not that I know of. We usually recommend <= 1.5 mm if you can do it
Bruce
On Tue,
25 May 2010, Mishkin Derakhshan wrote:
> Hi,
> I'm wondering if anyone has looked at the accuracy/reproducibility of
> cortical thickness measurements using 3mm slice data. I found the Han
> 2006 paper in NeuroImag
Hi,
I'm wondering if anyone has looked at the accuracy/reproducibility of
cortical thickness measurements using 3mm slice data. I found the Han
2006 paper in NeuroImage comparing different sequences, but it doesn't
compare different slice thicknesses.
If not, does anyone have anecdotal experience u
I tried the recommended syntax below for looking at the surfaces and
they look fine in all three views (coronal, horizontal and sagittal).
And the surfaces seem consistent with other subjects I've processed.
Thanks,
Elias
On Tue, 2010-05-25 at 14:40 -0400, Douglas N Greve wrote:
> And all the sur
Yes, you would just run the command for the fix that happens earliest on
in the processing stream. The order these fixes occur in the processing
stream is:
control points
wm edits
pial edits
So if you've done all 3, you only need to run
recon-all -autorecon2-cp -autorecon3 -s
and it will take
How do I convert between the two coordinate systems?
Yigal
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it
Hello all,
I am new to FreeSurfer and still trying to understand how things work.
I am currently trying to understand how the manual correction works.
Following the online tutorials I was able to fix the brainmask and
wm.mgz, and also add control points in the wm so that low intensity wm
is also
And all the surfaces look ok? Try looking at them with
tkmedit subjectname orig.mgz -seg aseg.mgz -surfs
Elias Kersten wrote:
> The subcortical structures, brainstem, thalamus, cerebellum appear to be
> labeled correctly, but the rest of the brain and background are labeled
> as Left-Cerebral-W
The subcortical structures, brainstem, thalamus, cerebellum appear to be
labeled correctly, but the rest of the brain and background are labeled
as Left-Cerebral-White-Matter.
On Tue, 2010-05-25 at 11:51 -0400, Douglas N Greve wrote:
> How does the aparc+aseg.mgz look?
>
> Bruce Fischl wrote:
>
Thanks Krish. Unfortunately, I had seen your earlier posting about this
and tried that. It hung for a long time, then produced this output:
[vantz:functional] (nmr-std-env) gzip -d fsfast-tutorial.tar.gz
gzip: fsfast-tutorial.tar.gz: invalid compressed data--crc error
gzip: fsfast-tutorial.tar.g
Hi Jesse
Can you do
gzip -d fsfast-tutorial.tar.gz
and then do
tar -xf fsfast-tutorial.tar
If this works, I am guessing it might be an error of the command "tar"
itself ( how it's implemented across platforms )
Best
Krish
On May 25, 2010, at 1:37 PM, Jesse Friedman wrote:
> Thanks... I di
Thanks... I did use wget.
> how did you download it? If you just used your browser, then the file
> might have been truncated. Try using the wget command.
>
> doug
>
> Jesse Friedman wrote:
>> Hi,
>>
>> I'm following instructions from:
>> http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialData
how did you download it? If you just used your browser, then the file
might have been truncated. Try using the wget command.
doug
Jesse Friedman wrote:
> Hi,
>
> I'm following instructions from:
> http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialData
>
> The anatomical data extracts succes
Hi,
I'm following instructions from:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialData
The anatomical data extracts successfully, but the functional data hangs
on this command:
tar xvfz fsfast-tutorial.tar.gz
The process extracts files for a while and produces this output:
./fsfast-tu
If you load in the white surface in to matlab with read_surf, the
coordinates are mni305. You can also convert the surface to ascii with
mris_convert, then extract the vertex you need (also in mni305).
doug
Yigal Agam wrote:
> Hi,
>
> Is there a way to get the Tal and MNI coordinates of a given
It is the input data (ie, the diffusion weighted 4D "time" series) you
collect from each subject, so it will be different for each subject.
doug
Weisinger, Brian (NIH/OD) [E] wrote:
>
>
> Hello,
>
> I am trying to run the dt_recon with the fractional anisotropy to do a
> project with white mat
Hi,
Is there a way to get the Tal and MNI coordinates of a given fsaverage
vertex through matlab or the unix command line, without opening tksurfer?
Thanks,
Yigal
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.e
Hello,
I am trying to run the dt_recon with the fractional anisotropy to do a project
with white matter.
I am running into a problem actually getting the command to work. I am trying
to follow the example online dt_recon --i 6-1025.dcm --s M87102113 --o dti
dt_recon --i f.nii --b f.bvals f
How does the aparc+aseg.mgz look?
Bruce Fischl wrote:
> Not sure then. Krish: can you take a look?
>
> On Tue, 25 May 2010, Elias Kersten wrote:
>
>
>> I loaded in lh.white and rh.white and the white and pial surfaces look
>> fine, as does the aseg.mgz.
>>
>> Thanks,
>> Elias
>>
>> On Tue, 2010
Not sure then. Krish: can you take a look?
On Tue, 25 May 2010, Elias Kersten wrote:
> I loaded in lh.white and rh.white and the white and pial surfaces look
> fine, as does the aseg.mgz.
>
> Thanks,
> Elias
>
> On Tue, 2010-05-25 at 09:08 -0400, Bruce Fischl wrote:
>> Hi Elias,
>>
>> have you lo
I loaded in lh.white and rh.white and the white and pial surfaces look
fine, as does the aseg.mgz.
Thanks,
Elias
On Tue, 2010-05-25 at 09:08 -0400, Bruce Fischl wrote:
> Hi Elias,
>
> have you looked at the surfaces? Are they correct?
>
> Bruce
> On Mon, 24 May 2010,
> Elias Kersten wrote:
>
Hi,
We're having problems untarring the tutorial data. Are the uncompressed
data available anywhere?
Thanks,
Yigal
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information
Hi Elias,
have you looked at the surfaces? Are they correct?
Bruce
On Mon, 24 May 2010,
Elias Kersten wrote:
> Hi,
>
> I am trying to run a subject through the entire recon-all pipeline.
> However, I noticed the second to last step, "-wmparc", was taking a very
> long time (days).
>
> Looking o
Yes, that's fine.
--
On Tue, 25 May 2010, [GB2312] Àîèª wrote:
Hi, all
Bruce has suggested that we can directly give recon-all dcm file as input.
However, I have done recon-all with mgz file as input. Is that input file
OK?
For example, sub1 has 128 dcm files, 001~128, I just ran a syntax:
mri
Dear FreeSurfer experts,
I want to run the simulation script with qdec, but I always get the following
error message:
'error in simulation script generation command failed: chmod u+x' and then the
adress of the 'mri_glmfit-sim-mc-z.abs.2' - file. This it what the file
contains:
mri_glmfit-si
Hi, all
Bruce has suggested that we can directly give recon-all dcm file as input.
However, I have done recon-all with mgz file as input. Is that input file
OK?
For example, sub1 has 128 dcm files, 001~128, I just ran a syntax:
mri_convert 001 sub1.mgz
then the computer read 128 dcm files and conve
25 matches
Mail list logo
