Hi Freesurfer list,
My group is switching to the fsfast functional connectivity pipeline. We would
like to continue regressing out the six-parameter rigid body head motion as a
nuisance variable. In order to do this, which file should we flag: is it
fmcpr.mcdat or mcprextreg?
Thank you!
Best,
Actually, it is on by default (thanks to Emma for pointing it out). The
smoothing helps to blur anatomical differences which reduces the chance
that it will get stuck in a local minimum. It will usually only smooth
the reference, and only if it is high res; this can help the reference
look a li
Dear FreeSurfer Developers,
I am using FreeSurfer 5.3 to analyze whether a risk factor explains variation
in brain structures related to surface area, mean thickness, and subcortical
volumes.
Documentation suggests using estimated Total Intracranial Volume (eTIV) as a
covariate to adjust for
We'll try to process it on a blade server tongiht... if it succeeds we can edit
any incorrect results as needed.
The image is from a separate site, it has OK resolution (1x1x1.5) but has an
enormous amount of gibbs ringing compared to our on-site images, which is
probably causing the issue...
Is that your design matrix or the contrast matrix? To test for the
interaction between two continuous variables, one usually creates a new
variable by multiplying them together and then just testing for the
regressor for that variable being different than zero
On 08/23/2017 12:34 PM, Timothy H
does this happen every time you run it? The message said that the job
was killed, which suggests something outside of recon-all (eg, if you
were running it on a cluster, sometimes a job will get killed if it runs
out of memory or runs too long).
On 08/23/2017 02:30 PM, Cara Bohon wrote:
> I h
Hi K,
I would recommend to use the data from the longitudinal directories also
for the cross sectional analysis. That data will be less noisy than from
independent processing (which is what you also find).
Since the longitudinal stream goes through many different processing
steps than the re
Hi,
healthy controls usually show 0.5% atrophy per year or less. You have
very young subjects, and the expectation there would be near to 0
change. Due to acquisition noise, hydration effects, head motion etc,
you will of course always find individual cases with volume / thickness
increase or
Hi Ann-Kathrin,
for age you should use age at baseline (should be fixed for all time
points per subject). You have the time_from_baseline variable to model
the time. (maybe that is what you are already doing).
I don't know why more survives with the voxelwise model, I usually see
the opposit
Hi Kasper,
1) yes correct
2) for generic the time delta is always 1 ( 2-1, 3-2, 4-3 ..)
Best, Martin
Am 16.08.2017 um 08:22 schrieb Kasper Jessen:
Dear Freesurfer,
The following is a follow-up, on a previous discussion
(http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51582.h
Freesurfer experts,
I have created a design matrix in order to test for whether there is an
interaction effect between two continuous co-variates controlling for a
categorical variable.
So I have one categorical variable with two levels, and two continuous
co-variates.
My design matrix is as fol
Hi Chethana
are you sure it is a problem with the volume? It may just be a
visualization issue. Try changing the window levels
cheers
Bruce
On Wed, 23 Aug
2017, Chethana wrote:
> To,
> The Freesurfer experts,
>
> I am analysing a set of MRI images in freesurfer 6. In the step 1 of
> freesurf
That defect is so big you probably ran out of memory.
> On Aug 23, 2017, at 11:21 AM, Rockers, Elijah D.
> wrote:
>
> We encountered a hard failure, below is the tail of the log. We are currently
> running Freesurfer 6 again locally to see if it succeeds on a desktop machine
> (this is the fi
Dear Antonietta,
I don’t know of any official statement in that regard, however, Yong Li (CC’ed)
seems to have updated the QA tools working with FS 6 in April. He may share his
code.
Best,
Falk
Von: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auft
We encountered a hard failure, below is the tail of the log. We are currently
running Freesurfer 6 again locally to see if it succeeds on a desktop machine
(this is the first time encountering a hard failure on the XNAT server). Any
suggestions?
-merging segment 180 into 178
160 defects t
Dear FreeSurfer list,
is any of you aware of a new version of the QA (quality assessment) tools < [
https://surfer.nmr.mgh.harvard.edu/fswiki/QATools |
https://surfer.nmr.mgh.harvard.edu/fswiki/QATools ] > working for FS vs 6.0?
Should I expect a new release in the near feature?
Kind regards,
Hi Moji:
1. Absolutely. You can use standard FreeSurfer tools for extracting masks from
a segmentation, resample them to whatever space, etc.
2. A lot of people have been making this question, so we’re now writing a bunch
of merged segmentations to the mri directory of the subjects for convenie
Dear Freesurfer Developers,
I have some questions regarding hippocampal and amygdalar subregional
segmentation in the latest Freesurfer version:
1) Can one use the segmentation outputs as ROI masks, register those to native
space functional image, and extract functional time courses in order
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