OrthoView has a point and click feature where you can click on a voxel and
it will tell you the anatomical location of that voxel.
Peak_nii does the same thing for all peaks in your image above your
thresholds.
Best Regards, Donald McLaren
=================
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
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On Tue, Mar 19, 2013 at 5:51 PM, James Lee <[log in to unmask]> wrote:
> Luigi,
>
> For a long time I have wanted a routine that would look up anatomic
> locations directly in MNI coordinates, without the need to convert to
> Talairach coordinates, with the known weakness of the single-subject
> Talairach atlas.
>
> So I wrote a simple matlab script, included below, which is based on
> the more accurate probabilistic Hammers_mith_atlas_n30r83 atlas. The
> script essentially loads the atlas image, and the list of labels, and
> then "looks up" the label at the voxel coordinates requested by the
> user.
>
> Thought you might find this useful!
>
> Jim
>
>
>
> % Script to find anatomic location in MNI coords using Hammers_mith n30r83
> atlas
> % Written Mar 19, 2013 by James Lee, Imaging and Neuroscience center,
> % University of Utah
> % Known to run with spm5, not tested on any other version
> %
> % Run this from the directory that has the
> Hammers_mith_atlab_n30r83_SPM5.img
>
> addpath('/Users/jim/spm5_1782');
>
> % Load the atlas image
>
> disp('Loading Hammers_mith atlas n30r83 ...')
> P = char('Hammers_mith_atlas_n30r83_SPM5.img');
> V = spm_vol(P);
> for k=1:V.dim(3),
> d = V.dim(1:2);
> M = spm_matrix([0 0 k]);
> img = spm_slice_vol(V,M,d,0);
> ham(:,:,k)=img; % THE slice index can go first OR last
> end
>
> % Enter array of all labels -- better check this for typos
> % ODD NUMBERS = RIGHT SIDE
>
> labels{1}='R hippocampus';
> labels{2}='L hippocampus';
> labels{3}='R amygdala';
> labels{4}='L amygdala';
> labels{5}='R anterior temp lobe, medial part';
> labels{6}='L anterior temp lobe, medial part';
> labels{7}='R anterior temp lobe, lateral part';
> labels{8}='L anterior temp lobe, lateral part';
> labels{9}='R parahippocampal and ambient gyri';
> labels{10}='L parahippocampal and ambient gyri';
> labels{11}='R superior temp gyrus, posterior part';
> labels{12}='L superior temp gyrus, posterior part';
> labels{13}='R middle and inferior temporal gyrus';
> labels{14}='L middle and inferior temporal gyrus';
> labels{15}='R fusiform gyrus';
> labels{16}='L fusiform gyrus';
> labels{17}='R cerebellum';
> labels{18}='L cerebellum';
> labels{19}='brainstem';
> labels{20}='L insula';
> labels{21}='R insula';
> labels{22}='L lateral remainder of occipital lobe';
> labels{23}='R lateral remainder of occipital lobe';
> labels{24}='L cingulate gyrus, anterior part';
> labels{25}='R cingulate gyrus, anterior part';
> labels{26}='L cingulate gyrus, posterior part';
> labels{27}='R cingulate gyrus, posterior part';
> labels{28}='L middle frontal gyrus';
> labels{29}='R middle frontal gyrus';
> labels{30}='L posterior temporal lobe';
> labels{31}='R posterior temporal lobe';
> labels{32}='L inferiolateral remainder of parietal lobe';
> labels{33}='R inferiolateral remainder of parietal lobe';
> labels{34}='L caudate nucleus';
> labels{35}='R caudate nucleus';
> labels{36}='L nucleus accumbens';
> labels{37}='R nucleus accumbens';
> labels{38}='L putamen';
> labels{39}='R putamen';
> labels{40}='L thalamus';
> labels{41}='R thalamus';
> labels{42}='L pallidum';
> labels{43}='R pallidum';
> labels{44}='corpus callosum';
> labels{45}='R lateral ventricle (excluding temporal horn)';
> labels{46}='L lateral ventricle (excluding temporal horn)';
> labels{47}='R lateral ventricle, temporal horn';
> labels{48}='L lateral ventricle, temporal horn';
> labels{49}='third ventricle';
> labels{50}='L precentral';
> labels{51}='R precentral';
> labels{52}='L straight gyrus';
> labels{53}='R straight gyrus';
> labels{54}='L anterior orbital gyrus';
> labels{55}='R anterior orbital gyrus';
> labels{56}='L inferior frontal gyrus';
> labels{57}='R inferior frontal gyrus';
> labels{58}='L superior frontal gyrus';
> labels{59}='R superior frontal gyrus';
> labels{60}='L postcentral gyrus';
> labels{61}='R postcentral gyrus';
> labels{62}='L superior parietal gyrus';
> labels{63}='R superior parietal gyrus';
> labels{64}='L lingual gyrus';
> labels{65}='R lingual gyrus';
> labels{66}='L cuneus';
