If I do "3dcopy ortho+orig ortho.nii" then 3dinfo shows that the two datasets
share the same coordinate system, however when I use mri_info, the results differ. For
example,
3dinfo, both .BRIK and .nii:
Geometry String: "MATRIX(0,0,-1,127,1,0,0,-127,0,-1,0,180):256,256,256"
R-to-L extent: -1
As far as I can see the levels file should have
Male
Female
as its contents.
Check if the you have used in the qdec.table.dat file, is it
the with same name? E.g. if you have the field as SEX, then the
file should be called
Hth,
Shantanu
PS: could you CC freesurfer list as well?
On Mon,
Hi Pietro,
See if using an empty newline after
886 7.386721424 Male ADHD 72 8 25
in your Qdec table solves the problem.
Hth,
Shantanu
On Mon, November 19, 2012 3:28 pm, pietro de rossi wrote:
> Hi all,
>
> I tried to load a tiny data table in qdec following directions on the wiki
> online
>
>
Hi, Doug
I tried bbregister and checked the registration using tkregister2. It seems
that this program registers the diffusion image with the anatomical *volume*
images in FreeSurfer, such as brain.mgz. My problem is a little unique: I am
working on monkey data and I found that my ?h.white surf
Hi all,
I tried to load a tiny data table in qdec following directions on the wiki
online
I get this error
Loading data table
/Users/derossip/desktop/Subjects_ABC_Proc/qdec/ABC_Cortex.qdec.table.dat...
QdecDataTable::Load: will attempt to open as Mac text file...
Number of columns: 7
fsid colum
Hello,
I'm using Freesurfer on Windows 7 using VirtualBox. I want to import DICOM
files based on the "FreeSurfer Troubleshooting Reconstruction Work Flow", but
I'm facing problems. This is what I have done:
1. Tried to use the source command like this: source
C:\FreeSurfer_data\SetUpFreeSurfer
Thanks a lot!
2012/11/19 Douglas N Greve
> It should be in the current directory.
> doug
>
> On 11/19/2012 12:47 PM, pietro de rossi wrote:
> > Hi FreeSurfer users and developers,
> >
> > I'm trying to export aseg.stats values for a preliminary analysis. I
> > would like to export them to an exc
It should be in the current directory.
doug
On 11/19/2012 12:47 PM, pietro de rossi wrote:
> Hi FreeSurfer users and developers,
>
> I'm trying to export aseg.stats values for a preliminary analysis. I
> would like to export them to an excel spreadsheet.
>
> My command line was
>
> asegstats2tabl
Please find the Xtmp.mat in the attachment.Thank you, Doug.
Best
Wei
Can you send me the Xtmp.mat file?
dloug
On 11/16/2012 01:01 PM, Zhou, Wei wrote:
> Hi Doug,
>
> It seems the previous fieldsign-sess problem is due to that I stored
> data on one server while freesurfer is on the other
Hi Donald and Doug,
Thanks for advice. Can I be a little bit clearer as I suspect I need a little
more guidance.
When comparing controls (gp c) and whole patient group (gp p) I see interesting
differences in area (DOSS model after checking for no interaction and with age
and ICV as correction
Fair enough Bruce. Thanks for the quick response.
John Lilley
Lead Systems Administrator - Cloud Computing
IMSS High Performance Computing
California Institute of Technology
Cell 323.252.2370
john...@caltech.edu
vcard
https://s3-us-west-1.amazonaws.co
Hi John
our preference would be that each user register, but then you can use any
one license for everyone. That lets us keep track of the total number of
users relatively accurately
cheers
Bruce
On Mon, 19 Nov 2012, Lilley, John F. wrote:
> Hi,
>
> We have setup a central install of free surf
Hi,
We have setup a central install of free surfer but are having some difficulty
with the license management aspect. Is there a way to run a single install
instance yet have each user provide individual license location variables out
side of $FREESURFER_HOME? (~/.license etc.) If not, would re
Hi FreeSurfer users and developers,
I'm trying to export aseg.stats values for a preliminary analysis. I would
like to export them to an excel spreadsheet.
My command line was
asegstats2table --subjects 119 123 125 135 141 145 146 147 151 159 160 163
164 167 171 174 178 186 196 198 218 221 224 2
Doug and Mahinda,
Since the assumption is that the slope is the same across all
subjects, I would demean once. I would use one model with 1 control
group and N patient group. The model will then test whether or not the
covariate-adjusted group means are the same or different. By doing it
in a sing
Dear list,
I am quite new in the use of freesurfer and I have two doubts.
