Dear all,
is the amygdala subfields segmentation available or you are working on it?
Thanks,
Stefano ___
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The information in this e-mai
Hi Stefano,
we are working on an algorithm to segment the nuclei, but unfortunately I do
not think it is going to be released any time soon.
Kind regards,
/Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl
Hi Freesurfer experts,
I want creat some ROI masks or parcellation from Caret
PALS_B12_Visuotopic.annot file in fsaverage's label folder.
I used the command mri_label2vol,
mri_label2vol --annot $Dir/label/lh.PALS_B12_Visuotopic.annot --temp
$Dir/mri/T1.nii --fillthresh .5 --o PALS_B12_Visuotopic
sorry, I think >=5 is in brain
On Mon, 24 Nov 2014, Gunjan Gautam wrote:
Hi Bruce,
What about the voxels having value equal to 5 (if exists) ?
Gunjan
On Sun, Nov 23, 2014 at 10:39 PM, Gunjan Gautam
wrote:
Ok thank you Bruce
On Nov 23, 2014 10:37 PM, "Bruce Fischl"
wro
Dear Anastasia,
Thank you very much for your answer.
In my analysis I have two groups 23 patients and 27 controls. My problem right
now is that this change in the results (from the output of trac-all -path -c)
gave me different P values between the groups, sometimes the results are
significant
Hi Graham
have you tried freeview? We stopped development on the tktools some time
ago.
cheers
Bruce
On Fri, 21 Nov 2014, Graham Wideman wrote:
> Hi all,
>
> I'm having some issues (some possibly mine, some possibly tksurfer's) getting
> tksurfer (5.3c6) to display curvature the way I think i
What is the full terminal output and error msg?
On 11/21/2014 04:14 AM, Anna Jonsson wrote:
> hi, I have tried to make prefrotnal cortex label by doing first
>
>
>
> mri_annotation2label --subject "$subject" --hemi rh --outdir
> "$subject"/label
>
>
>
> mri_mergelabels -i lh.caudalanteriorcingula
Have you looked at
mri_glmfit-sim --help
On 11/21/2014 01:51 PM, Jon Alan Wieser wrote:
>
>
> hi
>
> please explain the differece between --sim-sign abs, neg, and pos
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://m
I have not read that paper, but I think it can do what you want. Have
you seen?
http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough
On 11/22/2014 11:55 AM, std...@virgilio.it wrote:
> Dear all,
>
> is FS-FAST able to perform seed-based fcMRI analysis between thalamus
Would mris_decimate work?
On 11/24/2014 01:53 AM, 婷 wrote:
> Thanks for your reply with detailed explanation. I am interested in what if
> we apply analysis on native surface first. Still wondering:)
>
> Ting
>
>
>> On Nov 23, 2014, at 8:23 PM, Thomas Yeo wrote:
>>
>> Hi Ting,
>>
>> What I usual
Try using mri_aparc2aseg. This is what creates aparc+aseg.mgz from the
aparc annot. You can look in the recon-all.log file for the command line
(just make sure to change the output file name too so that you don't
overwrite aparc+aseg.mgz)
doug
On 11/24/2014 07:54 AM, wangzhiwei3233 wrote:
> H
yes I looked at mri_glmfit-sim -- help
it says:
--sim-sign sign : ,pos,neg
and:
6. Select the threshold sign (--sim-sign). This is the sign of the
threshold used to create the clusters for cluster-wise correction
of multiple comparisons. Options are abs (unsigned), pos
(positive), and
yes
On 11/24/2014 12:30 PM, Jon Alan Wieser wrote:
> yes I looked at mri_glmfit-sim -- help
>
> it says:
> --sim-sign sign : ,pos,neg
>
> and:
>
> 6. Select the threshold sign (--sim-sign). This is the sign of the
> threshold used to create the clusters for cluster-wise correction
> of mu
There are two things that are considered. One is the tesselation which
smoothing is one. The other is the registration that is used. Using
-target Something only specifies the smoothing target (if doing
smoothing in mris_preproc). If you want to spec a registration target,
you need to first ru
Hi Christopher, sorry for the delay. I had a write a new program. You
can download it from here
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/cluster-sess
Let me know how it goes
doug
On 11/14/2014 06:05 AM, Milde, Christopher wrote:
> Dear Freesurfer experts,
>
> I performed fMR
Dear all,
After running the recon-all on a subject, I needed to create a 'pial'
surface to include the hippocampi, which are not included well in the pial
reconstruction. So I generated a mask and used it to mask brain.mgz.
1. All well, except that in both the mask and the masked brain volume
(re
What do you mean apply it to your functional data? Analyzed fMRI? In
what package? In what space is the fMRI?
On 11/20/2014 08:01 AM, chenchunhuichina wrote:
> Dear freesurfer experts,
> I searched on the wiki but can not figure out how to solve this
> problem: I found some significant clusters
Hi all,
I am trying to download the latest version of Tracula from this site
http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula.
This seems not to be possible at the moment. Are there server problems?
Thanks,
Janosch
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Freesurfer mailing list
Freesu
It works! Thanks, Doug.
At 2014-11-25 01:19:13, "Douglas N Greve" wrote:
>
>Try using mri_aparc2aseg. This is what creates aparc+aseg.mgz from the
>aparc annot. You can look in the recon-all.log file for the command line
>(just make sure to change the output file name too so that you don't
>o
It works! Thank you, Doug.
Ting
> On Nov 24, 2014, at 12:17 PM, Douglas N Greve
> wrote:
>
> Would mris_decimate work?
>
>> On 11/24/2014 01:53 AM, 婷 wrote:
>> Thanks for your reply with detailed explanation. I am interested in what if
>> we apply analysis on native surface first. Still wond
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 as MGH dicoms
("This looks like an MGH DTI volume"). Could this be the reason why it fails?
Thanks,
Janos
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