Hello everyone,
I am trying to extract clusters showing significant correlation between LGI and a behavioral measure. I am able to extract PCC and sig.mgh but at the last step when I try to run simulation command to view corrected results and I run:
mri_glmfit-sim --glmdir lh.MEQ_LGI.glmdir --cache 4 neg --cwp 0.05 --2spaces
I get following error:
ERROR: cannot find /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm35/neg/th40/mc-z.csd
But I can see mc-z.csd file in fwhm30 etc.
Full message on terminal window is attached following.
Any help would be really appreciated.
----- Full message ----
cmdline mri_glmfit.bin --y lh.MEQ_LGI.10.mgh --fsgd MEQ.fsgd dods --C Corr-MEQ-cor.mtx --surf fsaverage lh --cortex --glmdir lh.MEQ_LGI.glmdir
WARNING: unrecognized mri_glmfit cmd option mri_glmfit.bin
SURFACE: fsaverage lh
log file is lh.MEQ_LGI.glmdir/cache.mri_glmfit-sim.log
/usr/local/freesurfer/bin/mri_glmfit-sim
--glmdir lh.MEQ_LGI.glmdir --cache 4 neg --cwp 0.05 --2spaces
$Id: mri_glmfit-sim,v 1.60 2016/04/30 15:13:36 greve Exp $
Mon Mar 6 11:11:13 MST 2017
setenv SUBJECTS_DIR /data/emot/Freesurfer/FreeSurferSegmentation/SB_AgingAll
FREESURFER_HOME /usr/local/freesurfer
Original mri_glmfit command line:
cmdline mri_glmfit.bin --y lh.MEQ_LGI.10.mgh --fsgd MEQ.fsgd dods --C Corr-MEQ-cor.mtx --surf fsaverage lh --cortex --glmdir lh.MEQ_LGI.glmdir
DoSim = 0
UseCache = 1
DoPoll = 0
DoPBSubmit = 0
DoBackground = 0
DiagCluster = 0
gd2mtx = dods
fwhm = 35.073391
ERROR: cannot find /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm35/neg/th40/mc-z.csd
This is a problem with using LGI in that it is already extremely smooth that the smoothness exceeds the limit of the look up table that we supply. I recommend that you not use a gaussian-based correction for LGI. Instead, use permutation (see mri_glmfit-sim --help).
On 03/06/2017 01:36 PM, Martin Juneja wrote:
Hello everyone,
I am trying to extract clusters showing significant correlation between LGI and a behavioral measure. I am able to extract PCC and sig.mgh but at the last step when I try to run simulation command to view corrected results and I run:
mri_glmfit-sim --glmdir lh.MEQ_LGI.glmdir --cache 4 neg --cwp 0.05 --2spaces
I get following error:
ERROR: cannot find /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm35/neg/th40/mc-z.csd
But I can see mc-z.csd file in fwhm30 etc.
Full message on terminal window is attached following.
Any help would be really appreciated.
----- Full message ----
cmdline mri_glmfit.bin --y lh.MEQ_LGI.10.mgh --fsgd MEQ.fsgd dods --C Corr-MEQ-cor.mtx --surf fsaverage lh --cortex --glmdir lh.MEQ_LGI.glmdir
WARNING: unrecognized mri_glmfit cmd option mri_glmfit.bin
SURFACE: fsaverage lh
log file is lh.MEQ_LGI.glmdir/cache.mri_glmfit-sim.log
/usr/local/freesurfer/bin/mri_glmfit-sim
--glmdir lh.MEQ_LGI.glmdir --cache 4 neg --cwp 0.05 --2spaces
$Id: mri_glmfit-sim,v 1.60 2016/04/30 15:13:36 greve Exp $
Mon Mar 6 11:11:13 MST 2017
setenv SUBJECTS_DIR /data/emot/Freesurfer/FreeSurferSegmentation/SB_AgingAll
FREESURFER_HOME /usr/local/freesurfer
Original mri_glmfit command line:
cmdline mri_glmfit.bin --y lh.MEQ_LGI.10.mgh --fsgd MEQ.fsgd dods --C Corr-MEQ-cor.mtx --surf fsaverage lh --cortex --glmdir lh.MEQ_LGI.glmdir
DoSim = 0
UseCache = 1
DoPoll = 0
DoPBSubmit = 0
DoBackground = 0
DiagCluster = 0
gd2mtx = dods
fwhm = 35.073391
ERROR: cannot find /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm35/neg/th40/mc-z.csd
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Dr. Greve,
I tried to run: mri_glmfit-sim --glmdir lh.MEQ_LGI.glmdir --sim perm 1000 3 permcsd --sim-sign abs --cwpvalthresh .05 It gives error that ERROR: design matrix is not orthogonal, cannot be used with permutation.
But when I run: mri_glmfit-sim --glmdir lh.MEQ_LGI.glmdir --sim perm 1000 3 permcsd --sim-sign abs --cwpvalthresh .05 --perm-force, it works.
I am not sure whether I will have to make the design matrix orthogonal. If so, could you please tell me how that can be done?
Or using --perm-force should be fine?
Thanks.
On Mon, Mar 6, 2017 at 1:58 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
This is a problem with using LGI in that it is already extremely smooth that the smoothness exceeds the limit of the look up table that we supply. I recommend that you not use a gaussian-based correction for LGI. Instead, use permutation (see mri_glmfit-sim --help).
