says: "If you want to restrict the correction to a smaller area to
reduce the severity of the correction, you can specify a mask or a label
and change the output folder".
Dear users,
I have been using FreeSurfer for a while now, but am working in a new lab and
their goals fall outside of my realm of experience.
We are using both MRI imaging as well as FNIRs. We have multiple vitamin E
capsules placed during both and would like to be able to view them in
FreeSurf
Hi,
FWIW, I've looked at a number of these measures in 500+ subjects from HCP
data -- wm-anat-snr, pctsurfcon, G/W cnr, G/CSF cnr -- to see how they
relate to each other, and whether they correlate with mean cortical
thickness, white matter surface area, or number of SurfaceHoles (prior to
topolo
probably similar, although maybe Doug can comment. You probably want to run
it on the orig.mgz as the intensity normalization can artificially increase
the SNR (which is kind of the point)
Bruce
On Mon, 19 Oct 2015, John
Anderson wrote:
Hi Bruce,
Thanks a lot!! this is really great!
I ran
Hi Kasper,
if you use the same file formats and conversion tools across both time
points, the images should be identical. Even after conversion to nii.
Not sure why they are not.
Yes, both warnings are related to the acquisition parameters. The second
should better say that header informatio
Hi Bruce,
Thanks a lot!! this is really great!
I ran the command as the following :
mri_cnr subj_01/surf subj_01/mri/norm.mgz
processing MRI volume subj_01/mri/norm.mgz...
white = 97.2+-9.5, gray = 69.0+-16.1, csf = 47.8+-16.5
gray/white CNR = 2.291, gray/csf CNR = 0.848
lh CNR = 1.56
Hi Daniel,
sorry for the late reply; I was on vacation.
It seems that the T1-T2 registration failed. Can you please send me the .log
files for the hippocampal subfields? They should be in the following directory:
media/orlandi/Ub4_Shared_HD/orlandi/PharmaCog-Volontari/CARTELLE-avg+base+long+T2/
Hi John
I guess you could run recon-all through to the skull stripping, then copy
your skull-stripped volume to brainmask.mgz in the subject's mri dir, then
restart recon-all from there.
cheers
Bruce
On Fri, 16 Oct 2015, John Anderson wrote:
Dear experts,
I want to run recon-all on a stri
Hi John
there is also a binary called mri_cnr that will compute the
contrast-to-noise ratio (CNR), which is really the more interesting
metric. It will also spit out the WM means+- std, and the ratio of these
two can be used as an SNR measure.
cheers
Bruce
On Mon, 19 Oct 2015, John Anderso
Dear Jürgen
This really helps!
I highly appreciate your input on this.
Bests,
John Anderson
Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419
Sent: Monda
Hi Jorge and FS experts,I have run again the analysis and still get the
convergence problem.I am assuming the issue has to do with the preprocessing
steps, as I had doubts on how to follow from the instructions if I am not using
qdec and have a cross sectional design.
Instructions on lme in the
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