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 CautionDear experts,
I am preparing my data for longitudinal statistical analysis following the steps in https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalStatistics#LinearMixed....
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
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