Add --no-fixmni to the mri_surfcluster command

On 8/4/17 3:03 PM, Martin Juneja wrote:

Hi Douglas,

When I checked the summary created by FreeSurfer by running FS commands:

For cortical gyrification I get (here co-ordinates are in TalX TalY and TalZ):

# ClusterNo Max VtxMax Size(mm^2) *TalX TalY TalZ * NVtxs WghtVtx Annot 1 -2.108 44783 1067.81 -28.3 -0.4 41.8 2111 -3503.03 caudalmiddlefrontal 2 -1.837 87895 505.11 -29.8 -85.0 1.6 724 -1114.00 lateraloccipital 3 -1.731 60125 335.00 -24.1 38.5 27.8 541 -799.69 rostralmiddlefrontal 4 -1.660 157315 236.93 -20.1 -60.7 52.0 529 -766.88 superiorparietal 5 1.457 79262 93.31 -45.7 2.4 -17.9 173 237.80 superiortemporal 6 -1.440 34463 88.73 -46.9 3.8 41.2 170 -231.97 precentral

For cortical thickness I get (here co-ordinates are in MNIX MNIY and MNIZ): # ClusterNo Max VtxMax Size(mm^2) *MNIX MNIY MNIZ * CWP CWPLow CWPHi NVtxs WghtVtx Annot 1 6.658 102251 3976.09 -42.7 -8.6 54.9 0.00020 0.00000 0.00040 9234 19027.15 precentral 2 3.368 44083 3096.64 -28.8 -43.8 -17.3 0.00020 0.00000 0.00040 5273 7856.00 fusiform 3 2.808 156481 1476.57 -64.4 -30.5 2.8 0.00818 0.00659 0.00978 3169 4837.73 superiortemporal

Command to save these summaries were as following:

For gyrification: mri_surfcluster --in sig.mgh --subject fsaverage --hemi lh --surf white --annot aparc --thmin 1.3 --sum LH_Perform_LGI.summary1.3 For thickness: mri_glmfit-sim --glmdir xyz --cache 1.3 neg --cwp 0.05 --2spaces

Before these, I used general FS commands: mris_preproc, mri_surf2surf and mri_glmfit for both.

Only difference is I did not run mri_glmfit-sim on gyrification measures but ran this on thickness, area and volume measures due to orthogonal/non-orthogonal differences between gyrification and (thickness, area and volume) measures.

Thanks.

On Fri, Aug 4, 2017 at 11:24 AM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

How do you know one is MNI and one it Tal? can you send a summary
of your commands?


On 8/4/17 2:09 PM, Martin Juneja wrote:

...

Hi FreeSurfer experts,

I am trying to correlate my behavioral data with whole brain
cortical measures using cortical measures as IVs and behavioral
data DV.

Somehow the significant clusters I get from cortical thickness,
area and volume are in MNI co-ordinates but significant clusters
from local gyrification-behavioral data are in Talairach
co-ordinates.

I used identical procedures to preprocess my data but still I am
getting my results in different co-ordinate systems (thickness,
volume, area in MNI and gyrification in Tal).

I would really appreciate any help.
MJ


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