[FieldTrip] Fieldtrip Compatibility with FSL generated meshes

Berdakh Abibullaev berdakho at gmail.com
Sun Feb 8 17:43:47 CET 2015

Hello Jan-Mathijs,

My apologies for not being constructive in posing my question.
By anatomy folder I meant the MRI segmentation results (scalp, outer skull,
inner skull (CSF) and brain) generated by FSL.

*Can I use the FieldTrip to load those segmentation results to generate
meshes and model BEM for source estimation? *

As you know that extracting cortical matters from infant MRI is an
extremely difficult task as

most MRI segmentation tools are developed using adult brain parameters.
And, I presume that "ft_volumesegment" cannot handle infant MRI

Thanks again,

On Sun, Feb 8, 2015 at 3:08 AM, Schoffelen, J.M. (Jan Mathijs) <
jan.schoffelen at donders.ru.nl> wrote:

>  Hi Berdakh,
>  What do you mean with 'import anatomy folder'? Please check out the links
> below in order to formulate your question more constructively.
> http://fieldtrip.fcdonders.nl/faq/how_to_ask_good_questions_to_the_community
> http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002202
>  Note that FieldTrip's low-level fileio functions know how to deal with
> compressed nifti files, so if your question means 'can I use FieldTrip to
> load in images that have been constructed with FSL', the answer would be
> yes.
> For information about supported dataformats, see:
> http://fieldtrip.fcdonders.nl/dataformat
> Best wishes,
>  Jan-Mathijs
>  On Feb 7, 2015, at 7:32 PM, Berdakh Abibullaev <berdakho at gmail.com>
> wrote:
>  Hi there,
>  Is there any way to "Import anatomy folder" generated by FSL into the
> FieldTrip
> ?
> We are trying to work with infant MRI data pre-processed by FSL for infant
> EEG source estimation.
> The data description is available here:
>  http://jerlab.psych.sc.edu/NeurodevelopmentalMRIDatabase/description.html
> And, I am copying it below:
> Description.
> The database consists of MRI average templates for a number of ages; in
> 1-3 month increments through 18 months; then half-year increments through
> 19-5 years; then 5 year increments through 89 years. The templates were
> done separately for brain and head. Also included are segmentation PVE
> volumes for gm/wm/csf; T2W-derived CSF; and non-myelinated axons (NMA) for
> infants. Access to the dataset is separated by ages (infants; 0-12 mo;
> preschool, 15 mo through 4-0 years; children 4-5 through 10-5 yrs;
> adolescents 11-0 through 17-5 yrs; adults 20-89 years).
> The segment data for ages 15-months and older consists of GM, WM, CSF, and
> T2W-derived CSF. The best combination of segments would be the
> image_aposteriori_seg data, using GM, WM, and T2W-derived CSF for priors.
> For 3 through 12 months, the best combination of segments would be the
> nma_seg data; using GM, WM, NMA, and T2W-derived CSF. The "CSF" PVE
> segments are "Other Matter" in a 3-class segmentation (GM, WM, "Other
> Matter") and does not reflect actual CSF. The T2W-derived CSF is identified
> as bright voxels in the T2W scan and represent actual CSF in the brain or
> head. There is an atlas derived from FSL "Harvard-Oxford" cortical and
> subcortical atlas for the infants, 8 10 12 14 16 18, and 20-24 year old
> templates.
> Overview:
> ANTS....brain.nii.gz: Average MRI template derived from extracted brain
> ANTS....head.nii.gz: Average MRI template derived from whole head
> ANTS....brain-head: brain extracted from head template
> ANTS....T2W_brain: MRI template separate for extracted brain T2W
> ANTS....T2W_head: MRI template separate for whole head T2W
> Segments
> AVG...T2W_brain...: T2W for individual participants, warped to template,
> averaged
> AVG...image_seg_...: Image-based segment averages
> AVG...image_aposteriori_seg_.. : Age-template priors with a posteriori FAST
> AVG...MNI_aposteriori_seg_...: AVG of MNI-template priors, with a
> posteriori FAST
> AVG...nma_seg_: For infants, non-myelinated axons separate from gray matter
> AVG....seg_csf: "Other matter" in 3-class segmentation
> AVG....seg_t2wcsf: T2W-derived CSF
> Atlas:
> ANTS...brain...brainstem: The individual files have the brain areas
> ANTS...brain_atlas: Segmented atlas for all brain areas
>   Please help.
>  Thanks,
> Berdakh.
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