Hi Freesurfer experts,
When I perform the statistical analysis, I am very confused with the following
questions:
My experimental design includes 3 discrete factors: diagnosis with two levels
(A, B); genotype with two levels (G, T); gender (F, M), and two covariates.
So I can get 8 classes: AGF,
Hi Freesurfers,
I'm trying to extracting thickness value for a ROI which is created by afni.I
follow the workflows of "Cortical Thickness of a Volume-defined ROI". The ROI
mask and T1 volume file are all talairach transformed.
When I map the thickness data to the fsaverage subject with mri_surf
Hi Zhu
what is your command line?
Bruce
On Thu, 6 Sep 2012, zzy7...@mail.ustc.edu.cn wrote:
> Hi Freesurfers,
>
> I'm trying to extracting thickness value for a ROI which is created by afni.I
> follow the workflows of "Cortical Thickness of a Volume-defined ROI". The ROI
> mask and T1 volum
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OK. So do you have any other suggestions? Is there some minor difference
between my version and yours that would explain this behavior. Other
settings to try?
Darren
On Wed, Sep 5, 2012 at 4:28 PM, Bruce Fischl wrote:
> our internal development version.
> On Wed, 5 Sep 2012, Darren Gitelman
> wr
On 09/06/2012 04:42 AM, Meng Li wrote:
> Hi Freesurfer experts,
> When I perform the statistical analysis, I am very confused with the
> following questions:
>
> My experimental design includes 3 discrete factors: diagnosis with two
> levels (A, B); genotype with two levels (G, T); gender (F, M
Hi Bruce
My command line is
cd $SUBJECTS_DIR/subjid/surf
mri_surf2surf \
--s con_52 \#It is my Processed freesurfer date
--trgsubject fsaverage \
--hemi lh \
--sval lh.thickness \
--tval lh.thickness.fsaverage.mgh \
--reshape #or reshape-factor 7
Zhu
> -Original E
can you send the full screen output as well?
On Thu, 6 Sep 2012,
zzy7...@mail.ustc.edu.cn wrote:
>
> Hi Bruce
> My command line is
> cd $SUBJECTS_DIR/subjid/surf
> mri_surf2surf \
> --s con_52 \#It is my Processed freesurfer date
> --trgsubject fsaverage \
> --hemi lh \
> --sval lh.t
Try using --srcsubject instead of --s. Also, remember to include the
terminal output. Also, there's probably no need to reshape it.
doug
On 09/06/2012 10:54 AM, zzy7...@mail.ustc.edu.cn wrote:
> Hi Bruce
> My command line is
> cd $SUBJECTS_DIR/subjid/surf
> mri_surf2surf \
>--s con_52 \
Hi Doug,
As Bruce suggested, you may give me some help.
My question is: I paint SPM results onto Freesurfer surface, is it possible
to get the size and name of clusters on the surface?
Thanks
Karry
On Mon, Sep 3, 2012 at 10:16 PM, keepmoon wrote:
>
> Hi Bruce,
>
> Thanks for your answer! Yes
The command line to get the aseg was:
Mri_convert -rt nearest -c .nii.gz
aseg.mgz
Fslmaths was used to match label values to the colour lut and combine them all
into one file.
Thanks,
Jeff
On 2012-09-05, at 1:05 PM, Bruce Fischl wrote:
> what is your mri_convert command line?
>
> On We
and when you say it is "way off" what do you mean? Is the intensity volume
conformed in the same way?
On Thu, 6 Sep 2012, Jeff
Thompson wrote:
>
> The command line to get the aseg was:
>
> Mri_convert -rt nearest -c .nii.gz
> aseg.mgz
>
> Fslmaths was used to match label values to the colour l
Yes, it is probably best to do it with those as those have the averages
across the subjects used to create the atlas. If you just use the area
of the cluster on the pial, it will be somewhat smaller.
doug
On 09/06/2012 01:53 PM, Ritobrato Datta wrote:
> Hi Doug,
>
> I need to dump the surfa
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