Dear Martin,
Yes I think so, and I run the mri_glmfit with fsaverage as the subject like:
mri_glmfit --glmdir lh.thickness.rmanova --y lh.thickness.sm05.mgh --fsgd
rmanova.fsgd doss --C tp1-vs-tp2.mtx --C tp1-vs-tp3.mtx --C tp2-vs-tp3.mtx
--C tp-effect.mtx --C mean.mtx --surf fsaverage lh
it
Hi Sophie
mris_spherical_average is an alternative to mri_label2label and takes
labels in the individual subject spaces, not fsaverage.
cheers
Bruce
On Thu, 30 Jan
2014, Sophie Maingault wrote:
Dear FS experts,
I have some troubles when I'm trying to use the command
Hi,
Would you please advise if it is possible to do longitudinal statistical
analysis within a group with two time points in Qdec. And if it is not
possible in Qdec how I suppose to do it?
Best regards,
Amirhossein Manzouri
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Dear Kaiming,
how many subjects do you have? only 1? You need to have more data to run
a glm (your degrees of freedom is 0 , see error message).
Your other question:
you can select any target for running your analysis. But usually people
do not select one of the subjects from the study,
Hello,
I am running reg-feat2anat and facing some problems.
First I ran the command in its default mode using FSL initialisation
reg-feat2anat --feat featdir.feat --subject s. That gave me a bad registration.
There is a warning coming up
WARNING: initial G-W contrast is negative, but
Technically, you are on safe ground using DODS in that I don't think a
reviewer would object. However, I would be a little worried as to
whether the group difference is real. Does DOSS start to look like DODS
if you lower the threshold? Try running DODS with and without demeaning
the
Hi Sophie
can you visualize each of the individual subject labels to make sure that
they look ok? You also need to specify -o fsaverage to use fsaverage as the
output subject, otherwise it will assume that the last subject in your list
is the output subject (this is why your output label
you can't do it in qdec, use the command line stream, ie,
mris_preproc, mri_surf2surf to smoooth, mri_glmfit, and mri_glmfit-sim
doug
On 01/30/2014 09:18 AM, amirhossein manzouri wrote:
Hi,
Would you please advise if it is possible to do longitudinal
statistical analysis within a group with
The second warning you don't need to worry about. I should change that
to not be a warning. reg-feat2anat is only registering the functional
and anatomical. If the registration to mni152 does not look good, then
that is an FSL issue
doug
On 01/30/2014 11:06 AM, Mariam Sood wrote:
Hello,
I
Can you post a screenshot?
Ruopeng
On 01/30/2014 12:58 PM, Markus Gschwind wrote:
Dear Experts,
I have installed Freesurfer 5.3 under ubuntu 12.04.
It is running fine except for Freeview which is causing heavy graphic
trouble (thousands of colored squares in the black fields where the
Dear Experts,
I have installed Freesurfer 5.3 under ubuntu 12.04.
It is running fine except for Freeview which is causing heavy graphic
trouble (thousands of colored squares in the black fields where the brains
should be displayed.
Tksurfer is working fine.
Glxgears is showing the rotating
Hi Christine
if you upload this subject we will take a look
cheers
Bruce
On Thu, 30 Jan 2014,
Christine Smith wrote:
Hello,
The parcellation of grey and white matter appears to be off in several
T1-weighted structural scans I have been processing. The effect is observed
in the temporal
You might also want to read about mean centering and same or different
slopes here:
*http://mumford http://mumford*.fmripower.org/*mean*_*centering*/
Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Hi Kaiming,
thickness is not a surface, it is a function defined on a surface. Don't
add it as a surface name to the command line.
Best, Martin
On 01/30/2014 11:12 AM, Kaiming Yin wrote:
Dear Martin,
Make sense now. thanks for this. Yes I only have one subject with 3
different time
Hi Wanda, I can see that it is failing, I just can't see why it is
failing (and cannot replicate it here). Can you try a couple of things.
First, make sure that the disk is not filling up. Next, can you try it
with, say, half the subjects? Does this always occur or is it just recently?
doug
Hi Doug,
I currently have 40.64 GB of disk space (is this enough)?
