External Email - Use Caution Dear experts,
I am preparing my data for longitudinal statistical analysis following the steps in https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalStatistics#LinearMixedEffectsModel. I try running the following comand : mris_preproc --qdec-long qdec/long.qdec.table-test.dat --target fsaverage --hemi lh --meas area --out output/lh.area.stack.mghmris_preproc --qdec-long qdec/long.qdec.table-test.dat --target fsaverage --hemi lh --meas area --out output/lh.area.stack.mgh but it crashes because it looks for /fsaverage/label/lh.cortex.label How can I create this label file? Thank you very much in advance for your help, please find below the whole output. Best, Diana nsubjects = 25 INFO: turning on jacobican correction tmpdir is output/tmp.mris_preproc.21054 /home/neuroimagen/AnalisisLongitudinalLMM Log file is output/lh.area.stack.mris_preproc.log lun jun 8 17:41:42 CEST 2020 setenv SUBJECTS_DIR /home/neuroimagen/AnalisisLongitudinalLMM/ cd /home/neuroimagen/AnalisisLongitudinalLMM /usr/local/freesurfer/bin/mris_preproc --qdec-long qdec/long.qdec.table-test.dat --target fsaverage --hemi lh --meas area --out output/lh.area.stack.mgh Linux localhost 4.4.0-179-generic #209-Ubuntu SMP Fri Apr 24 17:48:44 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.76.2.1 2016/08/12 17:55:45 zkaufman Exp $ freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c tmpdir is output/tmp.mris_preproc.21054 Src lh sphere.reg Trg lh sphere.reg --------------------------------------------------- #@# 1/25 100_001.long.100 lun jun 8 17:41:42 CEST 2020 -------------- ----------------------- mri_surf2surf --srcsubject 100_001.long.100 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval output/tmp.mris_preproc.21054/100_001.long.100.1.mgh --sval /home/neuroimagen/AnalisisLongitudinalLMM//100_001.long.100/surf/lh.area --jac --sfmt curv --noreshape --cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /home/neuroimagen/AnalisisLongitudinalLMM/ cd /home/neuroimagen/AnalisisLongitudinalLMM mri_surf2surf --srcsubject 100_001.long.100 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval output/tmp.mris_preproc.21054/100_001.long.100.1.mgh --sval /home/neuroimagen/AnalisisLongitudinalLMM//100_001.long.100/surf/lh.area --jac --sfmt curv --noreshape --cortex sysname Linux hostname localhost machine x86_64 user neuroimagen srcsubject = 100_001.long.100 srcval = /home/neuroimagen/AnalisisLongitudinalLMM//100_001.long.100/surf/lh.area srctype = curv trgsubject = fsaverage trgval = output/tmp.mris_preproc.21054/100_001.long.100.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /home/neuroimagen/AnalisisLongitudinalLMM//100_001.long.100/surf/lh.sphere.reg Loading source data Reading curvature file /home/neuroimagen/AnalisisLongitudinalLMM//100_001.long.100/surf/lh.area Reading source subject label mask lh.cortex.label masking the input Reading target surface reg /home/neuroimagen/AnalisisLongitudinalLMM//fsaverage/surf/lh.sphere.reg Done Using surf2surf_nnfr() Mapping Source Volume onto Source Subject Surface with Jacobian Correction surf2surf_nnfr_jac: building source hash (res=16). Surf2SurfJac: 1st Forward Loop (163842) Surf2SurfJac: 2nd Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2SurfJac: Reverse Loop (149877) Reverse Loop had 29625 hits INFO: nSrcLost = 0 surf2surf_nnfr_jac() done No such file or directory mri_surf2surf: could not open label file /home/neuroimagen/AnalisisLongitudinalLMM//fsaverage/label/lh.cortex.label nTrg121 = 141330, nTrgMulti = 22512, MnTrgMultiHits = 2.31596 nSrc121 = 115191, nSrcLost = 0, nSrcMulti = 34686, MnSrcMultiHits = 2.2567 Reading target space mask label lh.cortex.label Invalid argument
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