thank you. and one other question; rather than putting years as the time
variable, can i do time 1 (for baseline) and 2 (for follow-up), and jsut
control for time between scans instead?
On Fri, Jun 13, 2014 at 5:42 PM, Martin Reuter
wrote:
> Hi Anna, whenever it says qdec-long the table is in q
Hi Anna
I am not a statistician, but I would not control for duration separately, but
rather use the time variable for that.
It does not need to be in years (can be days out months).
Measures closer in time are more correlated than measures further apart. Lme
makes use of that information throug
HI Liesel
is it possible you are running out of RAM? Or disk space?
cheers
Bruce
On Tue, 24 Jun
2014, Liesel-Ann Meusel wrote:
Hi,
I am running recon-all and I am getting the following error during the
mri_ca_register step (full log
file is attached). Please let me know what I need to do t
Hi Freesurfer experts,
I tried running trac-all with my config file and received the following
error :
Segmentation fault
Linux 129-x-xx-xxx 3.4.33-2.24-desktop #1 SMP PREEMPT Tue Feb 26 03:34:33
UTC 2013 (5f00a32) x86_64 x86_64 x86_64 GNU/Linux
trac-paths exited with ERRORS at Tue Jun 24 11:15:
Thank you. I just another question about the fsid groupings for the qdec
table for lme. If in the qdec I specify only the fisid (eg nt the
longitudinally processed subject with XX.long), and the XX.longs are in a
different folder, than how when I do the matlab lme tools does freesurfer
know to use
Hi Dorian
if you want to avoid overlap you might need to cobble together a procedure
yourself - probably converting the annots to labels then removing the
overlap and recombining into an annot. It wouldn't be that hard to do in
matlab.
For you second question you are probably best off drawin
Hi Freesurfer experts,
Is it possible to change the dependent variable of a whole hemisphere's
thickness to a specific brain region's thickness? For example I wish to
test one of my independent variables with right hemisphere superior
parietal region's thickness as opposed to the whole right hemis
You can run aparcstats2table to get a table of the means of each ROI for
each subject. Then pass that to mri_glmfit with --table instead of --y
with the other options being the same
doug
On 6/24/14 12:05 PM, Chris Wertz wrote:
Hi Freesurfer experts,
Is it possible to change the dependent
That will work, thank you very much.
Chris
On Tue, Jun 24, 2014 at 10:29 AM, Douglas Greve
wrote:
>
> You can run aparcstats2table to get a table of the means of each ROI for
> each subject. Then pass that to mri_glmfit with --table instead of --y with
> the other options being the same
> doug
Dear Freesurfer experts,
My dataset was processed by Brainsuite, so that after registration they are
in .dfs format.
Now I wanted to do multiple comparison correction. How do I import the data
to freesurfer and do the corrections?
Thanks.
Miao
___
Freesur
Hi Anna,
the matlab tools don't know. They only look at the other co-variates that you
might want to include into your study (the fsid-base for grouping, the time
variable and others from the table). The stack of thickness maps needs to be in
the same order as the rows in the qdec table. That
Hi Freesurfers,
I am reposting this as my last email bounced.
I have conducted a DODS analysis in qdec with group (controls vs patients)
set as my fixed factor and age as a nuisance variable to determine if my
groups differ in cortical thickness. Controls were added first in the
.levels file follo
Hi Mio, sorry, I have no clue, I've never used Brainsuite. If you have
each subject's thickness in a common space, you could convert it to mgh
format and then run mri_glmfit and mri_glmfit-sim
doug
On 06/24/2014 01:16 PM, Miao Wei wrote:
> Dear Freesurfer experts,
> My dataset was processed b
Hi Douglas,
Thanks for getting back to me. Which software can help me to convert the
files to mgh format? I found one called MNE. Do you happen to have any
experience with this one?
Miao
Douglas N Greve
>于2014年6月24日星期二写道：
>
> Hi Mio, sorry, I have no clue, I've never used Brainsuite. If you have
I have not used MNE. I'm cc'ing Matti who is the MNE author
doug
On 06/24/2014 04:32 PM, Miao Wei wrote:
> Hi Douglas,
> Thanks for getting back to me. Which software can help me to convert
> the files to mgh format? I found one called MNE. Do you happen to have
> any experience with this one?
Hi Doug,
Is it possible that I need to use an f-contrast or input the weights in a type
of matrix? I’ve been asking around and I’ve gotten that as a suggestion,
although I’m not exactly sure what that means and how I’d do it.
Thanks,
Stephanie
Stephanie N. DeCross
Clinical Research Coordinator
Hello!
I'm a begginer user with this programm and i need some help, please!
I was wondering if it's possible to get an output only for WM segmentation
but excluding the filling in of CSF and/or hyperintensities? And if so,
would it be possible to convert this to nii ?
Thank you!
Ale
_
Hi Ale
I guess the best way to do this would be to use mris_fill to fill the
interior of the ?h.white surface, then remove every voxel in the
resulting volume that isn't one of:
left/right cortex, left/right white matter, any callosum label
cheers,
Bruce
On Wed, 25
Jun 2014, Alejandra Machado
Dear FreeSurfer Experts:
I have question regarding extracting the individual or average cortical
thickness value of significant cluster after multiple compression
correction by FDR. For example I have 100s of subjects in an analysis and
several blobs showing significant difference between groups a
Thank you. Hopefully I can do this since my data won't survive fdr
correction in matlab. And there are no other options available for the
correction.
Miao
On Tue, Jun 24, 2014 at 1:19 PM, Douglas N Greve
wrote:
>
> Hi Mio, sorry, I have no clue, I've never used Brainsuite. If you have
> each s
Thanks.
I would like to start learning and using freesurfer.
I have a DICOM MRI of the brain which has a tumor in it. I would like to
segment this tumor as automatically as possible. Can I segment only one
slice so it propagates through the adjacent slices? Which tool in
freesurfer do I need to use
Dear list,
I am resending this message as I don’t know if it went through.
Does the OS version, hardware or MatLab version (i.e., 2013a vs. 2014a) impacts
in the results from the LME processing (Bernal-Rusiel et al.)?
The LME is to be used for a Freesurfer 5.1/5.3 longitudinal pipeline.
Regards,
P
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