Hi,
I have calculated the group differences for volume using both
FreeSurfer GLM and SPSS GLM. I have used gender and group as fixed
factor and intercranial volume and age at MRI scan as covariate.
GroupDescriptorFile 1
Title group_difference_between_group1_and_group2_gender_age
DeMeanFlag 1
C
HI,
I solve my problem. The FreeSurfer GLM model is easier to use than SPSS
GLM. I had force SPSS to look at my model by selecting group differences
between group1 and group2 and look at interactions between the three
groups. I then got similar results as in FreeSurfer glm for the group
diffe
Dear Dr. Fischl,
Thank you for your respone. What would the --reg and the --temp be in this case?
Massieh
> Original message --
>From: Bruce Fischl
>To: mmoay...@uhnres.utoronto.ca->
>cc: freesurfer@nmr.mgh.harvard.edu->
>Subject: Re: [Freesurfer] Label to ROI
Ok I will. Thanks for your help! :)
Sergio.
2012/7/30 Anastasia Yendiki
>
> Hi Sergio - Sorry, if this occurs independently of trac-all, whenever you
> run bedpostx directly, you're better off asking for help on the FSL list.
> We've never run into this problem with bedpostx up till now.
>
> a.
it depends what volume geometry you want the output in. If our standard
one you would do
--identity --temp $SUBJECTS_DIR/$subject/mri/orig.mgz
although Doug is the expert!
cheers
Bruce
On Tue, 31 Jul 2012, mmoay...@uhnres.utoronto.ca wrote:
> Dear Dr. Fischl,
>
> Thank you for your respone.
Anastasia,
We might try installing FSL + FreeSurfer in another machine, because the
one we were using was too slow anyway.
Would you mind telling us exactly which versions of FreeSurfer and FSL I
need to install?
As I will mostly/only use Tracula then I would rather install the version
of FSL that
Yes, default is fine! Just run bedpostx with the path to the dmri
directory as the only argument, that should work.
On Mon, 30 Jul 2012, Gonzalo Rojas Costa wrote:
> Hi Anastasia:
>
> And, which options do you think I must use with bedpostx ?... The default
> ?...
>
> Sincerely,
>
>
> Gonzal
Well, when the current version of tracula was being developped we had FSL
4.1.5 installed here. But now that the next version (you know, the one
that will be available "soon") is being developped we have FSL 4.1.9. So
I'd suggest going with the latest version of FSL. The only thing that
shoul
Dear FreeSurfer Experts,
I am using Freesurfer version 5.1 over at the University of Pennsylvania,
and I have been running into issues with the optic chiasm. Despite having
edited it out on both the brainmask.mgz and wm.mgz volumes, FreeSurfer has
been insisting that it be included as a surface on
Hi Peter
what did you run after editing it out of the wm.mgz? You should be running
-autorecon2-wm -autorecon3
cheers
Bruce
On Tue, 31 Jul 2012,
Peter McNally wrote:
> Dear FreeSurfer Experts,
>
> I am using Freesurfer version 5.1 over at the University of Pennsylvania,
> and I have been run
Hi Bruce,
Thank you for your speedy response. Yes, I ran -autorecon2-wm -autorecon3.
Best,
Peter
On Tue, Jul 31, 2012 at 2:03 PM, Bruce Fischl wrote:
> Hi Peter
> what did you run after editing it out of the wm.mgz? You should be running
> -autorecon2-wm -autorecon3
>
> cheers
> Bruce
>
>
>
> O
hmmm. And are the edits reflected in the filled.mgz? Is the chiasm gone?
How about in the ?h.orig and ?h.orig.nofix?
On Tue, 31 Jul 2012, Peter
McNally wrote:
> Hi Bruce,
>
> Thank you for your speedy response. Yes, I ran -autorecon2-wm -autorecon3.
