Dear freesurfer team,
I’m trying to use freesurfer LME tools to check whether baseline BMI scores
(BMI scores at the first timepoint) have a statistically significant
effect/impact on longitudinal thickness changes accounting for baseline age and
gender. The model I’m thinking of is:
Y_ij = b0
[POSTED ON BEHALF OF RUCHIKA PRAKASH]
Dear Colleagues:
The Department of Psychology at Ohio State University is looking to hire a
tenure-track assistant professor in the area of clinical
neuropsychology/neuroscience. We are specifically looking for candidates with
the potential to establish a
Hi Freesurfer People,
The aim is get ROI masks for my functional images and to achieve that for
each of the subjects in my data, I am:
1. Running freesurfer for segmentation of structural scan,
2. Running feat analysis that would give me transformation matrices
including structural2functional and
Hi,
Writing this question helped me find my own mistake. I have been using
output_better.nii.gz instead of output_better.nii. Running gunzip
extraction before nii2mnc solves the problem.
Thanks alot,
Usman Ayub Sheikh
On Thu, Sep 7, 2017 at 4:32 PM, Usman Ayub wrote:
> Hi Freesurfer People,
>
Hello,
Is it possible to use cluster-defining thresholds such as p = 0.025 with
mri_glmfit-sim? (This would roughly correspond to a negative log value of 1.6.)
My design doesn't allow the use of permutations for simulating cluster sizes,
so I have to use the mczsim option; however, from what I
Hello FreeSurfer expert,
I have a binarized stroke masks of 200 stroke patients that were hand
traced. Since, we have a lot of patients, it will take a lot of time to
edit the aseg.presurf.mgz. The stroke masks were drawn in the native space
and I want to bring them into the freesurfer space, and
try something like
mergeseg --src aseg.presurf.mgz --merge stroke.mgz --o aseg.manedit.mgz
--segid 77
This will model the strokes as WM hypointensities
On 09/07/2017 11:54 AM, miracle ozzoude wrote:
> Hello FreeSurfer expert,
>
> I have a binarized stroke masks of 200 stroke patients that wer
Thanks doug. If I run the recon-all -autorecon2-noaseg -autorecon3. Will it
incorporate the stroke? Also, does it matter if it's a cortical stroke and
i am using v6.0 and i don't see aseg.manedit.mgz.
Best,
Paul
On Thu, Sep 7, 2017 at 12:38 PM, Douglas N Greve
wrote:
>
> try something like
>
>
sorry, should be
mergeseg --src aseg.auto.mgz --merge stroke.mgz --o aseg.presurf.mgz
--segid 77
when you re-run recon-all, it will create the manedit file
On 09/07/2017 12:49 PM, miracle ozzoude wrote:
> Thanks doug. If I run the recon-all -autorecon2-noaseg -autorecon3.
> Will it incorporat
If you want to use that threshold, you will have to create tables for
that threshold using mri_mcsim. See
https://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo
Alternatively, I have a version of mri_glmfit-sim that will run
permutation with non-orthogonal designs.
https://gate.nmr.
what version of FS are you using?
On 09/07/2017 03:19 PM, Aidan Murphy wrote:
>
> We're running QA on Freesurfer's aseg and aparc+aseg volumes. On the
> aparc volume we're noticing fairly large unknown regions in what
> should be entorhinal cortex, specifically where it comes up against
> the
Thanks, I will try later.
Bo
发件人: freesurfer-boun...@nmr.mgh.harvard.edu
代表 Bruce Fischl
发送时间: 2017年9月7日 4:56:23
收件人: Freesurfer support list
主题: Re: [Freesurfer] 答复: ROI
Hi Bo
have you tried freeview? We don't support tksurfer any more.
cheers
Bruce
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