You can use --proj frac 0 1 .1
See the --help for more info
doug
On 11/29/14 8:22 PM, Bruce Fischl wrote:
> Hi Angela
>
> that actually looks ok. It should follow the gray/white boundary I
> believe. Have you looked at it in the individual subject space without
> mapping it to the MNI coords? I t
thank you!
> Hi Angela
>
> that actually looks ok. It should follow the gray/white boundary I
> believe. Have you looked at it in the individual subject space without
> mapping it to the MNI coords? I think there are options in mri_label2vol
> to
> fill in the whole cortical ribbon instead of just
Hi Angela
that actually looks ok. It should follow the gray/white boundary I
believe. Have you looked at it in the individual subject space without
mapping it to the MNI coords? I think there are options in mri_label2vol to
fill in the whole cortical ribbon instead of just painting the gray/whi
Hi Bruce,
I have followed your suggestions using the 'custom fill' botton and then
saving the label and using mri_label2vol. This is the command I used:
mri_label2vol --label gyrif_lh.label --temp MNI152_T1_1mm_brain.nii.gz
--reg $FREESURFER_HOME/average/mni152.register.dat --o gyrif_lh.nii.gz
Ho
great!
thank you so much
Angela
>
> Sorry, the input should be area, not thickness, ie,
>
> mri_segstats --i $SUBJECTS_DIR/fsaverage/lh.white.avg.area.mgh --seg
> gyrbin.mgh --id 1 --sum gyrbin.sum
>
>
> On 11/2/14 11:30 AM, Douglas Greve wrote:
>>
>> First, create binary masks, something like (
Sorry, the input should be area, not thickness, ie,
mri_segstats --i $SUBJECTS_DIR/fsaverage/lh.white.avg.area.mgh --seg
gyrbin.mgh --id 1 --sum gyrbin.sum
On 11/2/14 11:30 AM, Douglas Greve wrote:
>
> First, create binary masks, something like (for a threshold of 2 = p <
> .01)
>
> mri_bina
First, create binary masks, something like (for a threshold of 2 = p < .01)
mri_binarize --i gyrification/sig.mgh --abs --min 2 --binval 1 --o
gyrbin.mgh
mri_binarize --i thickness/sig.mgh --abs --min 2 --binval 2 --o
thickbin.mgh
fscalc gyrbin.mgh mul thickbin.mgh mul 3 -o gyr_and_thick_bin.
Thank you Bruce!
I have another question:
I would like to show the statistical maps of differences in gyrification
and those of cortical thickness. Is it possible with freeview?
I would also like to calculate the degree of overlapping between these two
maps (percentage of vertices or mm2). Is it p
Hi Angela
in tksurfer you can show the overlay, and use the "custom fill" button to
fill the area that is above threshold on the surface. Then save it as a
label and use mri_label2vol to write it into a volume. If the output volume
you give has the extension .nii.gz it will save it in nifti for
Dear all,
I found some interesting findings about gyrification and I would like to
test any related problem in structural connectivity.
My idea was to use the area where I found significant lower gyrification
in my sample to perform probabilistic tracking with FSL.
My question is: is there any way
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