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Thank you Tim, the explanation and screenshot helped indeed.
Diana

El mar., 9 jun. 2020 a las 10:07, Tim Schäfer (<ts+ml@rcmd.org>) escribió:
        External Email - Use Caution       

These are different versions of the fsaverage template, but with reduced vertex count (mesh resolution). The default fsaverage subject has the highest resolution, and it gets lower for fsaverage6, 5, ... and so on.

Put another way, fsaverage3 is quite 'blocky', if that helps. I have attached a screenshot of fsaverage3.

Tim

> On June 9, 2020 at 9:59 AM Diana <diana.tordesillas@gmail.com> wrote:
>
>
>         External Email - Use Caution       
>
> Tim, my bad I do have it in the installation folder:
> ls -l $FREESURFER_HOME/subjects/fsaverage/label/lh.cortex.label
> -rwxrwxr-x 1 8481 1590 6117569 ago 14  2007
> /usr/local/freesurfer/subjects/fsaverage/label/lh.cortex.label
>
> Please, could you explain to me what fsaverage 3, 4, 5 and 6 are?
>
> Thank you!
>
> Diana
>
> p.d. I copied below the contents of $FREESURFER_HOME/subjects/
>
> localhost:/usr/local/freesurfer/subjects> ls fs
> fsaverage/     fsaverage3/    fsaverage4/    fsaverage5/    fsaverage6/
>  fsaverage_sym/
> localhost:/usr/local/freesurfer/subjects> ls fsaverage
> label  mri  mri.2mm  scripts  surf  xhemi
> localhost:/usr/local/freesurfer/subjects> ls fsaverage/label/
> lh.aparc.a2005s.annot      rh.aparc.a2009s.annot
> lh.aparc.a2009s.annot      rh.aparc.annot
> lh.aparc.annot      rh.aparc.label
> lh.aparc.label      rh.BA1_exvivo.label
> lh.BA1_exvivo.label      rh.BA1_exvivo.thresh.label
> lh.BA1_exvivo.thresh.label      rh.BA2_exvivo.label
> lh.BA2_exvivo.label      rh.BA2_exvivo.thresh.label
> lh.BA2_exvivo.thresh.label      rh.BA3a_exvivo.label
> lh.BA3a_exvivo.label      rh.BA3a_exvivo.thresh.label
> lh.BA3a_exvivo.thresh.label      rh.BA3b_exvivo.label
> lh.BA3b_exvivo.label      rh.BA3b_exvivo.thresh.label
> lh.BA3b_exvivo.thresh.label      rh.BA44_exvivo.label
> lh.BA44_exvivo.label      rh.BA44_exvivo.thresh.label
> lh.BA44_exvivo.thresh.label      rh.BA45_exvivo.label
> lh.BA45_exvivo.label      rh.BA45_exvivo.thresh.label
> lh.BA45_exvivo.thresh.label      rh.BA4a_exvivo.label
> lh.BA4a_exvivo.label      rh.BA4a_exvivo.thresh.label
> lh.BA4a_exvivo.thresh.label      rh.BA4p_exvivo.label
> lh.BA4p_exvivo.label      rh.BA4p_exvivo.thresh.label
> lh.BA4p_exvivo.thresh.label      rh.BA6_exvivo.label
> lh.BA6_exvivo.label      rh.BA6_exvivo.thresh.label
> lh.BA6_exvivo.thresh.label      rh.cortex.label
> lh.cortex.label      rh.entorhinal_exvivo.label
> lh.entorhinal_exvivo.label      rh.entorhinal_exvivo.thresh.label
> lh.entorhinal_exvivo.thresh.label      rh.Medial_wall.label
> lh.Medial_wall.label      rh.MT_exvivo.label
> lh.MT_exvivo.label      rh.MT_exvivo.thresh.label
> lh.MT_exvivo.thresh.label      rh.oasis.chubs.annot
