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 > -- > ------------------------------------------------- > 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.ne...@gmail.com <mailto:e-mail%3asahil....@gmail.com> > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
