[FieldTrip] Fieldtrip Compatibility with FSL generated meshes

Schoffelen, J.M. (Jan Mathijs) jan.schoffelen at donders.ru.nl
Sun Feb 8 10:08:07 CET 2015

Hi Berdakh,

What do you mean with ‘import anatomy folder’? Please check out the links below in order to formulate your question more constructively.



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,


On Feb 7, 2015, at 7:32 PM, Berdakh Abibullaev <berdakho at gmail.com<mailto:berdakho at gmail.com>> wrote:

Hi there,

Is there any way to "Import anatomy folder" generated by FSL into the

We are trying to work with infant MRI data pre-processed by FSL for infant EEG source estimation.

The data description is available here:
And, I am copying it below:


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.


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

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

ANTS...brain...brainstem: The individual files have the brain areas
ANTS...brain_atlas: Segmented atlas for all brain areas

Please help.


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