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#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
Invalid argument
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
Invalid argument _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 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
Invalid argument _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Tim Schäfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 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
Invalid argument _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Tim Schäfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 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
Invalid argument _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Tim Schäfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Tim Schäfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 CautionTim, 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
Invalid argument _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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External Email - Use Caution
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 CautionThese 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 CautionTim, 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
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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freesurfer@nmr.mgh.harvard.edu
-
Diana -
Tim Schäfer