yes, it is just like a "normal" group analysis. You create a stack of LI
maps, one for each subject, create an FSGD file, run mri_glmfit, then
mri_glmfit-sim.
doug
On 01/13/2014 06:22 PM, krista kelly wrote:
>
> Just wanted to repost this in case anyone else can give some advice.
> Thanks!
Just wanted to repost this in case anyone else can give some advice. Thanks!
Is there any way to analyze group differences with xhemi? I can get the
laterality indices per group, but I'd like to do a whole brain analyses
looking at group differences in laterality indices.
Thanks,
Krista
On Tue,
Greetings Freesurfer Community,
I am running a longitudinal study using Freesurfer v.5.3 to compare rate of
cortical thinning between 2 groups of subjects. I hope I can seek some
expert advice on the following situation:
All data (both the baseline and follow-up) has been processed independently
Hi Anastasia, thanks so much for your help. I downloaded the update to
calculate motion parameters for each participant. I now have Freesurfer
5.3 installed on my server but all the preprocessing was completed in
Freesurfer 5.1 (not 5.2 like I originally said). Can I run the motion
calculation step
Hi
I have a volume of diffusion index in freesurfer dimensions and I would
like to compare the left and right hemis.
That means I need to register the volume/surface to the fsaverage_sym using
xhemi?Is there more documentation about this tool?
Thnanks!
Shani
On Mon, Jan 13, 2014 at 6:12 PM, Do
The surface initially loads upside down, and if you load the annotations
the ensuing parcellations are mapped to an upside down surface
appropriately, but the label reported in the 'Tksurfer Tools' window
appears to be based on a right-side-up brain.
For example, if I position the cursor over the
Hi,
I had a strange problem trying to convert DTI dicoms. When I used the
following command to convert a raw dicom to nifti image, I obtained a
64-volume nifti that only contains one horizontal slice of the brain.
mri_convert [input Dicom] [output nifti name]
Does anyone have ideas for why this m
Hi Gari - Yes, fslmaths should be able to do it, with -thrp 20.
a.y
On Mon, 13 Jan 2014, Garikoitz Lerma-Usabiaga wrote:
Thanks Anastasia, I finally got it, I had to do mri_vol2vol twice to have it
in the diffusion space.
I have an additional question:
I want to create waypoint masks for pr
Hi Mike
what kind of mismatch do you mean?
Bruce
On Mon, 13 Jan 2014, Harms, Michael
wrote:
To add to this thread, I have this same problem (upside-down display in
tksurfer, with mismatch with the reported annotation labels in the Tools
window) when using a CentOS 6.4 system, using both FS 5
To add to this thread, I have this same problem (upside-down display in tksurfer, with mismatch with the reported annotation labels in the Tools window) when using a CentOS 6.4 system, using both FS 5.1 and FS 5.3, but not when using a CentOS 5.5 system.
If there is an easy fix for this (e
Sophie,
Try to add the line MEASURE1 = pial_lgi in the .Qdecrc in your home folder
instead, that should make pial_lgi automatically listed in qdec.
Let me know if it doesn't work,
Marie
On Jan 13, 2014, at 8:11 AM, Douglas N Greve
mailto:gr...@nmr.mgh.harvard.edu>>
wrote:
It has not been
-- Forwarded message --
From: "Salil Soman"
Date: Jan 12, 2014 1:28 PM
Subject: Re: problem with bvecs file with new (12/13) TRACULA code
To: "Anastasia Yendiki"
Cc:
Hi,
>
> Thank you for your email. Taking the .bval and bvec files outputed by
> dcm2nii (which are row format) and
On 01/13/2014 11:41 AM, amirhossein manzouri wrote:
> Dear Doug,
> I need also to correct for Age and Years of Education by using them as
> nuisance covariate. Would you please explain:
> Why the covariates should be demeaned?
Reduces correlation with the group term and so improves efficiency.
>
Thanks Anastasia, I finally got it, I had to do mri_vol2vol twice to have
it in the diffusion space.
I have an additional question:
I want to create waypoint masks for probtracx from Tracula tracts (for
example, uncinate).
Should I use mri_binarize on path.pd.nii to create the mask?
Should I use
Hi Francesco - The bvecs file that you're attaching has only 3 vectors,
while the bvals file has 65 b-values. Are these your original files, or
the ones saved by trac-all in the dmri/ directory?
a.y
On Mon, 13 Jan 2014, Francesco Baldacchini wrote:
> Hi everybody,
> I'm trying to run the trac
Dear Doug,
I need also to correct for Age and Years of Education by using them as
nuisance covariate. Would you please explain:
Why the covariates should be demeaned?
Is subtracting the mean from each individual the only way of demeaning?
How Qdec regress out the effect of the covariates , linear o
Hi Chris
you need to use mri_surf2surf
cheers
Bruce
On Mon, 13 Jan 2014, Chris McNorgan wrote:
> Hi,
>
> I wanted to confirm whether spherical inflation generates meshes with
> the same number of vertices across individuals? Or would you have to use
> something like mri_surf2surf to map everyone'
Hi,
I wanted to confirm whether spherical inflation generates meshes with
the same number of vertices across individuals? Or would you have to use
something like mri_surf2surf to map everyone's sphere to a template sphere?
Thanks,
Chris
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It has not been incorporated into QDEC. You will have to use mri_glmfit.
doug
On 01/13/2014 03:59 AM, Sophie Maingault wrote:
> Dear FS experts,
>
> I followed this page to measure LGI : http://freesurfer.net/fswiki/LGI
> I wanted to use it in QDEC, so after running recon-all –cache for
> pial_l
If there is no interaction, then either DODS or DOSS is appropriate.
DOSS will be more powerful and a little more interpretable. If there is
an interaction then DODS must be used, and the interpretation of the
difference between groups becomes more problematic. Eg, if age is the
covariate, and
What do you mean by a volume of a single subject? We have tools to do
surface-based interhemispheric analysis
http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
doug
On 01/13/2014 05:28 AM, Shani Ben Amitay wrote:
> Hello freesurfers
>
> I would like to preform inter-hemispheric comparison (or
> he
Hi all,
I have 4 years of structural scans from children and 2 from adults. I would
like to analyze the data both cross-sectionally and longitudinally. In the
recommendations for the longitudinal analysis, it says one should process all
images in one folder with the time point in the subjectID/
Hello freesurfers
I would like to preform inter-hemispheric comparison (or
hemispheric asymmetry) for a volume of a single subject.
what would be the best way to do it?
Thanks
Shani
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Freesurfer@nmr.mgh.harvard.edu
https://mai
thank you
Von: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu]
Gesendet: Sonntag, 12. Januar 2014 03:10
An: Roschinski, Benjamin
Cc: freesurfer@nmr.mgh.harvard.edu; gerit.pf...@gmail.com
Betreff: Re: b value for TRACULA
Hi Benjamin - The ball-and-stick mod
Dear FS experts,
I followed this page to measure LGI : http://freesurfer.net/fswiki/LGI
I wanted to use it in QDEC, so after running recon-all cache for pial_lgi,
I created the $SUBJECTS_DIR/qdec/.Qdecrc with MEASURE1 = pial_lgi but I
don't see it in the measures menu. Do you know why ?
Best reg
Hey All,
I am sorry to jump into this discussion. I know how to check the slope
difference between groups. I want to ask help from you to confirm that if
difference in thickness in some brain areas arising from (0 0 1 -1)
happens, it means that there is a group * age interaction, right?
Then, th
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