On 03/06/2017 01:36 PM, Martin Juneja wrote:
Hello everyone,
I am trying to extract clusters showing significant correlation between LGI and a behavioral measure. I am able to extract PCC and sig.mgh but at the last step when I try to run simulation command to view corrected results and I run:
mri_glmfit-sim --glmdir lh.MEQ_LGI.glmdir --cache 4 neg --cwp 0.05 --2spaces
I get following error:
ERROR: cannot find /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/
cortex/fwhm35/neg/th40/mc-z.csd
But I can see mc-z.csd file in fwhm30 etc.
Full message on terminal window is attached following.
Any help would be really appreciated.
----- Full message ----
cmdline mri_glmfit.bin --y lh.MEQ_LGI.10.mgh --fsgd MEQ.fsgd dods --C Corr-MEQ-cor.mtx --surf fsaverage lh --cortex --glmdir lh.MEQ_LGI.glmdir
WARNING: unrecognized mri_glmfit cmd option mri_glmfit.bin
SURFACE: fsaverage lh
log file is lh.MEQ_LGI.glmdir/cache.mri_glmfit-sim.log
/usr/local/freesurfer/bin/mri_glmfit-sim
--glmdir lh.MEQ_LGI.glmdir --cache 4 neg --cwp 0.05 --2spaces
$Id: mri_glmfit-sim,v 1.60 2016/04/30 15:13:36 greve Exp $
Mon Mar 6 11:11:13 MST 2017
setenv SUBJECTS_DIR /data/emot/Freesurfer/FreeSurferSegmentation/SB_AgingAll
FREESURFER_HOME /usr/local/freesurfer
Original mri_glmfit command line:
cmdline mri_glmfit.bin --y lh.MEQ_LGI.10.mgh --fsgd MEQ.fsgd dods --C Corr-MEQ-cor.mtx --surf fsaverage lh --cortex --glmdir lh.MEQ_LGI.glmdir
DoSim = 0
UseCache = 1
DoPoll = 0
DoPBSubmit = 0
DoBackground = 0
DiagCluster = 0
gd2mtx = dods
fwhm = 35.073391
ERROR: cannot find /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/
cortex/fwhm35/neg/th40/mc-z.csd
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
If you don't have an orthogonal design, then you can't use mri_glmfit-sim. I think you can use PALM:
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM
I have not tried it yet.
Anderson, can you use PALM with surfaces?
On 03/06/2017 05:23 PM, Martin Juneja wrote:
Hi Dr. Greve,
I tried to run: mri_glmfit-sim --glmdir lh.MEQ_LGI.glmdir --sim perm 1000 3 permcsd --sim-sign abs --cwpvalthresh .05 It gives error that ERROR: design matrix is not orthogonal, cannot be used with permutation.
But when I run: mri_glmfit-sim --glmdir lh.MEQ_LGI.glmdir --sim perm 1000 3 permcsd --sim-sign abs --cwpvalthresh .05 --perm-force, it works.
I am not sure whether I will have to make the design matrix orthogonal. If so, could you please tell me how that can be done?
Or using --perm-force should be fine?
Thanks.
On Mon, Mar 6, 2017 at 1:58 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
This is a problem with using LGI in that it is already extremely smooth that the smoothness exceeds the limit of the look up table that we supply. I recommend that you not use a gaussian-based correction for LGI. Instead, use permutation (see mri_glmfit-sim --help). On 03/06/2017 01:36 PM, Martin Juneja wrote: > Hello everyone, > > I am trying to extract clusters showing significant correlation > between LGI and a behavioral measure. I am able to extract PCC and > sig.mgh but at the last step when I try to run simulation command to > view corrected results and I run: > > mri_glmfit-sim --glmdir lh.MEQ_LGI.glmdir --cache 4 neg --cwp 0.05 > --2spaces > > I get following error: > > ERROR: cannot find > /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm35/neg/th40/mc-z.csd > > But I can see mc-z.csd file in fwhm30 etc. > > Full message on terminal window is attached following. > > Any help would be really appreciated. > > ----- Full message ---- > > cmdline mri_glmfit.bin --y lh.MEQ_LGI.10.mgh --fsgd MEQ.fsgd dods --C > Corr-MEQ-cor.mtx --surf fsaverage lh --cortex --glmdir lh.MEQ_LGI.glmdir > > WARNING: unrecognized mri_glmfit cmd option mri_glmfit.bin > > SURFACE: fsaverage lh > > log file is lh.MEQ_LGI.glmdir/cache.mri_glmfit-sim.log > > /usr/local/freesurfer/bin/mri_glmfit-sim > > --glmdir lh.MEQ_LGI.glmdir --cache 4 neg --cwp 0.05 --2spaces > > $Id: mri_glmfit-sim,v 1.60 2016/04/30 15:13:36 greve Exp $ > > Mon Mar 6 11:11:13 MST 2017 > > setenv SUBJECTS_DIR > /data/emot/Freesurfer/FreeSurferSegmentation/SB_AgingAll > > FREESURFER_HOME /usr/local/freesurfer > > Original mri_glmfit command line: > > cmdline mri_glmfit.bin --y lh.MEQ_LGI.10.mgh --fsgd MEQ.fsgd dods --C > Corr-MEQ-cor.mtx --surf fsaverage lh --cortex --glmdir lh.MEQ_LGI.glmdir > > DoSim = 0 > > UseCache = 1 > > DoPoll = 0 > > DoPBSubmit = 0 > > DoBackground = 0 > > DiagCluster = 0 > > gd2mtx = dods > > fwhm = 35.073391 > > ERROR: cannot find > /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm35/neg/th40/mc-z.csd > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 Partners Compliance HelpLine at http://www.partners.org/complianceline <http://www.partners.org/complianceline> . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Douglas N Greve -
Martin Juneja