[MINC-users] conversion and viewing of functional data (AFNI-BRIK and HEAD) to mnc

[Nameeta Lobo]

Hi Najmeh,

Thank you for that detailed explanation. However, I am having problems trying to
find the minc4dim3 command and the xdisp software. We have the 1.3 version of
MINC but I dont seem to find the above command anywhere. Also, where could I get
xdisp from? The only thing that I could find on google was something that I had
to sign up a lot for. 

Also, is there any other statistical analysis I should be carrying out on my
funtional data. I have just used deconvolution in AFNI and as I mentioned in my
previous e-mail, used the 3dAFNItoMINC to convert it. My data is in the short
format and has 43 sub bricks in AFNI. 

running the mincinfo command on this minc functional data gives me the following.

mincinfo story_motion_new.mnc
file: story_motion_new.mnc
image: signed__ float -4270.3427734375 to 287392.3125
image dimensions: time xspace zspace yspace
    dimension name         length         step        start
    --------------         ------         ----        -----
    time                       44      unknown      unknown
    xspace                     30            5        -71.1
    zspace                     64        -3.75      118.125
    yspace                     64        -3.75      133.825

with the original 3dinfo story_motion_new+orig.BRIK command line in AFNI gives me
Dataset File:    story_motion_new+orig
Identifier Code: XYZ_NLmqlhuH1PInWR8tBL7qRg  Creation Date: Wed Oct 13 15:46:39 2004
Dataset Type:    Func-Bucket (-fbuc)
Byte Order:      LSB_FIRST [this CPU native = LSB_FIRST]
Storage Mode:    BRIK file
Data Axes Orientation:
  first  (x) = Anterior-to-Posterior
  second (y) = Superior-to-Inferior
  third  (z) = Left-to-Right   [-orient ASL]
R-to-L extent:   -73.900 [R] -to-    71.100 [L] -step-     5.000 mm [ 30
voxels]A-to-P extent:  -133.825 [A] -to-   102.425 [P] -step- 3.750 mm [ 64
voxels]I-to-S extent:  -118.125 [I] -to-   118.125 [S] -step-     3.750 mm [ 64
voxels]Number of values stored at each pixel = 44

with values then printed for every sub brick. 

so far this is all that I have with me as I cannot view the minc funtional data
yet. Please do help and thank you for your time.

nameeta






Quoting "Najmeh Khalili M." <najma@bic.mni.mcgill.ca>:

> 
> Hi Nameeta,
> 
> In order to use register, you need to have your functional data analyzed
> and the dimension reduced from 4D to 3D.
> 
> Once you have your functional t-maps or effects in minc you just call
> 
> register structural.mnc functional-tmap.mnc
> 
> In register you can synchronize the functional and the structral and set
> the threshold of your t-values, put labels, and obtain stereotaxic
> coordinates.
> 
> Of course, display has more functionality but it is poorly documented and
> not too trivial to work with. It's very well worth exploring because it
> allows you to pain labels and to get 3D views of brain surface and etc.
> 
> If you want to look at your time-series, ie 4D fMRI data, use xdisp. It
> allows you to eyeball motion artifacts ans activations, but it does not
> ovrlay your functional data on anatomical data.
> 
> Hope this helps,
> Naj
> 
> 
> 
> 
> On Tue, 15 Mar 2005, Nameeta Lobo wrote:
> 
> >
> > Hello all,
> >
> > I am a newbie to this software. I have AFNI datasets which I want to
> convert to
> > the MNC format. I used the 3dAFNItoMINC command and converted a structural
> to
> > the mnc format and viewed it using mincview (which needed xv) as well as
> using
> > Display. I could see all the 3 views with Display which was good but with
> > mincview could see just one view . I want to look at my functional data
> too. I
> > have been going through your web page and came across Register. My question
> is
> > how do I view my functional data as an overlay on my structural. Should I
> be
> > using the 3dAFNItoMINC command, converting this functional data into mnc
> and
> > then use Register and merge the 2 datasets (structural and functional) or
> am I
> > totally off on this one. If yes, could you please give me some suggestions
> as to
> > how to go about working on this data. Any help will be really
> appreciated.
> >
> > thanks
> > N
> > _______________________________________________
> > MINC-users@bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >
> 
> 
> 
> 
> 
>