from isq to DICOM format

[Maura Monville]

    Dear All,
I browsed through ImageJ documentation on the wiki.
To my dismay not all the features are explained to my satisfaction.
Therefore, I would be grateful if someone could suggest a good updated ImageJ user's manual.

I am interested in
1. reading an isq file from Scanco micro-CT scan made up pf 856 slices)
2. save the file in DICOM format

I realized ImageJ can do step 1. but cannot do step 2.
I saw one of the possible output formats is "Analyze 7.5". Is this the format of Mayo/Clinic BIR
ANALYZE biomedical package ? If the answer is "yes" then I will be more than grateful as we
plan to use ANALYZE PRO (now version 11) to manipulate the micro-CT data.
Otherwise I can save the micro-CT data in TIF format as ANALYZE can read such format.
I tried to save selecting TIF output but if seems to have saved just one slice. Instead I need to save the whole
stack of slices (856). CAn someone help me with that ?

Thank you so much.
Best regards,
Maura
--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[ctrueden]

Hi Maura,

> I would be grateful if someone could suggest a good updated ImageJ
> user's manual.

Did you see the ImageJ User Guide? It is quite thorough:
http://imagej.nih.gov/ij/docs/guide/

And if you use the Fiji distribution of ImageJ, the Fiji wiki at
http://fiji.sc/ has additional information about many of the plugins it
provides.

> 2. save the file in DICOM format

The Tudor DICOM tools can save as DICOM:
http://santec.tudor.lu/project/dicom

But my understanding (from previous threads on this subject) is that the
saving is rather rudimentary. Consider saving to TIFF (which will
definitely save your entire multidimensional image, not just one slice).

If you have additional problems, I suggest you be very specific in
describing your difficulties. See
http://stackoverflow.com/help/how-to-askfor guidance.

Regards,
Curtis


On Wed, Mar 5, 2014 at 10:59 AM, Maura Monville <[hidden email]>wrote:

>     Dear All,
> I browsed through ImageJ documentation on the wiki.
> To my dismay not all the features are explained to my satisfaction.
> Therefore, I would be grateful if someone could suggest a good updated
> ImageJ user's manual.
>
> I am interested in
> 1. reading an isq file from Scanco micro-CT scan made up pf 856 slices)
> 2. save the file in DICOM format
>
> I realized ImageJ can do step 1. but cannot do step 2.
> I saw one of the possible output formats is "Analyze 7.5". Is this the
> format of Mayo/Clinic BIR
> ANALYZE biomedical package ? If the answer is "yes" then I will be more
> than grateful as we
> plan to use ANALYZE PRO (now version 11) to manipulate the micro-CT data.
> Otherwise I can save the micro-CT data in TIF format as ANALYZE can read
> such format.
> I tried to save selecting TIF output but if seems to have saved just one
> slice. Instead I need to save the whole
> stack of slices (856). CAn someone help me with that ?
>
> Thank you so much.
> Best regards,
> Maura
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html