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 <a...@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 > > > > > > > > > > _______________________________________________ > 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. > >
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