> labels{67}='R cuneus';
> labels{68}='L medial orbital gyrus';
> labels{69}='R medial orbital gyrus';
> labels{70}='L lateral orbital gyrus';
> labels{71}='R lateral orbital gyrus';
> labels{72}='L posterior orbital gyrus';
> labels{73}='R posterior orbital gyrus';
> labels{74}='L substantia nigra';
> labels{75}='R substantia nigra';
> labels{76}='L subgenual frontal cortex';
> labels{77}='R subgenual frontal cortex';
> labels{78}='L subcallosal area';
> labels{79}='R subcallosal area';
> labels{80}='L pre-subgenual frontal cortex';
> labels{81}='R pre-subgenual frontal cortex';
> labels{82}='L superior temp gyrus, anterior part';
> labels{83}='R superior temp gyrus, anterior part';
>
> addr(1) = 0;
>
> while addr(1) ~= 999
> addr(1:3)=input('Enter X Y Z voxel coordinates in brackets...or 999
> for exit >> ');
> if (addr(1) ~= 999) answer = ham(addr(1), addr(2), addr(3));
> else answer=0;
> end
> if (answer > 0) disp(labels(answer));
> else disp('No value found');
> end % End of if
> end % End of while
>
>
> On 3/12/13, John Ashburner <[log in to unmask]> wrote:
> >> I did custom pre-processing, so, of course, I normalized functional
> >> images
> >> with normalize fiunction of SPM.
> >>
> >> So, the coordinates I see in activations are MNI coordinates?
> >
> > If you spatially normalised the images by matching them to one of the
> > MNI-space template images supplied with SPM, then they should be in
> > MNI space, with co-ordinates in MNI space.
> >
> >
> >> In MNI space, are positive values of x coordinate related to right
> >> emisphere?
> >
> > They should be.
> >
> >
> >> I'm asking this, because, for example, for right hand task, I see
> >> more activations in right emisphere (positive value of x coordinate). Is
> >> it
> >> possible?
> >
> > This will depend on the file format of the original images. If you
> > have used NIfTI throughout, then the left and right sides should not
> > get mixed up. If they do come out wrong, then this would indicate a
> > bug (probably one of mine) somewhere in the code.
> >
> > If the original data were the old ANALYZE format, as would be used
> > with older versions of SPM (before SPM5), then there is a chance of
> > the laterality getting mixed up. However, if you converted your
> > original DICOM files using software that knows about NIfTI (and the
> > way it saves orientations in the headers), and all image manipulations
> > were with software that is NIfTI compatible, then there should not be
> > a problem.
> >
> > Note that the slices option of the stats results sometimes displays
> > the left side of the brain on the right side of the image. However,
> > the x coordinates reported should be correct.
> >
> > Best regards,
> > -John
> >
> > On 11 March 2013 20:08, Luigi Pavone <[log in to unmask]> wrote:
> >> Thanks Dr. Lee, thanks Dr. Ashburner., thanks Dr. Hammers.
> >>
> >> I did custom pre-processing, so, of course, I normalized functional
> >> images
> >> with normalize fiunction of SPM.
> >>
> >> So, the coordinates I see in activations are MNI coordinates?
> >>
> >> In MNI space, are positive values of x coordinate related to right
> >> emisphere? I'm asking this, because, for example, for right hand task, I
> >> see
> >> more activations in right emisphere (positive value of x coordinate). Is
> >> it
> >> possible?
> >>
> >> Thanks,
> >>
> >> Luigi
> >>
> >>
> >> 2013/3/11 James Lee <[log in to unmask]>
> >>>
> >>> Luigi,
> >>>
> >>> If you want the coordinates in Talairach space you can use mni2tal.
> >>> You may want to consider using icbm2tal, which is evidently more
> >>> accurate. See the comments at http://www.brainmap.org/icbm2tal.
> >>>
> >>> Jim
> >>>
> >>> On 3/11/13, John Ashburner <[log in to unmask]> wrote:
> >>> > If your data are spatially normalised to MNI space, then the reported
> >>> > coordinates will also be in MNI space.
> >>> > Best regards,
> >>> > -John
> >>> >
> >>> >
> >>> > On 11 March 2013 16:05, Luigi Pavone <[log in to unmask]>
> wrote:
> >>> >> Hi to all.
> >>> >>
> >>> >> I did fMRI analysis with spm v.8. Now I need to translate
> coordinates
> >>> >> coming
> >>> >> from fMRI results (button "whole brain" in panels "p value") in
> >>> >> tailarach
> >>> >> coordinates.(please see tha attached file)
> >>> >>
> >>> >> Are they MNI coordinates, so i can use mni2tal m file?
> >>> >>
> >>> >> Thanks,
> >>> >>
> >>> >> Luigi
> >>> >
> >>>
> >>
> >
>
