users > RE: Affine registration stops after generating cmd.sh
Jun 30, 2018  05:06 PM | Rob Kozol - Dept. of Biology, University of Miami
RE: Affine registration stops after generating cmd.sh
Sorry I should have explained those output files. Yes you are right that the cluster aborts the files due to the time limits I put in the job file. However, I have tried giving them more and more time with no results. Usually one brain with two .nrrd files goes through an affine, warp and two registrations in about two hours. Also I have run these on my computer with the same results, CMTK starts, creates an affine directory and then stops. I have left a terminal up for days with no change. 

As for the headers, I have tried and cannot determine anything specific. for example here is one that did not work

NRRD0004
# Created by Nrrd_Writer at Thu Jun 28 15:09:56 EDT 2018
type: uint8
encoding: raw
endian: big
dimension: 3
sizes: 1030 1411 138
space dimension: 3
space directions: (0.891265,0,0) (0,0.891265,0) (0,0,1.976)
space units: "microns" "microns" "microns"
------------------------------------------------------
(Fiji Is Just) ImageJ 2.0.0-rc-67/1.52d; Java 1.8.0_172 [64-bit]; Mac OS X 10.13.5; 360MB of 5333MB (6%)

Title: WTBG5_01.nrrd
Width: 918.0029 microns (1030)
Height: 1228.1632 microns (1378)
Depth: 272.688 microns (138)
Size: 187MB
Resolution: 1.1220 pixels per microns
Voxel size: 0.8913x0.8913x1.976 microns^3
ID: -2
Bits per pixel: 8 (grayscale LUT)
Display range: 0-255
Image: 1/138
No threshold
Magnification: 0.50
ScaleToFit: false
Uncalibrated
Path: /Users/robkozol/Desktop/WT_MS222_06/WT_BG_062518/WTBG5_01.nrrd
Screen location: 12,23 (1440x900)
SetMenuBarCount: 4 (261ms)
Coordinate origin: 0,0,0
No overlay
No selection

Here is one that worked

NRRD0004
# Created by Nrrd_Writer at Wed Jun 27 12:44:09 EDT 2018
type: uint8
encoding: raw
endian: big
dimension: 3
sizes: 1030 1381 138
space dimension: 3
space directions: (0.891265,0,0) (0,0.891265,0) (0,0,1.976)
space units: "microns" "microns" "microns"
------------------------------------------------------
(Fiji Is Just) ImageJ 2.0.0-rc-67/1.52d; Java 1.8.0_172 [64-bit]; Mac OS X 10.13.5; 1853MB of 5333MB (34%)

Title: WTBG4_01.nrrd
Width: 917.1117 microns (1029)
Height: 1214.7942 microns (1363)
Depth: 272.688 microns (138)
Size: 185MB
Resolution: 1.1220 pixels per microns
Voxel size: 0.8913x0.8913x1.976 microns^3
ID: -5
Bits per pixel: 8 (grayscale LUT)
Display range: 0-255
Image: 91/138
No threshold
Magnification: 0.50
ScaleToFit: false
Uncalibrated
Path: /Users/robkozol/Desktop/WT_MS222_06/WT_BG_062518/WTBG4_01.nrrd
Screen location: -40,72 (1440x900)
SetMenuBarCount: 49 (269ms)
Coordinate origin: 0,0,0
No overlay
No selection

The only difference I see are the height sizes because I am stitching two images together, but that doesn't seem to affect those that work (e.g. files are shorter and longer than the reference and work fine). 

Otherwise I agree that there is something odd about the files, but I cannot seem to figure it out.

Thanks,
Rob

Threaded View

TitleAuthorDate
Rob Kozol Jun 18, 2018
Rob Kozol Jun 28, 2018
Greg Jefferis Jun 28, 2018
Rob Kozol Jun 29, 2018
Greg Jefferis Jun 29, 2018
RE: Affine registration stops after generating cmd.sh
Rob Kozol Jun 30, 2018
Greg Jefferis Jun 30, 2018
Rob Kozol Jun 19, 2018
Greg Jefferis Jun 19, 2018
Rob Kozol Jun 19, 2018
Greg Jefferis Jun 19, 2018
Rob Kozol Jun 21, 2018
Greg Jefferis Jun 23, 2018
Rob Kozol Jun 19, 2018
Greg Jefferis Jun 19, 2018