Thank you for the clarification!Another question that I have concerns the one-sample t-test. If I conduct this test with my 42 subjects on their FA data, the one sample t-test is testing if the mean of each of the subject's FA data is greater than 0, correct?
On Tue, Apr 30, 2013 at 12:43 AM, Stephen Smith <[log in to unmask]> wrote:
HiOn 29 Apr 2013, at 19:20, Dana Wagshal <[log in to unmask]> wrote:Hi FSL group,
I successfully applied randomise to a group of 42 subjects in a one-sample t-test. When I looked at my results (OneSampleTTest_tfce_corrp_tstat1.nii.gz) I found some tracts that were significant at p < 0.05. Next, I wanted to know which tracts they corresponded to so that I could report this in a table. So I went under Atlas tools and chose the JHU ICBM-DTI-81 White Matter Labels and JHU White-Matter Tractography Atlas and manually went through OneSampleTTest_tfce_corrp_tstat1.nii.gz to find significant tracts and their coordinates.
I also read through the Randomise user guide and saw that you could get this same information by using the cluster command, and so I did:
fslmaths OneSampleTTest_tfce_corrp_tstat1 -thr 0.95 -bin -mul OneSampleTTest_tstat1 OneSampleTTest_tfce_thresh_tstat1 (I got a mask from the significant voxels from corrp)
cluster --in=OneSampleTTest_tfce_thresh_tstat1 --thresh=0.0001 --oindex=OneSampleTTest_cluster_index --olmax=OneSampleTTest_lmax.txt --osize=OneSampleTTest_cluster_size --mm (then I used the cluster command to get a list of significant clusters and their coordinates, called OneSampleTTest_lmax.txt)
These are my questions:
1) In my terminal screen a list of significant clusters appeared that corresponded to OneSampleTTest_lmax.txt, but the list on my screen only displayed 1 significant value for each cluster while the OneSampleTTest_lmax.txt displayed multiple values for a significant cluster:
On my screen:
Cluster Index Voxels MAX MAX X (mm) MAX Y (mm) MAX Z (mm) COG X (mm) COG Y (mm) COG Z (mm)
33 586 82 36 -37 31 31.4 -42 39.3
32 362 66.7 -27 -41 41 -31.1 -36.8 37.2
31 206 51.2 -11 24 51 -10.3 26.2 51
30 176 44.1 -28 -42 45 -30.7 -43.7 49.6
...
In OneSampleTTest_lmax.txt:
Cluster Index Value x y z
33 82 36 -37 31
33 68 35 -35 33
33 65.8 34 -45 31
33 65 33 -34 35
33 64.2 39 -36 33
33 59.4 33 -39 34
32 66.7 -27 -41 41
32 57.6 -27 -44 40
32 55.3 -35 -33 33
32 54.7 -33 -29 40
32 53.9 -35 -36 32
32 49.8 -27 -45 35
...
Which one should I use?That's up to you. The first is showing a single summary set of values for each cluster, the second is showing multiple (where present) local maxima within each cluster. Both valid pieces of information.2) I also saw in another post (https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1302&L=FSL&D=0&1=FSL&9=A&I=-3&J=on&X=388D5638851C577653&Y=danawagshal%40gmail.com&d=No+Match%3BMatch%3BMatches&z=4&P=231460) that a person was able to get probability percentages of certain tracks from the JHU White-Matter Tractography Atlas. I had to do this manually and I would love it if someone could tell me how I could obtain this from a command.
I'm not sure - maybe with Featquery or atlasquery….?Cheers.
Best,
Dana
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Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
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-Dana