[HCP-Users] Cifti to gifti conversion

[LEVI SOLOMYAK]

Dear All,

I am working with a cifti dlabel.nii file. I'm attempting to use those
labels to create ROI's but i need those files to be in gifti. I have tried
various ways of doing this with no success.

I have been relying on the following two commands:
wb_command -cifti-label-to-roi
wb_command -cifti-convert -to-gifti-ext

but am guessing that I have not been implementing them properly.

I have tried first creating the ROIs and then converting them to gifti and
vice versa. When I convert the dlabel file to label.gii file I get an
invalid structure error.
When I create the rois and then attempt to convert them to gifti surface
files I get a "Number of data arrays MUST be two in a SurfaceFile" error.

Any help would be much appreciated!

Best,
I.S.

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Re: [HCP-Users] Cifti to gifti conversion

[Donna Dierker]

I use wb_command -cifti-separate for this purpose.


On Nov 11, 2015, at 10:52 AM, LEVI SOLOMYAK  
wrote:

> Dear All,
> 
> I am working with a cifti dlabel.nii file. I'm attempting to use those labels 
> to create ROI's but i need those files to be in gifti. I have tried various 
> ways of doing this with no success. 
> 
> I have been relying on the following two commands: 
> wb_command -cifti-label-to-roi 
> wb_command -cifti-convert -to-gifti-ext
> 
> but am guessing that I have not been implementing them properly. 
> 
> I have tried first creating the ROIs and then converting them to gifti and 
> vice versa. When I convert the dlabel file to label.gii file I get an invalid 
> structure error. 
> When I create the rois and then attempt to convert them to gifti surface 
> files I get a "Number of data arrays MUST be two in a SurfaceFile" error. 
> 
> Any help would be much appreciated!
> 
> Best,
> I.S. 
> 
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
> 


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Re: [HCP-Users] Cifti to gifti conversion

[Timothy Coalson]

-cifti-convert is not intended to make files that will work nicely as
single-surface files, it is more of a hack for software that can't read
cifti yet:

-cifti-convertDUMP CIFTI MATRIX INTO OTHER FORMATS

The -cifti-separate command is how you take a structure from a cifti file
and turn it into a non-cifti file that will load and display nicely.

Cifti does not store surface geometry, so .surf.gii files must be derived
from something else (like freesurfer or other provided files).  Surface
files also don't store ROIs, those go in .func.gii files, just like other
surface data besides geometry.

Tim


On Wed, Nov 11, 2015 at 10:59 AM, Donna Dierker 
wrote:

> I use wb_command -cifti-separate for this purpose.
>
>
> On Nov 11, 2015, at 10:52 AM, LEVI SOLOMYAK 
> wrote:
>
> > Dear All,
> >
> > I am working with a cifti dlabel.nii file. I'm attempting to use those
> labels to create ROI's but i need those files to be in gifti. I have tried
> various ways of doing this with no success.
> >
> > I have been relying on the following two commands:
> > wb_command -cifti-label-to-roi
> > wb_command -cifti-convert -to-gifti-ext
> >
> > but am guessing that I have not been implementing them properly.
> >
> > I have tried first creating the ROIs and then converting them to gifti
> and vice versa. When I convert the dlabel file to label.gii file I get an
> invalid structure error.
> > When I create the rois and then attempt to convert them to gifti surface
> files I get a "Number of data arrays MUST be two in a SurfaceFile" error.
> >
> > Any help would be much appreciated!
> >
> > Best,
> > I.S.
> >
> > ___
> > HCP-Users mailing list
> > HCP-Users@humanconnectome.org
> > http://lists.humanconnectome.org/mailman/listinfo/hcp-users
> >
>
>
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>

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