The code that does this is hard-coded and hard for me to follow (eventhough I wrote it:). It might be faster to to try to change ROI5.mgh. How did you create */media/Storage/FTD_Data/fsaverage/surf/ROI5.mgh?*

On 03/04/2016 04:31 PM, Sahil Bajaj wrote:

Hello again,

To calculate cortical thickness, I am running step-4 & 5 following the instructions from https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness

So running step 4:

*mri_surf2surf --s S01_LP --trgsubject fsaverage --hemi lh --sval lh.thickness --tval lh.thickness.fsaverage.mgh --reshape*

where S01_LP is my subject ID, it runs as follow:

srcsubject = S01_LP srcval = lh.thickness srctype = trgsubject = fsaverage trgval = lh.thickness.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /media/Storage/FTD_Data/S01_LP/surf/lh.sphere.reg Loading source data Reading target surface reg /media/Storage/FTD_Data/fsaverage/surf/lh.sphere.reg Done Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (98973) Reverse Loop had 7939 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 157350, nTrgMulti = 6492, MnTrgMultiHits = 2.22289 nSrc121 = 49582, nSrcLost = 0, nSrcMulti = 49391, MnSrcMultiHits = 2.47411 Saving target data Reshaping 6 (nvertices = 163842) Saving to lh.thickness.fsaverage.mgh

Next when I run step 5 as follow:

*mri_segstats --seg /media/Storage/FTD_Data/fsaverage/surf/ROI5.mgh --in lh.thickness.fsaverage.mgh --sum segstats-ROI5.txt*

It runs as follows:

$Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --seg /media/Storage/FTD_Data/fsaverage/surf/ROI5.mgh --in lh.thickness.fsaverage.mgh --sum segstats-ROI5.txt sysname Linux hostname degas machine x86_64 user sahil UseRobust 0 Loading /media/Storage/FTD_Data/fsaverage/surf/ROI5.mgh Loading lh.thickness.fsaverage.mgh ERROR: dimension mismatch between input volume and seg input 27307 1 6 seg 23406 1 7

As mentioned in the instructions I also tried using --reshape-factor 7 in step 4 also but still I get exactly same error after running step 5. Could you please help me in figuring out this problem?

Thanks, Sahil

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Sahil Bajaj Post-doctoral Fellow Nantz National Alzheimer's Center, Department of Neurology The Houston Methodist Research Institute (THMRI) Houston, TX, USA. Office: 713-363-9003 E-mail:sahil.neuro@gmail.com mailto:E-mail%3Asahil.phy@gmail.com

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