Hi Katie
you can view data on a tal brain by mapping the data using the
talairach.xfm transform. Since you can also use the inverse of the
transform you can map both ways. I think there is a tcl command in tksurfer
for finding the vertex that is closest to a given tal coord. Try:
select_tal
Hi Shannon, sorry for the delay. There are several ways you can do this.
If you already have a slope for each subject, then just use that as
input and use the simple two group FSGD file. If you really want to do
the RM ANOVA, then there are two ways. The simpler way is to create a
"stack" of al
Instead of FTP, you could try getting the files via HTTP at
http://surfer.nmr.mgh.harvard.edu/ftp/dist/freesurfer/
-- Paul Raines (http://help.nmr.mgh.harvard.edu)
On Tue, 4 Sep 2012 6:19pm, Dix Meiberth wrote:
Thx for your responses. But no, I try to copy to my harddrive on my 1 year old
Hi Longchuan, when I asked for the terminal output, I meant the stuff
that gets printed to the screen when the command runs. Try running it
outside of your script to capture the output. Also, does the old program
require 20G ?
doug
On 08/27/2012 04:20 PM, Longchuan Li wrote:
> Hi, Doug
> Here i
Thanks Bruce,
Still no luck,this what I am getting
/freesurfer/subjects/test1> recon-all -i
/media/sf_freesurferstudys/raw/raw_scr/T1pre/Image1.dcm -subjid test7
-all Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0
Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0
INF
Is that the actual name of the file? Does it have a dcm extension?
On Wed, 5
Sep 2012, Varghese, Chikku wrote:
> Thanks Bruce,
> Still no luck,this what I am getting
>
>
> /freesurfer/subjects/test1> recon-all -i
> /media/sf_freesurferstudys/raw/raw_scr/T1pre/Image1.dcm -subjid test7 -all
>
Hi Clark, I just made a modification to mri_binarize to make it take an
FDR as input. It computes the threshold and binarizes the input based on
the threshold. I've put a copy here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_binarize.linux
Run it with --help to get more
Nick, List:
Still no luck with this data. See attached as an example.
To get to this point I had run:
recon-all -all
This ran to the error: mri_watershed Error: GLOBAL region of the brain
empty !
Then I followed your recommendation below
recon-all -s -skullstrip -no-wsgcaatlas
Hi Susan, I've updated that web page to demonstrate how to run the
random effects analysis. Let me know if that is clear or not.
doug
On 08/23/2012 12:38 PM, Susan Alice McLaughlin wrote:
> Hi,
>
> I'm resending this e-mail, as it didn't seem to go through correctly
> yesterday:
>
> I’m a Freesu
Hi again,
This is a follow-up question to my previous email -- the method I used may
not be the most efficient or the correct way to extract cortical thickness
from manually created ROIs. I'm unfamiliar with how to obtain thickness
data from a label, so I'm not sure if what I did is correct or if
Hi Darren
can you describe your input data? What format, resolution, etc... is it?
If you upload it we'll take a look
cheers
Bruce
On Wed, 5 Sep 2012, Darren Gitelman
wrote:
Nick, List:
Still no luck with this data. See attached as an example.
To get to this point I had run:
r
Bruce:
Thank you for looking. I have uploaded the files:
I uploaded them in Dicom Format.
This is a T1, MPRAGE, image, acquired with GRAPPA, resolution 1x1x1.
Name: 3157.tar.gz
Darren
On Wed, Sep 5, 2012 at 11:27 AM, Bruce Fischl wrote:
> Hi Darren
>
> can you describe your input data? What f
Hello,
I got mri_ca_train to complete and to produce a .gca file, which looks to be
what is expected after splitting it up into means/labels/priors files.
The problem was the norm.mgz file. I ended up copying and renaming the T1.mgz
file to replace the norm.mgz file, and it seemed to work in mr
Ok, I am trying to use the select_talairach_point command, and I have it
in part of a script that uses tksurfer to load up a subject's inflated
surface, load the curvature, and load an overlay, but it doesn't seem to be
doing anything. Is there a step I am missing? What should I see if it
works
I don't think you actually want to do the full conformation as that will
change the type to uchar, which is probably what is messing up your
values. Instead, try this
mri_vol2vol --mov aseg.mgz --targ orig.mgz --regheader --interp nearest
--precision int --o aseg.conf.mgz
doug
On 09/05/2012
what is your mri_convert command line?
