Dear Davide,
I have checked the FLICA documentation more carefully and now I see the
issue: FLICA is expecting Freesurfer surface data in mgh format.
However, it’s not very straightforward tp provide this format with
CAT12 surface data that are always saved as gifti files. You can try to
use the mris_convert tool from Freesurfer to convert - and more
importantly - to combine data of all subjects into one mgh file:
mris_convert --combinesurfs FWHM.mesh.TYPE.RESAMP.SUBJECT1.gii
FWHM.mesh.TYPE.RESAMP.SUBJECT2.gii …
FWHM.mesh.TYPE.RESAMP.SUBJECTx.gii FWHM.mesh.TYPE.mgh
while the names are that from the resampled and smoothed data:
FWHM filtersize in FWHM after smoothing (e.g. s15)
SURF left, right, or both hemispheres [ lh | rh | mesh ]
TYPE surface data file [ thickness | gyrification | fractaldimension |
... ]
RESAMP resampling to 164k (Freesurfer) or 32k (HCP) mesh [ resampled |
resampled_32k ]
SUBJECTx subject names
However, I am not sure whether you can use the combined hemipsheres
(e.g. „mesh“) or you have to deal with the hemispheres separately
(change the resampling options for that).
Best,
Christian
Christian Gaser, Ph.D.
Professor of Computational Neuroscience/Neuroimaging
Biomagnetic Center
Structural Brain Mapping Group
Department of Neurology
Jena University Hospital
Am Klinikum 1, D-07747 Jena, Germany
Tel: ++49-3641-9325778 Fax: ++49-3641-9325772
e-mail: [log in to unmask]
http://www.neuro.uni-jena.de
On 12 Feb 2020, at 16:26, Davide Fedeli wrote:
> Dear Christian, thank you for your fast reply.
>
> From the paper by Maglanoc et al., (2020) it seems possible to combine
> multimodal data in FLICA (https://doi.org/10.1002/hbm.24802) (e.g they
> used grey matter volume, cortical thickness, surface area, mean
> diffusivity, radial diffusivity, fractional anisotropy and
> resting-state data).
> In their paper GMV is extracted with CAT, while the surface data are
> obtained from freesurfer's processing pipeline (and it seems to me
> that surface maps are then registered to fsaverage template)
> We have used CAT12 (we love CAT12!) for our cortical processing. Our
> problem is that we cannot find how to convert CAT12 .gii surface data
> (e.g. cortical thickness and gyrification) into .mgh surfaces in
> FreeSurfer. In fact, when we use the mris_convert function, the output
> is not correctly read by FLICA.
>
> Do you have any thoughts on how to solve this problem? Does this
> "joint" metodology seems to be reliable?
>
> Many thanks and best whishes
> Davide
>
> ========
> Maglanoc, L. A., Kaufmann, T., Jonassen, R., Hilland, E., Beck, D.,
> Landrø, N. I., & Westlye, L. T. (2020). Multimodal fusion of
> structural and functional brain imaging in depression using linked
> independent component analysis. Human Brain Mapping, 41(1), 241-255.
> https://doi.org/10.1002/hbm.24802
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