24 Jan
2018
24 Jan
'18
2:59 p.m.
can you send the terminal output of mri_glmfit?
On 01/24/2018 02:52 PM, miracle ozzoude wrote:
Hello Doug,
I looked at the fwhm.dat and fwhm value = 0. I have attached the mri_glmfit.log file. How do i solve this problem?
Best, Paul
On Mon, Jan 22, 2018 at 11:57 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
If your fwhm is 0, then something is wrong. Look in the fwhm.dat file in the glmfit output to see what the value is. Also, send the terminal output from mri_glmfit (not mri_glmfit-sim) On 01/22/2018 11:43 AM, miracle ozzoude wrote: > > ---------- Forwarded message ---------- > From: *miracle ozzoude* <miracooloz@gmail.com <mailto:miracooloz@gmail.com> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>> > Date: Sat, Jan 20, 2018 at 1:56 PM > Subject: Re: [Freesurfer] monte-carlo error in longitudinal pipeline > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > > Hello Doug, > > I tried using the MC tables that FS distributed. However, i got an > error about " cannot find /fwhm00/pos/th30/mc-z.csd ". I checked and > there's no fwhm00, the table starts from fwhm01 to fwhm30. Below are > my script and cache.mri_glmfi-sim.log files. My FreeSurfer version is > stable version 5.3 on mac. Thank you. > > Best, > Paul > > mri_glmfit-sim --glmdir lh.paired.diff.glmdir --cache-dir > $SUBJECTS_DIR/average/mult-comp-cor/fsaverage/lh/cortex --cache 3 pos > --cwpvalthresh 0.05 --2spaces --overwrite > mri_glmfit-sim --glmdir rh.paired.diff.glmdir --cache-dir > $SUBJECTS_DIR/average/mult-comp-cor/fsaverage/rh/cortex --cache 3 pos > --cwpvalthresh 0.05 --2spaces --overwrite > > On Thu, Jan 18, 2018 at 5:23 PM, Douglas Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > Why are you doing your own MC simulation? You can just use the > tables that we distribute ... > > > On 1/17/18 6:12 PM, miracle ozzoude wrote: >> Hello Experts, >> >> I am running a paired t-test cortical thickness analysis based on >> the instruction on the wiki page >> (https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis> >> <https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis <https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis>>). >> However, the monte carlo files weren't not created when i >> corrected for multiple comparisons. Below are my script, fsgd >> files, mc-z log file, and a screenshot of contrast folder missing >> mc.z maps. Please can you help me figure out why the error is >> happening. Thank you. >> >> Best, >> Paul >> >> *Script*: >> pairs=pairs.fsgd paired=paired_diff.fsgd martrix1=mean.mtx >> martrix2=age.mtx >> #resample each subjects's left and right hemisphere data to >> fsavarage. >> mris_preproc --target fsaverage --hemi lh --meas thickness --out >> lh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff >> mris_preproc --target fsaverage --hemi rh --meas thickness --out >> rh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff >> # #smoothen the concatenated file by 5mm FWHM. --cortex means >> only smooth areas in the cortex. N:B. FWHM changes based on study >> type. >> mri_surf2surf --hemi lh --s fsaverage --sval >> lh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval >> lh.paired-diff.thickness.sm05.mgh >> mri_surf2surf --hemi rh --s fsaverage --sval >> rh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval >> rh.paired-diff.thickness.sm05.mgh >> # #Run GLM analysis >> mri_glmfit --y lh.paired-diff.thickness.sm05.mgh --fsgd $paired >> --C $martrix1 --C $martrix2 --surf fsaverage lh --cortex --glmdir >> lh.paired-diff.glmdirir >> mri_glmfit --y rh.paired-diff.thickness.sm05.mgh --fsgd $paired >> --C $martrix1 --C $martrix2 --surf fsaverage rh --cortex --glmdir >> rh.paired-diff.glmdir >> # # #Run Clusterwise correction for multiple comparisons using >> MONTE CARLO. First create a table for of simulations >> mri_glmfit-sim --glmdir lh.paired-diff.glmdir --sim mc-z 10000 2 >> mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite >> mri_glmfit-sim --glmdir rh.paired-diff.glmdir --sim mc-z 10000 2 >> mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite >> *Fsgd file 1:pairs.fsgd* >> >> GroupDescriptorFile 1 >> >> Class ADEX >> >> Input 1000_1 ADEX >> >> Input 1000_2 ADEX >> >> Input 1001_1 ADEX >> >> Input 1001_2 ADEX >> >> Input 1003_1 ADEX >> >> Input 1003_2 ADEX >> >> Input 1005_1 ADEX >> >> Input 1005_2 ADEX >> >> Input 1008_1 ADEX >> >> Input 1008_2 ADEX >> >> Input 1013_1 ADEX >> >> Input 1013_2 ADEX >> >> Input 1014_1 ADEX >> >> Input 1014_2 ADEX >> >> *Fsgd file 2: paired_diff.fsgd* >> >> GroupDescriptorFile 1 >> >> Class ADEX >> >> Variables Age >> >> Input 1000 ADEX 72 >> >> Input 1001 ADEX 76 >> >> Input 1003 ADEX 72 >> >> Input 1005 ADEX 80 >> >> Input 1008 ADEX 72 >> >> Input 1013 ADEX 80 >> >> Input 1014 ADEX 80 >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> <mailto: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> >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto: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> > <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. 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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>
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--
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/