Posted by
Michael Cundell on
Apr 24, 2009; 7:24pm
URL: http://imagej.273.s1.nabble.com/Reslice-from-line-selection-tp3692795p3692796.html
Sorry my response to wayne did not go to the list So I included it below.
v1.42 does not give me this problem and the lines do not go beyond the boundary of the box. Has the input and output spacing been replaced with just "line spacing" as there is now only one box for that?
Now using v1.42 I have tried to use the macro recorder to record a macro but with no luck. Can someone help me out with a macro for loading one of 20 ROIs in the ROI manager, reslicing it (0.1103 input and output spacing and a slice count of 50) and then creating a max projection of that and then saving the MAX projection as a TIFF, then close the reslice and max intensity of the reslice windows and then move on to the next ROI and do the same. Then I should be left with a folder that contains my Max intensity projections of the reslices.
I have no idea what im doing but I tried anyway by using the macro recorder for myself and came up with:
roiManager("Select", 0);
run("Reslice [/]...", "slice=0.1103 slice=50 rotate");
selectWindow("Reslice of SSC789_timelapse_01_R3D_D3D");
run("Z Project...", "start=1 stop=50 projection=[Max Intensity]");
saveAs("Tiff", "/data1/roi0.tif");
close();
close();
I was going to just copy and paste that 20 times and change the roiManager select numbers and increment the .tif file name because I have no idea how to automate that. But anyway, that macro alone doesnt work as it tells me that "Output Z-spacing (1pixels) is too large" when I try to run it. When recording the macro I did get an error from the macro recorder saying:
Duplicate keyword:
command: "Reslice [/]
Keyword: "slice"
Value: 1
add an underscore to the corresponding label in the dialog to make the first word unique.
Thanks
Mike
---------------------------
Hi,
I am using imageJ run on CentOS linux v1.41o which had the problem. I just
checked using my laptop which has v1.40g running on windows XP and that had
the same problem using a different deltavision image that was only 126MB
instead of the 2.6GB file i was opening in CentOS. However, I just updated
to v1.42 on my laptop by downloading ij.jar from
http://rsbweb.nih.gov/ij/upgrade/index.html and overwritting my old ij.jar
and the problem is now gone. Sorry I should have tried upgrading first.
All I was doing was drawing a line in my deltavision file, then reslice with
0.11micron input and output and a slice count of 10 (although all slice
counts i tried the lines went beyond the box). It was the same on both
versions of imageJ mentioned previously on separate machines with different
OS's.
Anyway, hopefully problem solved. I will go upgrade the linux computers
imageJ and try that. Should work
Thanks
Mike
_________________________________________________________________
View your Twitter and Flickr updates from one place – Learn more!
http://clk.atdmt.com/UKM/go/137984870/direct/01/