Hi Octavian
I wouldn't use control points since it really isn't healthy wm. The only
thing you can do is edit the wm.mgz and possibly also the brainmask, but
it's so abnormal looking you may not be able to get accurate surfaces.
How does the aseg look? If it is ok there may be one other option.
so the GM is properly labeled by the aseg there? What about the faint wm?
On
Tue, 25 Nov 2014, Octavian Lie wrote:
> Dear Bruce,
>
> I am not sure how an ok aseg.mgz would look like for a lesion like that, but
> it looks like it includes one larger gyrus excluded by the pia, see
> attached, I wo
It looks like there is only gray matter (int 42), similar to cortical
ribbon gray, no white matter in that gyrus in aseg, both in the original
recon, and after painting gyral centers in brainmask.
Octavian
On Tue, Nov 25, 2014 at 7:51 AM, Octavian Lie
wrote:
> Dear Bruce,
>
> I am not sure how a
Hi Mihaela
if you want to upload a representative subject we will take a look
cheers
Bruce
On Tue,
25 Nov 2014, Mihaela Stefan wrote:
> Hello Freesurfers,
> We noticed that our subcortical segmentations have a poor quality (see
> attachment). Is there a way to improve the segmentation in an auto
Hi Bruce,
I uploaded a subject.
Thanks!
Mihaela
On Tue, Nov 25, 2014 at 10:13 AM, Bruce Fischl
wrote:
> Hi Mihaela
>
> if you want to upload a representative subject we will take a look
> cheers
> Bruce
> On Tue,
> 25 Nov 2014, Mihaela Stefan wrote:
>
> > Hello Freesurfers,
> > We noticed that
Can you send the full terminal output?
doug
On 11/24/14 10:18 PM, Janosch Linkersdörfer wrote:
> Hi experts,
>
> I wanted to play with Tracula. Strangely, already the first preprocessing
> step, i.e., conversion to .nii.gz, fails.
>
> Apparently, mri_convert (falsely) recognizes my dicom files a
Dear Tracula Team,
Quick question: Is Tracula able to to process diffusion kurtosis data, and
yield, let's say, 'mean kurtosis' parameters for specific fiber
tracts?cheers,Cat___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mg
The 64bit Lion version. It should probably be made a little more clear
that that version is for 10.7 and higher. Ill fix that.
https://surfer.nmr.mgh.harvard.edu/fswiki/Download
-Zeke
> Gentleman
> Which Version of Freesurfer should I download for use with the OS X
> Yosemite 10.10.1?
> Thanks
Thanks, Zeke!!!
On Tue, Nov 25, 2014 at 10:59 AM, wrote:
>
> The 64bit Lion version. It should probably be made a little more clear
> that that version is for 10.7 and higher. Ill fix that.
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/Download
>
> -Zeke
>
>
> > Gentleman
> > Which Version of Fr
Hi all,
I am running FS in a VM (Debian, wheezy) and I would like to create a 3D
reconstruction of the hippocampus in .png. For that, I executed the
following code lines:
>> mri_extract_label aseg.mgz 17 lh.nii
>> mri_extract_label aseg.mgz 53 rh.nii
>> freeview -slice 500 500 500 -v lh.nii:isosu
Hi list,
I recently switched to the digest mode for the mailing list. Since then, I
don't receive answers to my mails as mails anymore, making it harder to respond
to them (or any other mail on the list).
Does anybody experience the same issues? How did you solve them?
Thanks,
Janosch
__
At 11/24/2014 08:23 AM, Bruce Fischl wrote:
>Hi Graham
>
>have you tried freeview? We stopped development on the tktools some time
>ago.
>
>cheers
>Bruce
Hi Bruce, thanks for replying.
Yes, I did proceed to try the same task in Freeview (which in general has a
nicer UI, to be sure). Some notes:
Dear Freesurfer experts,
I have processed my subject with recon-all and subfields hippocampal
segmentation. . I have tried to use
kvlQuantifyHippocampalSubfieldSegmentations.sh on a subset of my
subjects. I have these subjects A B C D E fsaverage in a folder.
When I try to exclude fsaverage
Hi Bruce,
I've heard people saying that FS 5.3 is focusing on better output for
cortical thickness and that I should use 5.0 for subcortical segmentation
because it's better. Does that make sense?
Thanks!
Mihaela
On Tue, Nov 25, 2014 at 10:43 AM, Mihaela Stefan
wrote:
> Hi Bruce,
> I uploaded
No, I don't think so
Bruce
> On Nov 25, 2014, at 11:05 PM, Mihaela Stefan wrote:
>
> Hi Bruce,
>
> I've heard people saying that FS 5.3 is focusing on better output for
> cortical thickness and that I should use 5.0 for subcortical segmentation
> because it's better. Does that make sense?
>
Hi,
Is there a way to generate an intersection between a cortical thickness
stats map (e.g., sig.mgh) in fsaverage space and native space neuroanatomy
using FS parcellations (e.g., lh.apac.anot.)? We would like to plot
cortical thickness of the significant clusters for each subject, but
separate t
Hi Douglas,
How exactly should I upload the glmdir?
Kind regards,
Bronwyn Overs
Research Assistant
Neuroscience Research Australia
Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
*M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399
Dear FS experts
We would like to force FS's mri_glmfit-sim function of FS 5.3.0 to report
all results and not only the significant results.
This was the behavior of this function until FS version 4.5.0.
Please can you guide as to the relevant lines in the mri_glmfit-sim function
and indicate what
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