AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

History of AFNI updates  

|
June 17, 2009 08:56AM
If you REALLY want to use the AFNI GUI to export raw data slices, you have to do the following:

* In the image viewer, click on Disp
* In the Disp controller, click all the "Save to" buttons off
* Also click "Save One" off (unless you just want 1 slice)
* Now the "Save" button in the image viewer should read "Save:bkg" which means it will save the background image data.
* You can now use "Save:bkg" to write out the raw data from the Underlay dataset.

The format (usually) is a small ASCII header indicating the data type and image dimensions, and then the raw data.
The header (if present) is of the form

MRI d x y\n

where
* d = data type: 0=byte 1=short 2=int 3=float 4=double 5=complex 6=rgb
* x = number of pixels in each row
* y = number of rows
* \n means the ASCII newline character

Note that int and double are not supported AFNI dataset types, and so data type codes 2 and 4 will never be written by the image viewer!

However, the header described above will not be written if the data type is short or byte and the image dimensions are square and are both powers of 2 from 64..1024 -- then the file will be just the raw data and nothing else. This "feature" is a holdover from the early days of AFNI (1994-6) at the Medical College of Wisconsin, since these were the data formats we received from the EPI reconstruction software and there were a bunch of programs that expected "really raw" image data like this.

I don't believe this "save the raw slices" feature has been used in AFNI by anyone for many years. I have not explained it for well over 10 years, and you are basically lucky that I have an excellent memory.
Subject Author Posted

Exporting to bmp format

siamak yousefi June 15, 2009 06:18PM

Re: Exporting to bmp format

bob cox June 16, 2009 11:46AM

Re: Exporting to bmp format

siamak yousefi June 16, 2009 04:33PM

Re: Exporting to bmp format

rick reynolds June 16, 2009 05:00PM

Re: Exporting to bmp format

bob cox June 17, 2009 08:56AM

Re: Exporting to bmp format

siamak yousefi June 17, 2009 05:12PM

Re: Exporting to bmp format

rick reynolds June 18, 2009 10:34AM

Re: Exporting to bmp format

siamak yousefi June 18, 2009 05:15PM