Hi Freesurfer experts,
I am trying to run tracktography from freesurfer labels using
probtrackx2 in fsl. To convert the labels to surfaces I use the
label2surf command as recommended on the fslwiki. To use the label2surf
command I need to convert the surface, e.g. lh.white into a
Dear Freesurfer experts,
I want to know if possible when doing longitudinal stream to put subjects
with only one time-point through the processing (eg base and long runs) in
order to subsequently use with the Matlab lme tools? Or better is to leave
them out and only do those with 2+ times?
Thank
Dear FreeSurfer experts,
I have two binary factors (F1: F1L1 F1L2; F2: F2L1 F2L2), 1 covariate (COV),
and 1 nuisance factor (NUI). I want to make sense of some specification of the
regressors and contrasts.
Because they are not described in
http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G1V, I
Hi all
When you loaded the lowb into freeview and it looked registered with the
anatomical, did you load the lowb with the registration file? If not,
then the registration may be wrong. Things may look almost right when
you don't specify a registration file because you probably collected the
Hi all,
I am trying to run fReadQdec.m. My qdec.table.dat file is a tab delimited file.
However when it reads to Qdec variable it reads it as N(# of subjects)X1 cell
(discounting for all tabs and spaces). I tried debugging the code but it seems
to me like it is just a simple read file in
yes, it has a certain format. Look at the examples on the wiki
doug
On 02/18/2014 11:19 AM, sabin khadka wrote:
Hi all,
I am trying to run fReadQdec.m. My qdec.table.dat file is a tab
delimited file. However when it reads to Qdec variable it reads it as
N(# of subjects)X1 cell (discounting
That looks right to me
doug
On 02/18/2014 10:08 AM, Yang, Daniel wrote:
Dear FreeSurfer experts,
I have two binary factors (F1: F1L1 F1L2; F2: F2L1 F2L2), 1 covariate
(COV), and 1 nuisance factor (NUI). I want to make sense of some
specification of the regressors and contrasts.
Because
This GLIBCXX error appears when running our Centos 6 build on an older
OS. Try using our Centos 4 build.
Nick
On Mon, 2014-02-17 at 09:32 -0500, Bruce Fischl wrote:
yes, it certainly looks like a library problem. You should talk to your
sysadmin, or perhaps Zeke or Nick can comment
cheers
Thanks Doug! One follow-up question: since it's [0.25 0.25 0.25 0.25], would
the effect be biased toward large sample sizes in one of the groups (versus the
other groups)?
Or, does FreeSurfer qdec take care of the unequal cell, in a possible way
analogous to using Type III SS in the
It will tend to weight smaller groups by a proportion greater than the
number of subjects in the group.
On 02/18/2014 01:58 PM, Yang, Daniel wrote:
Thanks Doug! One follow-up question: since it's [0.25 0.25 0.25
0.25], would the effect be biased toward large sample sizes in one of
That helps a lot. Thanks Anastasia:
best,
Alan
On Mon, Feb 17, 2014 at 11:04 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
Hi Alan - If you're using a standard MGH diffusion sequence and you have a
Martinos account, look for the appropriate gradient table in this directory:
Hi Anna,
the linear mixed effects models can include subjects with a single time
point and it would be a shame to drop that information. That is why we
modified the longitudinal pipeline (use 5.3) to allow processing of
subjects with a single time point. However, it is necessary that these
Hi Doug,
Thanks for the reply. Yeah I have my
qdec.table.dat file in the same format as wiki says and in tab delimited
format. But when I try to run fReadQdec it reads it as
N(# of subjects)X1 cell (discounting for all tabs and spaces). I was
assuming it would give me N X M(no of columns for
where did you get this m file from? I don't see it in our distribution.
On 02/18/2014 03:29 PM, sabin khadka wrote:
Hi Doug,
Thanks for the reply. Yeah I have my qdec.table.dat file in the same
format as wiki says and in tab delimited format. But when I try to run
fReadQdec it reads it as
Its under freesurfer/matlab/lme/Qdec. This is what is suggested to use while
performing linear mixed effects models in freesurfer.
http://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels
On Tuesday, February 18, 2014 3:35 PM, Douglas N Greve
gr...@nmr.mgh.harvard.edu wrote:
where
Doug, sorry, I am not sure I can fully understand.
Do you mean the results are weighted MORE toward groups with smaller sample
sizes (than groups with larger sample sizes)?
--
Daniel (Yung-Jui) Yang, Ph.D.
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
Tel: (203) 737-5454
E-mail:
Let's say you have four groups with 10 20 30 40 (100 total). The first
group would get a weight of .25 where it only had 10% of the total. I
don't think there is any way around this.
On 2/18/14 4:07 PM, Yang, Daniel wrote:
Doug, sorry, I am not sure I can fully understand.
Do you mean the
Thanks SO much!
I'll let you know if I have further problems.
Thanks again.
Best,
Pietro
Inviato da iPhone
Il giorno 18/feb/2014, alle ore 16:38, Louis Nicholas Vinke
vi...@nmr.mgh.harvard.edu ha scritto:
Hi Pietro,
There were some disconnected pieces of wm on the wm.mgz which was
Hello Everyone,
I am facing small problem to create my own file
////
saurabh@saurabh-Precision-WorkStation-T3500:~/Desktop/saurabh_freesurfer/bert/sam$
mri_convert -i /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/IM_0001 -o
$SUBJECTS_DIR/bert/mri/orig/005.mgz
command i m using is
:mri_convert -i /home/saurabh/Desktop/saurabh_freesurfer/bert/sam/IM_0001
-o $SUBJECTS_DIR/bert/mri/orig/005.mgz
cheers
Saurabh Thakur,
On Wed, Feb 19, 2014 at 12:22 PM, Saurabh Thakur srbht...@gmail.com wrote:
Hello Everyone,
I am facing small problem to create
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