Hi Matthew,
Thanks for your answer. I have just another question.
Now I have my statistic images like that : 4x4x4mm (45x54x45) and I want to resample them in 2x2x2mm (91x109x91) in order to overlay them on the MNI152_T1_2mm standard T1 image
So I do that : flirt -ref $FSLDIR/data/standard/MNI152_T1_2mm_brain -in [my statistic image] -out [my new image resampled] -applyisoxfm 2
It seems to works, but looking at the histograms it changes a little bit. But I think it's due to the interpolation, right?
So is it the best way to do that ?
And do you think it is better to resample my data before or after randomise ?
Kind regards
Antoine
________________________________________
De : FSL - FMRIB's Software Library [[log in to unmask]] de la part de Matthew Webster [[log in to unmask]]
Envoyé : mardi 16 juillet 2013 15:05
À : [log in to unmask]
Objet : Re: [FSL] Randomise after dual regression
Hello Antoine,
Randomise does not currently preserve the pixdims in the output images when a mask is not supplied with -m option. We will look into changing this in a future patch, but for now you can use fslcpgeom to restore this information to statistic images..
Kind Regards
Matthew
> Hi Steve,
>
> Sorry for the delay, I did not see your answer.
> So, I do my t-test like that (I want to compare 2 groups resting state (ASD et CON) on a IC after a DR) :
>
> test_design.mat :
>
> /NumWaves 2
> /NumPoints 26
> /PPheights 1.000000e+00 1.000000e+00
>
> /Matrix
> 1.000000e+00 0.000000e+00
> 1.000000e+00 0.000000e+00
> 1.000000e+00 0.000000e+00
> 1.000000e+00 0.000000e+00
> 1.000000e+00 0.000000e+00
> 1.000000e+00 0.000000e+00
> 1.000000e+00 0.000000e+00
> 1.000000e+00 0.000000e+00
> 1.000000e+00 0.000000e+00
> 1.000000e+00 0.000000e+00
> 1.000000e+00 0.000000e+00
> 1.000000e+00 0.000000e+00
> 1.000000e+00 0.000000e+00
> 0.000000e+00 1.000000e+00
> 0.000000e+00 1.000000e+00
> 0.000000e+00 1.000000e+00
> 0.000000e+00 1.000000e+00
> 0.000000e+00 1.000000e+00
> 0.000000e+00 1.000000e+00
> 0.000000e+00 1.000000e+00
> 0.000000e+00 1.000000e+00
> 0.000000e+00 1.000000e+00
> 0.000000e+00 1.000000e+00
> 0.000000e+00 1.000000e+00
> 0.000000e+00 1.000000e+00
> 0.000000e+00 1.000000e+00
>
> test_design.con :
>
> /ContrastName1 all_mean
> /ContrastName2 ASD_mean
> /ContrastName3 Con_Mean
> /ContrastName4 CON>ASD
> /ContrastName5 CON<ASD
> /NumWaves 2
> /NumContrasts 5
> /PPheights 5.000000e-01 1.000000e+00 1.000000e+00 1.000000e+00 5.000000e-01
> /RequiredEffect 0.961 1.359 1.359 1.921 0.961
>
> /Matrix
> 1.000000e+00 1.000000e+00
> 0.000000e+00 1.000000e+00
> 1.000000e+00 0.000000e+00
> 1.000000e+00 -1.000000e+00
> -1.000000e+00 1.000000e+00
>
> and I do this command (e.g for the 16th IC) :
>
> $ randomise -i ~/Dr_grp_test3/dr_stage2_ic0015 -o ~/tests/rando_ic16 -d ~/Dr_grp_test3/test_design.mat -t ~/Dr_grp_test3/test_design.con -n 500 -T
>
> And if I check the nifti info of the intput :
>
> $ fslinfo Dr_grp_test3/dr_stage2_ic0015.nii.gz
> data_type FLOAT32
> dim1 45
> dim2 54
> dim3 45
> dim4 26
> datatype 16
> pixdim1 4.0000000000
> pixdim2 4.0000000000
> pixdim3 4.0000000000
> pixdim4 1.0000000000
> cal_max 0.0000
> cal_min 0.0000
> file_type NIFTI-1+
>
> and if I check one of the output I get that for example:
>
> $ fslinfo tests/rando_ic16_tfce_corrp_tstat1.nii.gz
> data_type FLOAT32
> dim1 45
> dim2 54
> dim3 45
> dim4 1
> datatype 16
> pixdim1 1.0000000000
> pixdim2 1.0000000000
> pixdim3 1.0000000000
> pixdim4 1.0000000000
> cal_max 0.0000
> cal_min 0.0000
> file_type NIFTI-1+
>
> So I don't know why randomise change the dimensions of my voxels.
>
> Best regards,
> Antoine
>
>
>
>
> ________________________________
> De : FSL - FMRIB's Software Library [[log in to unmask]] de la part de Stephen Smith [[log in to unmask]]
> Envoyé : mercredi 3 juillet 2013 14:57
> À : [log in to unmask]
> Objet : Re: [FSL] Randomise after dual regression
>
> How did you do the t-test? It seems like maybe whichever program you used has not kept the header size intact. FSL programs should not cause that.
> Steve.
>
>
> On 3 Jul 2013, at 11:05, Antoine BERNAS <[log in to unmask]<mailto:[log in to unmask]>> wrote:
>
> Hi everybody,
>
> I realised a two sample t-test with randomise on one component `dr_stage2_IC#` after a group-ica and a dual-regression.
> But for each contrast image randomise has changed the size. I get the same number of voxels (45x54x45) but I pass from 4mmx4mmx4mm to 1mmx1mmx1mm.
> So it causes some problems when I want to add a background with a standard image (because 64 times smaller). Is it normal that randomise does that ?
> Otherwise How can I enlarge my contrast images ?
>
> best regards,
>
> Antoine B.
>
>
>
> ---------------------------------------------------------------------------
> 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]<mailto:[log in to unmask]> http://www.fmrib.ox.ac.uk/~steve
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