[FieldTrip] fieldtrip Digest, Vol 51, Issue 6

RICHARDS, JOHN RICHARDS at mailbox.sc.edu
Sun Feb 8 21:09:39 CET 2015


The answer to the question about the ³Neurodevelopmental MRI database², is
yes you can import these files.  They are nifti.nii.gz files, and I have
used field trip to import them. I also have gone through the field trip
procedure to make source models, BEM and FEM head models from these data
(though that work is not available on the www site).  I have used these
head models in EMSE, BESA, CURRY, Fieldtrip.

FYI others on this list.  Each age has the complete information to make
head models for source analysis.  This includes:
Average MRI template
GM, WM, T2WCSF segmented priors
Fully segmented BEM-3, 4, or 5 compartment MRI volume
Fully segmented head volume for FEM model (e.g., gm, wm, csf, skull, skin,
eyes, muscle..)
10-10 electrode positions already co-registered on the head MRI volume
(created on the head as Virtual-10-10 electrodes)
EGI-GSN-128 and HGSN-128 electrode positions based on average electrodes
from individual participants.

See Richards, J.E. & Xie, W. (2015) Brains for all the ages: Structural
neurodevelopment in infants and children from a life-span perspective. In
J. Benson (Ed.), Advances in Child Development and Behavior (Volume 48,
chapter 7). Philadephia, PA: Elsevier. DOI:10.1016/bs.acdb.2014.11.001

Richards, J.E. Boswell, C., Stevens, M., & Vendemia, J.M.C. (2015).
Evaluating methods for constructing average high-density electrode
positions. Brain Topography, 28, 70-86, doi 10.1007/s01548-014-0400-8(pdf
<http://jerlab.psych.sc.edu/PDF/Expt80-adult.pdf>)

I am working on a paper describing the child and adolescent electrode
positions.


John

>
>Message: 1
>Date: Sat, 7 Feb 2015 12:32:30 -0600
>From: Berdakh Abibullaev <berdakho at gmail.com>
>To: fieldtrip at science.ru.nl
>Subject: [FieldTrip] Fieldtrip Compatibility with FSL generated meshes
>Message-ID:
>	<CAOjxBaoWOzRyHv-vx_5uHCj3Xf+umAr5m=Suw=O6HiSEXv9pKQ at mail.gmail.com>
>Content-Type: text/plain; charset="iso-8859-1"
>
>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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>------------------------------
>
>Message: 2
>Date: Sun, 8 Feb 2015 09:08:07 +0000
>From: "Schoffelen, J.M. (Jan Mathijs)" <jan.schoffelen at donders.ru.nl>
>To: FieldTrip discussion list <fieldtrip at science.ru.nl>
>Subject: Re: [FieldTrip] Fieldtrip Compatibility with FSL generated
>	meshes
>Message-ID: <DCFE72F8-BC60-4952-B92B-47CA4353B9BA at fcdonders.ru.nl>
>Content-Type: text/plain; charset="windows-1252"
>
>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_communi
>ty
>
>http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002
>202
>
>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<mailto: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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>fieldtrip at donders.ru.nl<mailto:fieldtrip at donders.ru.nl>
>http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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