[MINC-users] conversion and viewing of functional data (AFNI-BRIK and HEAD) to mnc
Nameeta Lobo
minc-users@bic.mni.mcgill.ca
Thu Mar 17 13:14:04 2005
Hi
I want to actually use the MNI-ROIs instead of manually drawing ROIs. I work
with AFNI and so thought I could convert my AFNI structurals and functionals
into the MNC format. I have 43 sub bricks in my functional dataset which I know
are present too in the mnc format as the mincinfo: time gives me the number 43.
Also, to check the data I converted from AFNI to MINC and then back to AFNI. I
had all my 43 sub bricks with the same values in AFNI (the activation map looked
a little smooth though). I just cannot figure out how to see these 43 sub bricks
in MINC. xdisp is still not available and I havent downloaded postf yet. Also,
the functional dataset (statistical map) is a 4D and not a 3D.
1. How do I make this 3D?
2. I guess to see 4D data I should be using postf as xdisp is not available. Can
I see it using any other software?
3. You also mentioned that
> > > In register you can synchronize the functional and the structral and
> set
> > > the threshold of your t-values, put labels, and obtain stereotaxic
> > > coordinates.
As of now, I managed to upload the 4D functional data in the register window.
Besides moving that intensity bar, is there any other way to adjust thresholds.
Besides I guess this step does not help me right now as I still dont know how to
adjust the threshold for 44 sub bricks (this probably gives the same threshold
for all sub bricks)
5. How do I identify tag points. Is there some web page that I could read this
up? I just tried registering 2 volumes (test and retest) and played safe by
marking 4 equidistant points on the brain.
I am sorry to be so confused at this moment but it has been just 2 days ago that
I have been asked to manage this task and so am just googling and reading up
matter on your website and asking you so many questions.
Thank you all for your time and patience.
Nameeta
Quoting "Najmeh Khalili M." <najma@bic.mni.mcgill.ca>:
>
> > 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
>
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