Re: [Freesurfer] ERROR: fast_mat2vol
External Email - Use Caution
I have resolved by eliminating the option -nowhiten
It looks like the anatomical analysis is out of sync with the functional
analysis. Is is possible that you ran the functional analysis, then edited the
subject, then tried to rerun the analysis? If so, try running preproc-sess with
-force to redo all the preprocessing.On 12/1/2022 12:45 PM, std...@virgilio.it
wrote:
> External Email - Use Caution I would extract the rs-fMRI timeseries
> from Yeo’s Network components. I’m running: preproc-sess -s ${1} -fsd rest
> -sliceorder up -surface self lhrh -fwhm 0 -per-runfcseed-config -wm -fcname
> wm.dat -fsd rest -pca -cfg wm.config fcseed-sess -s ${1} -cfg
> wm.configfcseed-config -vcsf -fcname vcsf.dat -fsd rest -pca -cfg
> vcsf.configfcseed-sess -s ${1} -cfg vcsf.config mkanalysis-sess -analysis
> fc.noseed.surf.lh -surface self lh -fwhm 0 -notask -nuisreg vcsf.dat 5
> -nuisreg wm.dat 5 -polyfit 5 -nskip 4 -mcextreg -fsd rest -TR 1.67 -per-run
> -hpf 0.01 -lpf 0.1 -nowhiten mkanalysis-sess -analysis fc.noseed.surf.rh
> -surface self rh -fwhm 0 -notask -nuisreg vcsf.dat 5 -nuisreg wm.dat 5
> -polyfit 5 -nskip 4 -mcextreg -fsd rest -TR 1.67 -per-run -hpf 0.01 -lpf 0.1
> -nowhitenThe line below produced this error: selxavg3-sess -s ${1} -a
> fc.noseed.surf.lh -no-con-ok -svres Saving rho1 ERROR: fast_mat2vol: szvol
> inconsistent with mat2d nv = 151008, size(mat,2) = 142954 run 2t=
> 1.6reading data ... 0.518631Temporally filteringSaving rho1 ERROR:
> fast_mat2vol: szvol inconsistent with mat2d nv = 151008, size(mat,2) =
> 142954Found 0 voxels with corrected AR1 > 0.90Not WhiteningFound 8054
> zero-valued voxelsComputing contrastsThe res folder in fc.noseed.surf.lh or
> fc.noseed.surf.rh contains res-001.nii.gz 158KB res-002.nii.gz 158KB that
> cannot be opended. Stefano
>
>
>
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Re: [Freesurfer] ERROR: fast_mat2vol
It looks like the anatomical analysis is out of sync with the functional
analysis. Is is possible that you ran the functional analysis, then
edited the subject, then tried to rerun the analysis? If so, try running
preproc-sess with -force to redo all the preprocessing.
On 12/1/2022 12:45 PM, std...@virgilio.it wrote:
External Email - Use Caution
I would extract the rs-fMRI timeseries from Yeo’s Network components.
I’m running:
preproc-sess -s ${1} -fsd rest -sliceorder up -surface self lhrh -fwhm
0 -per-runfcseed-config -wm -fcname wm.dat -fsd rest -pca -cfg
wm.config fcseed-sess -s ${1} -cfg wm.configfcseed-config -vcsf
-fcname vcsf.dat -fsd rest -pca -cfg vcsf.configfcseed-sess -s ${1}
-cfg vcsf.config
mkanalysis-sess -analysis fc.noseed.surf.lh -surface self lh -fwhm 0
-notask -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -polyfit 5 -nskip 4
-mcextreg -fsd rest -TR 1.67 -per-run -hpf 0.01 -lpf 0.1 -nowhiten
mkanalysis-sess -analysis fc.noseed.surf.rh -surface self rh -fwhm 0
-notask -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -polyfit 5 -nskip 4
-mcextreg -fsd rest -TR 1.67 -per-run -hpf 0.01 -lpf 0.1 -nowhiten
The line below produced this error:
selxavg3-sess -s ${1} -a fc.noseed.surf.lh -no-con-ok -svres
Saving rho1
ERROR: fast_mat2vol: szvol inconsistent with mat2d nv = 151008,
size(mat,2) = 142954 run 2 t= 1.6reading data ...
0.518631Temporally filteringSaving rho1
ERROR: fast_mat2vol: szvol inconsistent with mat2d nv = 151008,
size(mat,2) = 142954Found 0 voxels with corrected AR1 > 0.90Not
WhiteningFound 8054 zero-valued voxelsComputing contrasts
The res folder in fc.noseed.surf.lh or fc.noseed.surf.rh contains
res-001.nii.gz 158KB
res-002.nii.gz 158KB
that cannot be opended.
