External Email - Use Caution I think all you need to do is copy (or symlink) fsaverage to your data directory, the label file is in there already.
e.g.: cp -r $FREESURFER_HOME/subjects/fsaverage /home/neuroimagen/AnalisisLongitudinalLMM Best, Tim > On June 8, 2020 at 7:29 PM Diana <diana.tordesil...@gmail.com> wrote: > > > 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 > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Tim Schäfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