>
> Best,
> Peter
>
> On Tue, Jul 31, 2012
Hi Massieh, use something like
mri_label2vol --label lh.V1.label --regheader orig.mgz --temp orig.mgz
--o lh.V1.mgz
doug
On 07/31/2012 05:46 AM, mmoay...@uhnres.utoronto.ca wrote:
> Dear Dr. Fischl,
>
> Thank you for your respone. What would the --reg and the --temp be in this
> case?
>
> Mass
Subject 20 is definitely out of synch, but the "make all" feature is not
catching it. Try re-running this subject with -autorecon3
doug
On 07/25/2012 11:45 AM, Gibbard, Clare wrote:
> Hi Bruce,
>
> Thanks, I've attached the end of the recon-all.log file for one of the
> subjects (the whole thi
Whoops forgot to select reply all... Yes I am erasing the chiasm using
tkmedit--I'll rerun autorecon-wm now and send the recon-all.log results
when they finish (probably) tomorrow.
Thank you,
Peter
On Tue, Jul 31, 2012 at 2:34 PM, Bruce Fischl wrote:
> can you cc the list on these emails? And tr
make sure it creates the filled without error, and if so, check the
filled to make sure that the edits to the wm are present in it (I don't
know why they wouldn't be though)
On Tue, 31 Jul 2012, Peter McNally
wrote:
Whoops forgot to select reply all... Yes I am erasing the chiasm using
tk
Hello,
If I were to run a DODS -- say, an F-test looking for group
differences and interactions in thickness among drug users vs non-
users, dependents vs abusers, and drug use in the last month vs no use
in the last month -- how would I visualize the results? I assume
there's no intelligib
Right, that would be a post hoc analysis.
doug
On 07/31/2012 03:46 PM, Ian Carroll wrote:
> Hello,
>
> If I were to run a DODS -- say, an F-test looking for group
> differences and interactions in thickness among drug users vs non-
> users, dependents vs abusers, and drug use in the last month vs
Hi Doug,I re-installed freesurfer, and I still get the same error message (terminal output attached); bin files are still missing from bin folder.Shall I report this as a bug?Regards,Fidel
Last login: Tue Jul 31 12:51:32 on ttyp2
Welcome to Darwin!
a3128u:~ FVila$ export FREESURFER_HOME=/Applicatio
And there is nothing in /Applications/freesurfer/bin? Are there any files in
the other directories? Do you have permission to install it in that location?
If nothing is in the bin dir, then there is no need to try recon-all, it will
always fail.
doug
On 07/31/2012 04:05 PM, Fidel Vila wrote:
Hi All,
I am trying to do cortical thickness analysis on a single subject's
longitudinal data. I am attaching the design and group.diff.mtx could any one
tell me whether they are correct.
Thanks
venkat
===
Please consider the environment before printing this
yes they are, but it is going to fail because you will not have any
degrees of freedom. What are you trying to do? You can't make inferences
from a single subject like this.
doug
On 07/31/2012 05:10 PM, Rajagopalan, Venkateswaran wrote:
>
> Hi All,
>
> I am trying to do cortical thickness analys
Hi
also we have tools to compute within subject differences (or slopes in
case of several time points) as well as percent changes before mapping
to fsaverage (long_mris_slopes, see the longitudinal tutorial on the
wiki).
Best, Martin
On Tue, 2012-07-31 at 17:10 -0400, Rajagopalan, Venkateswaran
> And there is nothing in /Applications/freesurfer/bin?
There are 357 items in /Applications/freesurfer/bin
> Are there any files in the other directories?
Indeed, from /Application/freesurfer/average (50 items in here) to /
Applications/freesurfer/trctrain (35 items) as well as 'LICENSE' file,
Hi,
So when using command tkmedit *subjID* brainmask.mgz -aux -wm.mgz -surfs I
receive the message:
"Error: Parsing -aux option
Expected an argument
This option needs an argument: the image type, directory, or file name of
the data to load as the aux volume."
My apologies if there is an obvious
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