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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:
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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
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--
Tim Schäfer

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