> lh.oasis.chubs.annot      rh.oasis.chubs.ifc.label
> lh.oasis.chubs.ifc.label      rh.oasis.chubs.ipc.label
> lh.oasis.chubs.ipc.label      rh.oasis.chubs.ips.label
> lh.oasis.chubs.ips.label      rh.oasis.chubs.lateraltemporal.label
> lh.oasis.chubs.lateraltemporal.label      rh.oasis.chubs.medialpfc.label
> lh.oasis.chubs.medialpfc.label      rh.oasis.chubs.mtl.label
> lh.oasis.chubs.mtl.label      rh.oasis.chubs.retrosplenial.label
> lh.oasis.chubs.retrosplenial.label      rh.oasis.chubs.tp.label
> lh.oasis.chubs.tp.label      rh.PALS_B12_Brodmann.annot
> lh.PALS_B12_Brodmann.annot      rh.PALS_B12.labels.gii
> lh.PALS_B12.labels.gii      rh.PALS_B12_Lobes.annot
> lh.PALS_B12_Lobes.annot      rh.PALS_B12_OrbitoFrontal.annot
> lh.PALS_B12_OrbitoFrontal.annot      rh.PALS_B12_Visuotopic.annot
> lh.PALS_B12_Visuotopic.annot      rh.perirhinal_exvivo.label
> lh.perirhinal_exvivo.label      rh.perirhinal_exvivo.thresh.label
> lh.perirhinal_exvivo.thresh.label      rh.V1_exvivo.label
> lh.V1_exvivo.label      rh.V1_exvivo.thresh.label
> lh.V1_exvivo.thresh.label      rh.V2_exvivo.label
> lh.V2_exvivo.label      rh.V2_exvivo.thresh.label
> lh.V2_exvivo.thresh.label      rh.Yeo2011_17NetworksConfidence_N1000.mgz
> lh.Yeo2011_17NetworksConfidence_N1000.mgz
>  rh.Yeo2011_17Networks_N1000.annot
> lh.Yeo2011_17Networks_N1000.annot
>  rh.Yeo2011_7NetworksConfidence_N1000.mgz
> lh.Yeo2011_7NetworksConfidence_N1000.mgz
>  rh.Yeo2011_7Networks_N1000.annot
> lh.Yeo2011_7Networks_N1000.annot
>  rh.Yeo_Brainmap_10Comp_PrActGivenComp.mgz
> lh.Yeo_Brainmap_10Comp_PrActGivenComp.mgz
>  rh.Yeo_Brainmap_10to14Comp_Flexibility.mgz
> lh.Yeo_Brainmap_10to14Comp_Flexibility.mgz
>  rh.Yeo_Brainmap_10to14Comp_Specialization.mgz
> lh.Yeo_Brainmap_10to14Comp_Specialization.mgz
>  rh.Yeo_Brainmap_10to14Comp_SpecializationROI.mgz
> lh.Yeo_Brainmap_10to14Comp_SpecializationROI.mgz
>  rh.Yeo_Brainmap_10to14Comp_TopSpecializationComp.csv
> lh.Yeo_Brainmap_10to14Comp_TopSpecializationComp.csv
>  rh.Yeo_Brainmap_11Comp_PrActGivenComp.mgz
> lh.Yeo_Brainmap_11Comp_PrActGivenComp.mgz
>  rh.Yeo_Brainmap_12Comp_PrActGivenComp.mgz
> lh.Yeo_Brainmap_12Comp_PrActGivenComp.mgz
>  rh.Yeo_Brainmap_13Comp_PrActGivenComp.mgz
> lh.Yeo_Brainmap_13Comp_PrActGivenComp.mgz
>  rh.Yeo_Brainmap_14Comp_PrActGivenComp.mgz
> lh.Yeo_Brainmap_14Comp_PrActGivenComp.mgz      Yeo_Brainmap_fsaverage_README
> rh.aparc.a2005s.annot
>
> El mar., 9 jun. 2020 a las 9:37, Tim Schäfer (<ts+ml@rcmd.org>) escribió:
>
> >         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
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> > > >
> > > > --
> > > > Tim Schäfer
> > > >
> > > > _______________________________________________
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> >
> > --
> > Tim Schäfer
> >
> > _______________________________________________
> > Freesurfer mailing list
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