Hi Doug,
Many thanks for your help.
Can you please take a look and see if this is the correct way to do it. I want to overal in fact my QDEC clusters on the connectivity maps in FSL but I got them by registering on the MNI 152 so I suppose I can just transform or move my QDEC clusters on the MNI space since this is the template I use for my connectivity maps. I am not sure if I need to mention the label of my clusters for example the uncorrected clusters. Should I use the sig.mgh or I just run:
mri_label2vol --label lh-precentral --temp MNI152_T1_1mm_brain.nii.gz --reg $FREESURFER_HOME/average/mni152.register.dat --fillthresh .5 --o precentral-lh.nii
Also what threshold should I use with mri_label2vol if this are my uncorrected clusters? How can I do this if as below I have two clusters in the same region?
Contrast: 'lh-Diff-Class1-Class2-Intercept-thickness', 15fwhm, DOF: 69 ClusterNo Max VtxMax Size(mm2) TalX TalY TalZ NVtxs Annotation --------- --- ------ --------- ---- ---- ---- ----- ---------- 1 -3.8743 18231 944.60 -39.8 1.5 14.1 2631 precentral 2 -3.8065 47386 1445.46 -8.2 33.1 33.9 2421 superiorfrontal 3 -2.8630 158749 181.92 -12.7 -12.6 46.4 506 superiorfrontal 4 -2.7960 73670 222.37 -33.7 0.9 8.1 564 insula 5 2.7914 52279 204.80 -9.8 -98.6 4.6 248 pericalcarine 6 -2.7364 43605 173.45 -41.4 -79.2 21.8 288 inferiorparietal 7 -2.6316 17412 301.53 -38.3 5.6 -36.8 439 temporalpole 8 2.6050 150788 64.40 -24.0 -59.1 54.7 165 superiorparietal 9 -2.5570 106020 75.96 -22.8 -8.6 47.9 200 precentral 10 -2.5070 88002 66.59 -17.6 -31.2 37.8 198 posteriorcingulate 11 -2.4736 113974 181.87 -52.7 -10.3 -26.6 236 middletemporal 12 -2.4496 118370 142.88 -43.6 -18.0 -25.5 289 inferiortemporal 13 -2.3087 111885 55.43 -46.6 -36.2 -3.9 165 bankssts 14 -2.2179 153596 36.91 -11.3 3.4 42.0 103 superiorfrontal 15 -2.1861 145681 95.36 -11.3 60.1 19.1 147 superiorfrontal 16 -2.1733 29252 59.92 -42.6 37.5 -4.4 92 parstriangularis 17 -2.1689 155583 34.83 -45.3 -14.7 -11.2 87 superiortemporal 18 -2.1636 22443 27.76 -41.6 -79.0 -3.1 43 lateraloccipital 19 -2.1592 139736 21.75 -47.5 -25.1 37.0 61 postcentral 20 -2.0221 19174 4.10 -34.2 33.8 29.2 6 rostralmiddlefrontal
________________________________ From: Douglas N Greve greve@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, August 21, 2012 4:55 PM Subject: Re: [Freesurfer] Convert QDEC clusters on the MNI_152_T1 space
You can use mri_label2vol and $FREESURFER_HOME/average/mni152.register.dat doug
On 08/21/2012 11:06 AM, Antonella Kis wrote:
Dear All,
Is possible to overlap my QDEC clusters onto MNI_152_T1 _1mm_brain template?
Thank you. Antonella
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