1. I am studying the visual areas of the brain, but I do not know how to
perform a vertex analysis within a ROI. I already know how to obtain
thickness data on a ROI (either drawn by hand or labeled), but I would
like to res
If it is in mni152 space, you can use
$FREESURFER_HOME/average/mni152.register.dat
doug
On 11/19/2012 12:12 PM, Eun Young Choi wrote:
> Hi Doug,
>
> It's in MNI space.
>
> Thanks,
> Eun Young
>
> On Mon, Nov 19, 2012 at 11:05 AM, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
>
Hi Doug,
It's in MNI space.
Thanks,
Eun Young
On Mon, Nov 19, 2012 at 11:05 AM, Douglas N Greve wrote:
> what space is the spmT volume in?
>
> On 11/15/2012 04:58 PM, Eun Young Choi wrote:
> > Hi all,
> >
> > I'd like to convert SPM2 spmT files to FreeSurfer space. I have a
> > Colin template
Can you send me the Xtmp.mat file?
dloug
On 11/16/2012 01:01 PM, Zhou, Wei wrote:
> Hi Doug,
>
> It seems the previous fieldsign-sess problem is due to that I stored
> data on one server while freesurfer is on the other server.
> But when I put the data and freesurfer on the same server and run t
Hi Marie, if you run
mri_info --orientation file.dcm
it will print out the orientation string (eg, PIL). When you do the
conversion, you can tell it to make the output this orientation:
mri_convert file.dcm --out_orientation PIL 001.mgz
This will orthogonalize the vox2ras matrix (note that you wil
On 11/15/2012 05:13 PM, Mahinda Yogarajah wrote:
> Hi,
>
> Thanks for the reply. I am using the new script and I should correct myself
> in that my significant volume changes do seem to correspond (although they
> are not completely identical) to areas where there are significant area
> diffe
what space is the spmT volume in?
On 11/15/2012 04:58 PM, Eun Young Choi wrote:
> Hi all,
>
> I'd like to convert SPM2 spmT files to FreeSurfer space. I have a
> Colin template brain available to help with the conversion, as well.
> Has anyone done this before? Any suggestions on how to do this?
Hi Ted, can you use epidewarp.fsl to create the warp field (voxel shift
map (VSM))? If so, you can then use bbregister and mri_vol2surf with the
--vsm option to apply the warp simultaneously with determining or
applying the registration. It might work with the warp field that you
have (since e
On 11/19/2012 03:04 AM, Mahinda Yogarajah wrote:
> Dear Experts,
>
> I have a two groups - a control group and patient group. The patient group
> can also be divided into 4 subgroups (but not control gp). Both groups are
> evenly split between male and female. So far I have compared the patient
Hi, Bruce and Doug
Thank you very much for the information. I will try this command to register
the surfaces with my diffusion volumetric data.
Best
Longchuan
From: Douglas N Greve
To: freesurfer@nmr.mgh.harvard.edu
Sent: Monday, November 19, 2012 10:43 A
use bbregister, something like
bbregister --s subjectname --init-fsl --t2 --mov lowb.nii --reg register.dat
where lowb is the low b (usually b=0) volume from your DTI, the one that
you used as the template for motion correction.
doug
On 11/19/2012 10:30 AM, Bruce Fischl wrote:
> Hi Longchuan
>
>
Hi Longchuan
yes, I think you can do this with tkregister2. Doug can give you the
details
Bruce
On Mon, 19 Nov 2012, Longchuan Li wrote:
Hi, Bruce
Thank you for the information. I will re-run recon-all using "-cm" option to
see if the problem will be solved. In the mean time, do you have any
Hi, Bruce
Thank you for the information. I will re-run recon-all using "-cm" option to
see if the problem will be solved. In the mean time, do you have any
suggestions regarding finding a transformation between the mismatched surfaces
and the volume?
Thanks again.
Longchuan
__
this is because the aseg doesn't show any white matter, and so the pial
surface is "frozen", since it is adjacent to a noncortical gray matter
structure and assumed not to be part of cortex. What version are you
running? We did have some fixes for this, but it may be that you need to
draw a bit
Hi Longchuan
have you tried the -cm (conform to min) option in recon-all?
cheers
Bruce
On Sun, 18 Nov
2012, Longchuan Li wrote:
Hi, FreeSurfer experts
I have a question regarding coregistering white and pial surfaces with the
brain.mgz and would appreciate your help on this. I
am working
Dear Experts,
I have a two groups - a control group and patient group. The patient group can
also be divided into 4 subgroups (but not control gp). Both groups are evenly
split between male and female. So far I have compared the patient and control
groups as a whole (age and icv as continuous/
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