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up vote 17 down vote

added by Vladimir Feb 1 at 16:51

I used four manually labeled, human brain MRI datasets in an evaluation study and have links to the them here: mindboggle.info/papers/… – Arno Klein Feb 2 at 23:57

And there are MANY unlabeled brain MRI volumes available!: nitrc.org/projects/fcon_1000, oasis-brains.org, nitrc.org/projects/multimodal – Arno Klein Feb 3 at 0:05

Data from 101 manually labeled brain image volumes and surfaces will be released soon as part of the Mindboggle project: mindboggle.info – Arno Klein Feb 3 at 0:09

Both NIF (www.neuinfo.org) broadly for all of neuroscience and NITRC (www.nitrc.org) offer listings of available data. Searching NITRC for 'data resources' (nitrc.org/search/…) generates 45 data sources, including the ones nicely identified by Arno Klein in a prior comment. – dnkennedy Feb 3 at 20:39

up vote 12 down vote

added by Vladimir Feb 1 at 20:14

up vote 11 down vote

added by Vladimir Feb 1 at 16:54

One can always try checking NITRC (www.nitrc.com); and get a listing of all resources that claim to do statistical analysis (nitrc.org/search/…) – dnkennedy Feb 3 at 20:30

For a complete preprocessing stream that handles resting-state fMRI data you can check out the scripts that are part of the 1000 Functional Connectomes Project: fcon_1000.projects.nitrc.org – Maarten Feb 8 at 9:59

There are a growing number of neuroimaging tools for fMRI analysis in R. R is an open source project so no expensive license to purchase such as for matlab. Still not mature enough for a comprehensive neuroimaging platform. – Ian Feb 16 at 9:33

up vote 10 down vote

added by satra Jan 31 at 3:11

	e.g. a single subject fMRI dataset - 100MB - 2GB (uncompressed) what about mouse, rat, monkey, eeg, etc.,.? – satra Feb 3 at 19:53
	Single subject MEG recording ( ~ 10-25 minutes) on a CTF 275 channel systems are typically 200-500 Mb – Ian Feb 16 at 9:36
	anybody with estimates on microscopy datasets? – satra Feb 26 at 15:54
	1 cm^2 scanned with a zeiss mirax at 40x and stored as a pyramidal virtual slide with 7 layers is about 130-150MB. – Isaiah Apr 30 at 16:09

up vote 10 down vote

added by Isaiah Feb 1 at 17:39

I think the first question to ask is what kind of large imaging study are you trying to support? I'm guessing that this is for DICOM data, no? XNAT is the system I am most familiar with and most likely to recommend for a neuroimaging study, but NBIA might be better if you are working with an oncology study and the sites are already familiar with it. – Nolan Nichols Feb 3 at 0:12

up vote 10 down vote

added by Isaiah Feb 1 at 17:43

this looks like an awesome tools questions. These sort of questions are on-topic on cogsci.SE as are all other neuroscience and related tools questions. We are trying to test how receptive the community is to neuroinformatics questions. Do you have the time to write up a full question on the topic there? – Artem Kaznatcheev May 14 at 21:09

up vote 10 down vote

added by Ailton Andrade de Oliveira Feb 1 at 19:33

Well, any registration algorithm can be used to transform anatomical labels to an unlabeled target brain image. I performed several evaluation studies evaluating registration-based neuroanatomical labeling. Please see mindboggle.info/papers/… and mindboggle.info/papers/… – Arno Klein Feb 3 at 0:58

In a few months we'll be releasing the new Mindboggle software to automate cortical labeling: mindboggle.info – Arno Klein Feb 3 at 1:01

Sorry to beat the NITRC drum, but, hey, that's what I do... Searching NITRC for resources that claim to do 'segmentation' generates 48 answers (including mindboggle!) (nitrc.org/search/…) It would take a little more manual human intervention to resolve which of these offer an automated approach, and which support 'whole brain' analysis, but it seems like a good start... – dnkennedy Feb 3 at 20:33

up vote 10 down vote

added by unidesigner Feb 2 at 15:18

up vote 8 down vote

added by Isaiah Feb 1 at 17:58

	You should check out ANTS and Gang Song one of the developers has definitely done slice co-registration to build 3d mouse models. picsl.upenn.edu/ANTS – satra Feb 1 at 20:55
	TrakEM2 is your friend: ini.uzh.ch/~acardona/trakem2_manual.html – unidesigner Feb 5 at 13:57

up vote 8 down vote

added by dnkennedy Feb 2 at 15:58

up vote 5 down vote

added by memyself Feb 2 at 10:51

up vote 2 down vote

added by unidesigner Feb 4 at 8:59

This is also a good question for the proposed community "Digital Preservation". – Jennifer Davis Apr 25 at 4:33

up vote 1 down vote

added by unidesigner Feb 2 at 15:03

up vote 1 down vote

added by unidesigner Feb 4 at 9:16

up vote 1 down vote

added by memyself Feb 7 at 7:52

up vote 1 down vote

added by Nolan Nichols Feb 9 at 4:38

up vote 1 down vote

added by satra Feb 13 at 14:33

The human brain consumes between 20-25 W (hypertextbook.com/facts/2001/JacquelineLing.shtml). A Pentium 4 2.8 GHz consumes up to 85 W, but some low power CPUs such as the IXC1100 can consume as little as 2.4 W – Yann Apr 2 at 16:58

up vote 1 down vote

added by tdc Feb 16 at 21:11

	see nipy.org. within that umbrella we have been developing nipype which is a python framework for integrating analyses across existing tools. also see pymvpa.org for machine learning tools applied to neuroimaging data – satra Feb 26 at 15:58
	@satra thanks, will take a look – tdc Feb 27 at 8:31

up vote 1 down vote

added by satra Feb 26 at 15:56

	e.g., iRODS (+iDrop) - see: irods.org – satra Feb 26 at 16:01
	amazon S3 - aws.amazon.com/s3 – Nolan Nichols May 2 at 22:04

up vote 1 down vote

added by Nate Apr 27 at 15:28

up vote 1 down vote

added by Nate Apr 27 at 15:35

up vote 1 down vote

added by Nolan Nichols May 2 at 20:49

up vote 0 down vote

added by unidesigner Feb 4 at 9:06

Is this a neuroscience question or a neuroinformatics question? – Matt Feb 6 at 22:19

True, it is a neuroscience question. – unidesigner Feb 11 at 17:26

but if there was a database describing those tradoffs, i'd argue that would be a neuroinformatics tool – Nolan Nichols May 2 at 20:51

This question would be on-topic at cogsci.SE. That site is in public beta, so feel free to post it there as a full question. – Artem Kaznatcheev May 14 at 21:13