External Email - Use Caution       

Hm, if you do not have the file in $FREESURFER_HOME/subjects/fsaverage/label/, your FreeSurfer installation is incomplete I guess. The file should definitely come with the software.

What is the output of:

  ls -l $FREESURFER_HOME/subjects/fsaverage/label/lh.cortex.label

on your machine?

Best,

Tim

> On June 9, 2020 at 8:08 AM Diana <diana.tordesillas@gmail.com> wrote:
>
>
>         External Email - Use Caution       
>
> Dear Tim,
> Thank you for your fast response.
> I did not have it in my fsaverage directory but I did find it in
> "tutorial_data_20190918_1558/buckner_data/tutorial_subjs/fsaverage",  would
> it be correct to use that one or should I create a new one? If I have to
> create it, which are the steps to do so?
>
> Best wishes, Diana
>
>
> El lun., 8 jun. 2020 a las 19:36, Tim Schäfer (<ts+ml@rcmd.org>) escribió:
>
> >         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.tordesillas@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
> >
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--
Tim Schäfer

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