Hi Ahearn,

the base needs a few files from all cross time points for processing. An individual -long run needs files from the base and from *all* cross time points. What is needed and how the stream works is described on the wiki although that may not be complete, especially in situations with edits. Usually though, files are passed on the command line and not opened implicitly (at least not from a different subject/timepoint).

Your list below is not complete, I am certain transforms (talairach and transforms across the base and time points) are needed. Also it is unclear if below you talk about the first case (to run a base with data from all cross) or the second case (to run a long with data from base and all cross).

Why not run a bunch of subjects all the way through, then move them off the computer and run a bunch of other subjects rather than having partial data (which also makes things very hard to replicate if anything goes wrong)?

Best, Martin

On 03/04/2016 07:09 AM, Ahearn, T wrote:

Hello,

I need to process a good few thousand T1 images on a machine that I can’t store all the data on. I’d like to transfer as few files as possible to the processing machine so that I can perform longitudinal processing. I have successfully longitudinally processed some patients with a sub set of their data but others seem to hang (the template looks ok) during mri_ca_label. Is there a list of the minimum files that I’d need to perform longitudinal processing? The files I’ve had some success with are below:

/mri/orig/001.mgz

/mri/norm.mgz

/mri/wm.mgz

/mri/aseg.auto_noCCseg.mgz

/mri/rawavg.mgz

/mri/orig.mgz

/mri/brainmask.mgz

/mri/aseg.mgz

Thanks

Trev

Dr. Trevor Ahearn

Principal Physicist (MRI)

NHS Grampian

The University of Aberdeen is a charity registered in Scotland, No SC013683.
Tha Oilthigh Obar Dheathain na charthannas clàraichte ann an Alba, Àir. SC013683.
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Martin Reuter, PhD
Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
Web  : http://reuter.mit.edu