I tried just now with half the subjects and it gave me the same error. I
was successful in completing a thickness analysis using this same method,
the only thing difference this time is that I am trying to do a surface
area
Hi Daniel,
1. yes. But why not include 6 month in your study if you have those
scans??? You will get much more reliable slope estimates with 3 time
points compared to 2, so including that time point will not only help
for the image processing part, but also in your statistics (you gain
That should be enough space. Can you try it with the other half? I'm
thinking it might be one subject who is messing things up.
On 01/30/2014 04:04 PM, Wanda Truong wrote:
Hi Doug,
I currently have 40.64 GB of disk space (is this enough)?
I tried just now with half the subjects and it
Hi,
with one group you want to check if atrophy is significantly different
from zero? That is probably the case for any group (e.g. aging), so it
won't tell you anything really. Also, if you don't find atrophy in a
region it doesn't mean it's not there (only your group size is too small
to
Hello Marie,
I am trying to conduct a local gyrification index analysis, however I am
getting this error ERROR: make_roi_paths did not complete successfully!
Which is the same as the one posted earlier by someone else:
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-July/032203.html
Hi Doug,
Same thing happens with the other half. I'm wondering what file is used for
Y - is it lh.area.fwhm10.fsaverage.mgh? and why does it have an input
number that is different from X, which should be the number of subjects?
Thanks,
Wanda
On 30 January 2014 14:19, Douglas N Greve
Hi Wanda,
I'm not sure to understand your problem. Do you get an error because of using
matlab 2013? If yes, I'm not sure to understand whether you modified the
SearchProjectionOnPial.m function properly.
Can you download the updated function there:
I don't know, it is a bit bizarre. Can you run mri_info on both
lh.area.fwhm10.fsaverage.mgh and Untitled/y.mgh and send me the results?
On 01/30/2014 05:01 PM, Wanda Truong wrote:
Hi Doug,
Same thing happens with the other half. I'm wondering what file is
used for Y - is it
Linda, try demeaning your covariates and see if the problem goes away
doug
On 01/30/2014 03:24 PM, Linda Zhang wrote:
Dear all,
Whilst running mri_glmfit, the following error occurred:
ERROR: matrix is ill-conditioned or badly scaled, condno = 12375.1
I've attached the design matrix, the
Thanks Doug. Can that be done within the fsgd file/command line?
I've read threads on demeaning but was never clear on how to do it
automatically.
Linda
On 30 January 2014 14:34, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote:
Linda, try demeaning your covariates and see if the problem goes
No, sorry, you'll have to create a new FSGD. Just compute the mean of
each covariate, then subtract the mean from the value for each subject.
doug
On 01/30/2014 05:46 PM, Linda Zhang wrote:
Thanks Doug. Can that be done within the fsgd file/command line?
I've read threads on demeaning but
Hi Martin,
Thanks for the help of glm, I also try the QDEC table for the 3 times
points of 1 same subject k. k was scanned at Aug-2012, May-2013, and
Jul-2013. A little confusion here is should I record the time as which one
of these:
(1) --time years (2) --time months (3) --time ages
Hi all,
I used freesurfer to process my anatomical scans, followed by BBregister
to align my resting state scan to the anatomical and finally afni to
process the resting state fmri scans. After recon-all I used bbregister:
*bbregister -s ${sub}_FS --mov ${sub}.RS.nii --reg
Hi all,
I have an annotation for fsaverage that I would like to convert into a
subject's space.
Up to now, the only way I found to do that was to convert my annotation to all
its labels, and then rebuilt the annotation in the subject's space from the
labels, using the following 3 steps
Hi,
If control points are only added to one hemisphere, is it ok to use the -hemi
flag together with -autorecon2-cp -autorecon3 for recon-all?
Thanks,
P
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Freesurfer@nmr.mgh.harvard.edu
Hi Kaiming,
1. Depends on what you are interested in (atrophy per month or yearly rate ,
select 1 or 2). To include age I'd make a column with age at baseline or mean
age of the subject's time points, not time varying.
I have no clue what you are looking at, but the significance maps should not
Yes, it should be
Bruce
On Jan 30, 2014, at 8:18 PM, silve...@gmx.com silve...@gmx.com wrote:
Hi,
If control points are only added to one hemisphere, is it ok to use the -hemi
flag together with -autorecon2-cp -autorecon3 for recon-all?
Thanks,
P
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