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

[Najmeh Khalili M.]

> 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.

I don't think we have a minc4dim3 command. What I suggested was that after
statistical analyses, your 4D fMRI volume will be reduced to a 3D
statistical map.

Please take a look at visualization tools in
www.bic.mni.mcgill.ca/software. postf and xdisp should be a part of minc
package.

Also, it appears that your afni-to-minc conversion does not specify the
temporal dimension of your data. I am not familiar with AFNI format, bt I
cannot decipher the time-step/start from the 3dinfo output that you
have printed below either.

N.

>
> 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