[MINC-users] conversion and viewing of functional data (AFNI-BRIK
and HEAD) to mnc
Robert VINCENT
minc-users@bic.mni.mcgill.ca
Wed Mar 16 12:00:04 2005
Hi,
Andrew Janke and I are working to get postf and xdisp in distributable
form. They are not currently available on the website.
I'm also working on a new version of Register which will allow viewing of
4D and 3D data alongside one another.
-bert
On Wed, 16 Mar 2005, Najmeh Khalili M. wrote:
>
> > 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
>
> _______________________________________________
> MINC-users@bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>