Hi all,
I just loaded raw structural scans into one of my subject directories. They are
of siemens IMA format and I used the following command:
mri_convert -it siemens -ot mgz 001/ 001.mgz
I then got the following error:
reading from 001/...
ERROR: could not parse 001/
ERROR: siemensRead(): 001/
specify one slice in the series and it will find the rest (not the
directory)
On Fri, 2 Feb 2007, Binyam Nardos wrote:
Hi all,
I just loaded raw structural scans into one of my subject directories. They are
of siemens IMA format and I used the following command:
mri_convert -it siemens -ot mgz
Hi Binyam,
I think you need to give it the IMA file name, so something like:
mri_convert -it siemens -ot mgz 001/file.IMA 001.mgz
If that doesn't work there are other options we can try.
Jenni
On Fri, 2 Feb 2007, Binyam Nardos wrote:
Hi all,
I just loaded raw structural scans into one of my s
thanks Jenni .. I had to change my input file format to siemens_dicom although
they were IMAs. It seems to be working now.
Binyam
Binyam Nardos
Cognitive Rehabilitation Research Group
Washington University School of Medicine Box # 8505
Forest Park Blvd
St. Louis, MO 63108
Office: (314) 454-7
Hi,
Sorry to dredge up an old thread, I was curious about the details on
where randomness is introduced in the following programs (beyond the
normal floating points issues):
> mris_smooth -seed 1234
> mris_sphere -seed 1234
> mris_fix_topology -seed 1234
> mris_ca_label -seed 1234
I assume t
Yea, some siemens scanners/dicom servers produce dicom files with IMA
extensions, which fools our software into thinking it is the old ima
format.
doug
On Fri, 2 Feb 2007, Binyam Nardos wrote:
thanks Jenni .. I had to change my input file format to siemens_dicom although
they were IMAs. I
Hello all,
Is there some information on the wiki about the
srctoDst voxel-to-voxel transform and the rastoRAas
transform?
THAnks
Chacko.
Sucker-punch spam with award-winning protection.
Try the free Yahoo!
Chacko,
There is this page:
http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
and there, open Doug Greve's PowerPoint file, which describes the
transforms used within Freesurfer.
N.
On Fri, 2007-02-02 at 10:49 -0800, Chacko Cherian wrote:
> Hello all,
> Is there some information on
Hi Bruce:
Is there a way that I can load the MEG timecourse data on the freesurfer
surface? Is it possible that we could get the timecourse waveform for a
specific point on the surface?
Thanks!
Tao
___
Freesurfer mailing list
Freesurfer@nmr.mgh.ha
sure, if you save it in the right format. The easiest thing to do would
be to save it as a volume, where the 1st spatial dimension is # of
vertices on the surface, and the last (4th one) is the # of time points
(the 2nd and 3rd would both be 1). Or there are other formats you can save
in if you
If the time course is in the proper format, then you can. It needs to
be in one of the "volume" formats, eg mgh or mgh. The number of cols
should equal the number of vertices, the number of rows = # of slices
= 1, and the 4th dim is time.
Then run
tksurfer subject hemi surf -timecourse yourfile
Actually, I think the w file only holds one time point, so that prob
wont work. If you want to go the matlab route, you can do something
like:
mri_convert lh.curv lh.curv.mgh # convert to mgh for a template
then in matalb
f = MRIread('lh.curv.mgh');
f will be a struct
f.vol will be a 4d matr
oops, you're right. Anders wrote another format for multiple time points,
but I can't seem to find it. The volume is the best way to go these
days though.
Bruce
On Fri, 2 Feb 2007, Doug Greve
wrote:
Actually, I think the w file only holds one time point, so that prob
wont work. If you wa
I would like to calculate total brain volume (defined as: total white,
gray, and subcortical altogether). Should I take the BrainSegVol and
minus out cerebellum and ventricles, or add the white and gray matter
volumes from mris_anatomical_stats (it seems I remember hearing that white
matter from m
Hi Derin,
the aseg labeling of cortical gm is not that accurate - the surfaces are
quiet a bit more so. We have a new tool for generating the estimate of the
gm and wm volume from the surfaces called mris_volume and mris_wm_volume. I
think Doug or Nick has integrated it into the dev version of
Bruce,
So if I downloaded the dev version of the program I could use it to get
the volumes from subjects processed with 3.0.3? And would adding these
volumes together generate the total volume I'm looking for (including
subcoritical)? Thanks!
-Derin
> Hi Derin,
>
> the aseg labeling of cortica
you would need to add in whatever subcortical components you wanted to
include, as they are excluded from the wm volume
On Fri, 2 Feb 2007, Derin
Cobia wrote:
Bruce,
So if I downloaded the dev version of the program I could use it to get
the volumes from subjects processed with 3.0.3? And wo
I have not implemented it in recon-all yet.
doug
On Fri, 2 Feb 2007, Bruce Fischl wrote:
you would need to add in whatever subcortical components you wanted to
include, as they are excluded from the wm volume
On Fri, 2 Feb 2007, Derin Cobia wrote:
Bruce,
So if I downloaded the dev vers
Hello All,
After making changes using tkregister2 the input
registration matrix changes.IS there an 'optimum'
input registration matrix that i should try to get.I
notice that the closer the values(last column of the
input reg matrix) are to zero the better the outcome.
Thanks in advance.
Chacko.
.Bold { font-weight: bold; }
.Title { font-weight: bold; font-size: 18px; color: #cc3300; }
.Code { border: #8b4513 1px solid; padding-right: 5px; padding-left: 5px;color:
#66; font-family: 'Courier New' , Monospace;background-color: #ff9933; }
Dear Freesurfer experts.
I have some question
20 matches
Mail list logo
