Hi Antonin,
Thanks a lot for your reply.
Somehow, in the link you sent, I could not find any response to your email. But I can see your email to Anderson and command line parameters.
As I am not an expert in using FreeSurfer, so would it be possible for you to share detailed step-by-step guide and PALM command after I run mri_glmfit command and how and where to include '?h.white.avg.area.mgh' file?
I would really appreciate any help.
On Mon, Mar 6, 2017 at 4:28 PM, Antonin Skoch ansk@ikem.cz wrote:
Dear Martin,
I think yes, you can use PALM with FreeSurfer surfaces, see my conversation with Anderson on FSL list:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1604&L= FSL&D=0&1=FSL&9=A&J=on&d=No+Match%3BMatch%3BMatches&z=4&P=239088
but beware not to forget to include average the vertex area (?h.white.avg.area.mgh) file.
Antonin
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 <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu gr...@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 > >
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