Hi Dr. Greve,
I am sorry for reposting this. Could you please confirm the following steps
and correct me where I am wrong.
Thanks.
-- Forwarded message --
From: Martin Juneja
Date: Tue, May 9, 2017 at 12:15 PM
Subject: Re: [Freesurfer] Maps showing correlations between structura
Hello,
I'm writing because I have had an issue with QDEC and it's ability to
correctly read the number of subjects indicated on my data table. I have
about 70 subjects listed, but the program is only reading three. This is a
".dat" file that was created via a .csv template using Libre Calc.
Ben
Hi everyone. I’m unpacking dicoms collected on a 3T Tim Trio and I’m getting
segmentation errors (see below) with two of ~80 subjects when using either
unpacksdcmdir or dcmunpack (I’ve tried both commands with FreeSurfer 5.3.0 and
5.3.1, running on the Harvard NCF cluster). I’m not sure what to
I think that PALM may output simple p-values and not -log10(p), you can
convert it with
fscalc p.mgz log10 mul -1 -o sig.mgz
On 05/10/2017 01:27 PM, Sahil Bajaj wrote:
> Hello FreeSurfer experts,
>
> I used PALM toolbox to identify significant clusters after multiple
> comparison correction us
Hi Jerry
we have code that does this internally, but nothing that is easy to use
from the command line. You could do what you suggest using the lh.sphere
to compute distance. That will avoid the problem of crossing the banks of
a sulcus
cheers
Bruce
On Wed, 10 May 2017, Jerry Jeyachandra wro
yes
On 05/10/2017 12:50 PM, Jerry Jeyachandra wrote:
>
> Thanks and I presume that surfaceRAS coordinates are intrinsically in mm?
>
> Jerry
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
> on behalf of Douglas N Gre
Thanks and I presume that surfaceRAS coordinates are intrinsically in mm?
Jerry
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N Greve
Sent: May 10, 2017 12:42:29 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Obtaining surf
It will mean that the direction information in the file will not be
valid, so you will not be able to tell left from right or top from
bottom. The pixel data should be ok
On 05/10/2017 12:20 PM, shi yao wang wrote:
>
> Dear FS experts:
>
> There are some error message when I running recon-all a
We don't have a way to compute the exact distance from one vertex to
another along the surface (working on it!). If the distances are small,
then euclidian might work ok.
On 05/10/2017 12:35 PM, Jerry Jeyachandra wrote:
>
> Hi Bruce,
>
>
> To clarify, if I were to use:
>
> mris_convert lh.pial
Hi Bruce,
To clarify, if I were to use:
mris_convert lh.pial lh.pial.asc
That would give me surfaceRAS coordinates for the vertices for the lh.pial
surface which is consistent in order for the vertex normals in
lh.pial.normals.asc? I find this easier to work with than mri_surf2surf since
my
Dear FS experts:
There are some error message when I running recon-all as following:
WARNING: neither NIfTI-1 qform or sform are valid
WARNING: your volume will probably be incorrectly oriented
Are there any problem in raw data?
I am using MRICRON to convert DICOM to nii
thanks
Lawrence
__
Hi Freesurfer Developers,
I'm trying to map the vertices of caudal middle frontal in one subject into
the space of another subject by using mri_label2label. And I used the
method mentioned in this
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2015-November/042298.html
We are using freesur
Dear FS experts:
We generated a specific population of brain template.
Just wondering if FS can use these templates to measure brain volume.
thanks
Lawrence
Emory
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Hi Freesurfer team,
I wonder how calculate integrated rectified values of a ROI using
*mris_anatomical_stats. *
After reading lh.*.H.crv, lh.*.K.crv, lh.thickness,
and lh.aparc.DKTatlas40.annot files in matlab, I couldn't calculate same
output of the results using the command of "mris_anatomical
Dear Dr Doug,
I followed wiki to adjust the volumetirc measures to eTIV usign the command
mri_label_volume -eTIV \
$sdir/transforms/talairach.xfm 1948 \
$sdir/aseg.mgz 17 53
Kindly,
1. What is the saling factor stands for and why it is specifically "1948 " is
this only relevant to volumetrics?
Also, unless something is wrong with your processing or time point
naming, you should get different volumes also for each time point in the
longitudinal stream. Manually open the aseg.stats and check to determine
if the problem is in way you processed the longitudinal data or when
creating the
Hi Jahanvi,
long.testretest.qdec is a qdec table in the longitudional format (with
the fsid-base as the second column).
For test-retest (e.g. same session with subject removal), you usually
don't need a time column, that is why --generic-time is specified. the
qdec table would just look like
Hi Livia,
the Paired Analysis wiki page that you cite, contains the steps to
create the differences and then run a glm analysis on the difference
files. In your case you would to the first steps exactly as on the wiki
and then you can create a more complex Second FSGD File with more than
one
Hi,
I’ve a .mgh that is a volume projected on the surface of the same subject at
mid-thickness (output of mri_vol2surf) .
I would like to extract the mean hemipheric value in this X.mgh.
I guess it is possible with mris_anatomical stats but probably my command line
is incorrect (see below).
A
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