Stefano
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Mass General Brigham
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Please note that this e-mail is not secure (encrypted). If you do not wish to
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this message immediately. Continuing to send or respond to e-mail after
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[Freesurfer] ERROR: fast_mat2vol: szvol inconsistent with mat2d nv
External Email - Use Caution
I would extract the rs-fMRI timeseries from Yeo’s Network components.
I’m running:
preproc-sess -s ${1} -fsd rest -sliceorder up -surface self lhrh -fwhm 0
-per-run
fcseed-config -wm -fcname wm.dat -fsd rest -pca -cfg wm.config
fcseed-sess -s ${1} -cfg wm.config
fcseed-config -vcsf -fcname vcsf.dat -fsd rest -pca -cfg vcsf.config
fcseed-sess -s ${1} -cfg vcsf.config
mkanalysis-sess -analysis fc.noseed.surf.lh -surface self lh -fwhm 0 -notask
-nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -polyfit 5 -nskip 4 -mcextreg -fsd rest
-TR 1.67 -per-run -hpf 0.01 -lpf 0.1 -nowhiten
mkanalysis-sess -analysis fc.noseed.surf.rh -surface self rh -fwhm 0 -notask
-nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -polyfit 5 -nskip 4 -mcextreg -fsd rest
-TR 1.67 -per-run -hpf 0.01 -lpf 0.1 -nowhiten
The line below produced this error:
selxavg3-sess -s ${1} -a fc.noseed.surf.lh -no-con-ok -svres
Saving rho1 ERROR: fast_mat2vol: szvol inconsistent with mat2d nv = 151008,
size(mat,2) = 142954 run 2 t= 1.6reading data ... 0.518631Temporally
filteringSaving rho1 ERROR: fast_mat2vol: szvol inconsistent with mat2d nv =
151008, size(mat,2) = 142954
Found 0 voxels with corrected AR1 > 0.90Not WhiteningFound 8054 zero-valued
voxelsComputing contrasts
The res folder in fc.noseed.surf.lh or fc.noseed.surf.rh contains
res-001.nii.gz 158KB
res-002.nii.gz 158KB
that cannot be opended.
Thanks
Stefano
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Mass General Brigham
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline
.
Please note that this e-mail is not secure (encrypted). If you do not wish to
continue communication over unencrypted e-mail, please notify the sender of
this message immediately. Continuing to send or respond to e-mail after
receiving this message means you understand and accept this risk and wish to
continue to communicate over unencrypted e-mail.
[Freesurfer] ERROR: fast_mat2vol
External Email - Use Caution
I would extract the rs-fMRI timeseries from Yeo’s Network components.
I’m running:
preproc-sess -s ${1} -fsd rest -sliceorder up -surface self lhrh -fwhm 0
-per-runfcseed-config -wm -fcname wm.dat -fsd rest -pca -cfg wm.config
fcseed-sess -s ${1} -cfg wm.configfcseed-config -vcsf -fcname vcsf.dat -fsd
rest -pca -cfg vcsf.configfcseed-sess -s ${1} -cfg vcsf.config
mkanalysis-sess -analysis fc.noseed.surf.lh -surface self lh -fwhm 0 -notask
-nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -polyfit 5 -nskip 4 -mcextreg -fsd rest
-TR 1.67 -per-run -hpf 0.01 -lpf 0.1 -nowhiten
mkanalysis-sess -analysis fc.noseed.surf.rh -surface self rh -fwhm 0 -notask
-nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -polyfit 5 -nskip 4 -mcextreg -fsd rest
-TR 1.67 -per-run -hpf 0.01 -lpf 0.1 -nowhiten
The line below produced this error:
selxavg3-sess -s ${1} -a fc.noseed.surf.lh -no-con-ok -svres
Saving rho1
ERROR: fast_mat2vol: szvol inconsistent with mat2d nv = 151008, size(mat,2) =
142954 run 2t= 1.6reading data ... 0.518631Temporally filteringSaving rho1
ERROR: fast_mat2vol: szvol inconsistent with mat2d nv = 151008, size(mat,2) =
142954Found 0 voxels with corrected AR1 > 0.90Not WhiteningFound 8054
zero-valued voxelsComputing contrasts
The res folder in fc.noseed.surf.lh or fc.noseed.surf.rh contains
res-001.nii.gz 158KB
res-002.nii.gz 158KB
that cannot be opended.
Stefano ___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Mass General Brigham
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline
.
Please note that this e-mail is not secure (encrypted). If you do not wish to
continue communication over unencrypted e-mail, please notify the sender of
this message immediately. Continuing to send or respond to e-mail after
receiving this message means you understand and accept this risk and wish to
continue to communicate over unencrypted e-mail.
