File - Image - Import Sequence

[Ganesh Narayanasamy-2]

Hi,
 Here is a query from a newbie to the ImageJ listserv. I have a stack of CT
images with a naming sequence that I have never seen before. When I opened
it using File>Import>ImageSequence, the file stack opened in an incorrect
order.

 Here are the file names (and the order in which it got opened in
ImageSequence within brackets).

CT.rtp1.1.DAN.CHESTCT.T.137.CT.dcm (5)
CT.rtp1.1.DAN.CHESTCT.T.139.5.CT.dcm (1)
CT.rtp1.1.DAN.CHESTCT.T.142.CT.dcm (3)
CT.rtp1.1.DAN.CHESTCT.T.144.5.CT.dcm (6)
CT.rtp1.1.DAN.CHESTCT.T.147.CT.dcm (4)
CT.rtp1.1.DAN.CHESTCT.T.149.5.CT.dcm (2)

I would like to open the images in the sequence given above but don't know
how to. So, I tried these steps in vain.
Removed the dots,
Replaced dots with "_"
Appended a number to the end of the filename like
CTrtp11DANCHESTCTT137CT_1.dcm, CTrtp11DANCHESTCTT1395CT_2.dcm etc but that
did not help either.

I tried playing around with options in the Image sequence pop-up menu like
Starting Image:1, Increment:1; Sort Images Numerically etc, that did not
work either.

Can you help me with opening files in sequence given above. Thanks,
Ganesh

[ctrueden]

Hi Ganesh,

Did you try adding zeroes to the integer numbers, like so:

CT.rtp1.1.DAN.CHESTCT.T.137.0.CT.dcm
CT.rtp1.1.DAN.CHESTCT.T.139.5.CT.dcm
CT.rtp1.1.DAN.CHESTCT.T.142.0.CT.dcm
CT.rtp1.1.DAN.CHESTCT.T.144.5.CT.dcm
CT.rtp1.1.DAN.CHESTCT.T.147.0.CT.dcm
CT.rtp1.1.DAN.CHESTCT.T.149.5.CT.dcm

At least then the numbering will be consistent. If that doesn't work you
could also remove the decimal point like:

CT.rtp1.1.DAN.CHESTCT.T.1370.CT.dcm
CT.rtp1.1.DAN.CHESTCT.T.1395.CT.dcm
 CT.rtp1.1.DAN.CHESTCT.T.1420.CT.dcm
CT.rtp1.1.DAN.CHESTCT.T.1445.CT.dcm
CT.rtp1.1.DAN.CHESTCT.T.1470.CT.dcm
CT.rtp1.1.DAN.CHESTCT.T.1495.CT.dcm

And if all else fails, with this latter numbering scheme, the Bio-Formats
Importer should correctly identify the file group if you check the "Group
files with similar names" option.

-Curtis

On Mon, Mar 15, 2010 at 1:26 PM, Ganesh Narayanasamy
<[hidden email]>wrote:

> Hi,
>  Here is a query from a newbie to the ImageJ listserv. I have a stack of CT
> images with a naming sequence that I have never seen before. When I opened
> it using File>Import>ImageSequence, the file stack opened in an incorrect
> order.
>
>  Here are the file names (and the order in which it got opened in
> ImageSequence within brackets).
>
> CT.rtp1.1.DAN.CHESTCT.T.137.CT.dcm (5)
> CT.rtp1.1.DAN.CHESTCT.T.139.5.CT.dcm (1)
> CT.rtp1.1.DAN.CHESTCT.T.142.CT.dcm (3)
> CT.rtp1.1.DAN.CHESTCT.T.144.5.CT.dcm (6)
> CT.rtp1.1.DAN.CHESTCT.T.147.CT.dcm (4)
> CT.rtp1.1.DAN.CHESTCT.T.149.5.CT.dcm (2)
>
> I would like to open the images in the sequence given above but don't know
> how to. So, I tried these steps in vain.
> Removed the dots,
> Replaced dots with "_"
> Appended a number to the end of the filename like
> CTrtp11DANCHESTCTT137CT_1.dcm, CTrtp11DANCHESTCTT1395CT_2.dcm etc but that
> did not help either.
>
> I tried playing around with options in the Image sequence pop-up menu like
> Starting Image:1, Increment:1; Sort Images Numerically etc, that did not
> work either.
>
> Can you help me with opening files in sequence given above. Thanks,
> Ganesh
>