Thanks for answer Bruce,
does this mean that I will have to reanalyze all my subjects from the
beginning?
Martin
On Wednesday 11 July 2007 14:53:59 you wrote:
> Hi Martin,
>
> these are features we'll include in our next release, hopefully sometime
> this summer.
>
> I'll leave 3 for Doug.
>
>
Thanks for the answer Doug,
can still trust the aseg.stat values or I better wait? Will you release some
diff version of the files or we will have to start downloading 150GB from the
beginning?
Martin
On Wednesday 11 July 2007 20:09:59 Doug Greve wrote:
> #3 is an error in the osasis data set.
no, you should be able to just run these steps to add the wmparc and the cc
- as soon as we fix them!
On Thu, 12 Jul 2007, Martin Kavec
wrote:
Thanks for answer Bruce,
does this mean that I will have to reanalyze all my subjects from the
beginning?
Martin
On Wednesday 11 July 2007 14:53:5
When I type
tkregister2 --feat istlevel_FWIO_fmri_NYU_KB_Nov30_06_epi1swap_z2_3.feat
I get an error message saying ERROR: Option --feat unknown
I also did the second check you recommended and it looks good. But I just
realized - and this could be why it came out fine when I checked example_func
Hello Freesurfer Forum,
We have a question about the M matrix, found in the
.mgz file header.
We loaded an .mgz file into Matlab and took a look at
the affine transform matrix M from the header:
M(1,:) = [-1 0 0 132.7486];
M(2,:) = [ 0 0 1 -105.7281];
M(3,:) = [ 0 -1 0 131.7424];
M
Hi Jerry and Geoff,
when you compose a scaling and rotation matrix it's no longer so easy to
assign a meaning like "x scaling" to any one component.
cheers,
Bruce
On Thu, 12 Jul 2007, Jerry Yeou-Wei Chen wrote:
Hello Freesurfer Forum,
We have a question about the M matrix, found in the
.
Hello,
I just downloaded and installed the freesurfer and got up the step
where I tested it by trying "recon-all -s bert -autorecon1". This
works fine :-)
Now I (thoroughly) followed the instructions "Getting started with
your own data" in of https://surfer.nmr.mgh.harvard.edu/fswiki/
Te
Hi Birte,
you need to specify the name of a single DICOM file that is in the series
you want to use for building anatomical models, not just the directory
name.
cheers,
Bruce
On Thu, 12 Jul 2007, Birte
Schrader wrote:
Hello,
I just downloaded and installed the freesurfer and got up the
Hi Bruce,
thanks for replying so fast. But somehow I still don't get this
running. When I say:
"mri_convert avant/IM-0001-0001.dcm avant.mgz"
I get:
"mri_convert avant/IM-0001-0001.dcm avant.mgz
unknown file type for file avant/IM-0001-0001.dcm"
when saying:
"mri_convert -it dicom -ot m
Don,
If the file $subjdir/tmp/control.dat exists, then it is automatically
added to the mri_normalize and mri_ca_normalize steps. An explicit flag
is not needed.
Nick
On Wed, 2007-07-11 at 21:27 -0400, Bruce Fischl wrote:
> Hi Don,
>
> Nick actually just recently included something to allow yo
Try -siemens_dicom instead of -dicom
On Thu, 2007-07-12 at 21:44 +0200, Birte Schrader wrote:
>
> > Hi Bruce,
> >
> >
> > thanks for replying so fast. But somehow I still don't get this
> > running. When I say:
> >
> >
> > "mri_convert avant/IM-0001-0001.dcm avant.mgz"
> >
> >
> > I get:
>
yes, it is.
PS: Birte is a girl's name... :-)
On Jul 12, 2007, at 9:57 PM, Mithra wrote:
Hello Mr.Schrader,
Is is the "avant" folder saved in the path/folder from where you
are runnning this command?
Thanks.
On 7/12/07, Birte Schrader <[EMAIL PROTECTED]> wrote:
Hi Bruce,
thanks for
Thank you, Nick, But this doesn't work either. It then says:
"mri_convert -it siemens_dicom -ot mgz avant/IM-0001-0001.dcm avant.mgz
reading from avant/IM-0001-0001.dcm...
ERROR (ScanSiemensSeries): avant/IM-0001-0001.dcm is not a Siemens
DICOM file
ERROR: could not find any files (SeriesList=
Hello all. Thanks for the numerous replies and tips, none of them
solved the problem though. Another strange thing (maybe this is the
reason why it doesn't work): Though I have rwx-permits for all users
in my directory and on the dcm-files, the error message I get when
trying to convert the
what kind of dicoms are these? What version of freesurfer/mri_convert
are you using?
Birte Schrader wrote:
Thank you, Nick, But this doesn't work either. It then says:
"mri_convert -it siemens_dicom -ot mgz avant/IM-0001-0001.dcm avant.mgz
reading from avant/IM-0001-0001.dcm...
ERROR (ScanSie
you cannot do this, you have to save them separately
T. Song wrote:
Hi Doug:
Which command should I use to save a base image with an overlay together?
Thanks!
Tao
T. Song wrote:
Thanks! I was able to create a binary mask, and the result looks
good. Now how do I save a base image with an
use featdir/reg/freesurfer/anat2std.register.dat for the cross-run gfeat
registration, you can test it with something like:
tkregister2 --mov mean_func.nii --reg anat2std.register.dat --fsl-targ
Where mean_func is the mean functional for the individual in standard
space (I think this is crea
No, the aseg.stats should be fine. I don't know how they are going to
release the new set of files.
doug
Martin Kavec wrote:
Thanks for the answer Doug,
can still trust the aseg.stat values or I better wait? Will you release some
diff version of the files or we will have to start downloadin
These types of issues are discussed at length in:
https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems?action=AttachFile&do=get&target=fscoordinates.pdf
if you just want to get the voxel size from M, then you can compute the
sqrt of the sum of each col.
doug
Jerry Yeou-Wei Chen wrot
You may have an older version, I've put an update (for Linux) here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/tkregister2
Stacy Chu wrote:
When I type
tkregister2 --feat istlevel_FWIO_fmri_NYU_KB_Nov30_06_epi1swap_z2_3.feat
I get an error message saying ERROR: Option --fe
Hi Alex,
I see what you mean, but don't think I can diagnose it from one slice.
Can you drop the gzipped tarball of the subject on our website?
Bruce
On Fri, 13
Jul 2007, Alexander Fornito wrote:
Hi all,
I'm trying to run some 3T data through freesurfer and encouter a
consistent problem in
So then for redoing a recon with control points, it would be beneficial to
start again at the mri_normalize step?
From: Nick Schmansky <[EMAIL PROTECTED]>
To: Bruce Fischl <[EMAIL PROTECTED]>
CC: Freesurfer Mailing List ,Don
Hagler <[EMAIL PROTECTED]>
Subject: Re: [Freesurfer] control
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