On Wed, 5 Sep 2012, Jeff Thompson wrote:
Hello,
I got mri_ca_train to complete and to produce a .gca file, which looks to be
what is expected after splitting it up into means/labels/priors files.
The problem was the norm.mgz file. I ended up copying and
Hi Jeff, sorry, what do you mean to covary for a categorical variable?
doug
On 09/05/2012 12:43 AM, Jeff Sadino wrote:
> Hello,
>
> Is it possible to covary for a categorical variable in QDEC? I see
> other posters have said it is not possible, but I did not see
> any official documentation or
Nevermind, it turns out it was due to an permissions error.
Thanks again.
Katie
On Wed, Sep 5, 2012 at 12:53 PM, Katie Bettencourt wrote:
> Ok, I am trying to use the select_talairach_point command, and I have it
> in part of a script that uses tksurfer to load up a subject's inflated
> surfac
Darren,
I forgot to mention that you'll need to add
-clean-bm
after the -no-wsgcaatlas flag, otherwise the prior brainmask.mgz will be
retained and the new one will be saved as brainmask.auto.mgz.
Nick
On Wed, 2012-09-05 at 09:54 -0500, Darren Gitelman wrote:
> Nick, List:
>
>
>
> Still
Deirdre,
this is the infamous 'sliver' problem. consult this page for solutions:
https://surfer.nmr.mgh.harvard.edu/fswiki/TksurferDisplayProblems
Nick
On Wed, 2012-09-05 at 13:39 -0400, Deirdre O Shea wrote:
> Hello,
>
> I am just getting to get grips with using FreeSurfer to reconstruct
>
Hello,
I am trying to covary for Gender in mri_glmfit, but I am having errors pop
up. I tried to follow Doug's suggesting in this post:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg12272.html
but after modifying my Xg.dat file and rerunning mri_glmfit, it says:
ERROR: matrix is i
I still don't know what you mean by covarying for gender. What is your
design? Can you send your FSGD file?
doug
On 09/05/2012 04:44 PM, Jeff Sadino wrote:
> Hello,
>
> I am trying to covary for Gender in mri_glmfit, but I am having errors
> pop up. I tried to follow Doug's suggesting in this p
I'm running it now with the current dev version and it's passed the skull
stripping stage and it seems to have worked fine...
On Wed,
5 Sep 2012, Nick Schmansky wrote:
> Darren,
>
> I forgot to mention that you'll need to add
>
> -clean-bm
>
> after the -no-wsgcaatlas flag, otherwise the prior
Bruce
I used the following
version: freesurfer-x86_64-redhat-linux-gnu-stable5-20110522
Is that the same as the one you are using or are you referring to an
internal development version?
I will try Nick's suggestion as well.
Darren
On Wed, Sep 5, 2012 at 4:05 PM, Bruce Fischl wrote:
> I'm run
Nick
I ran: recon-all -skullstrip -no-wsgcaatlas -clean-bm -s 3157
and got the exact same problem with brainmask.mgz
Darren
On Wed, Sep 5, 2012 at 3:37 PM, Nick Schmansky wrote:
> Darren,
>
> I forgot to mention that you'll need to add
>
> -clean-bm
>
> after the -no-wsgcaatlas flag, otherwis
our internal development version.
On Wed, 5 Sep 2012, Darren Gitelman
wrote:
Bruce
I used the following
version: freesurfer-x86_64-redhat-linux-gnu-stable5-20110522
Is that the same as the one you are using or are you referring to an
internal development version?
I will try Nick's suggestion
Hello,
I think our emails were getting crossed in cyberspace. I have a group that
has a disproportionate number of females, and so there is a significant
difference in the number of females as compared to males (chi-square
p=.01). This must be accounted for. If I find that one group has a
small
Use gender as a discrete variable in the FSGD, ie, a class for M and a
class for F. If you have two other groups (say, normals and patients),
then use four classes (Mnormals, Mpatients, etc). Then test for the
normals vs patients with (Mnorm+Fnorm) - (Mpat+Fpat). This "regresses
out" gender.
28 matches
Mail list logo
