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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 CautionHm, 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 CautionDear 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 CautionI 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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