---------- Forwarded message ---------- From: miracle ozzoude <miracoo...@gmail.com> Date: Fri, Jan 26, 2018 at 7:08 PM Subject: Re: [Freesurfer] Fwd: monte-carlo error in longitudinal pipeline To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Hello Doug, Thanks for the patience. Here's the output from the terminal when I ran mri_glmfit. Best, Paul /Applications/freesurfer START: LONGITUDINAL CORTICAL THICKNESS 1000 1000_1 1000_1.long.1000 1000_2 1000_2.long.1000 1001 1001_1 1001_1.long.1001 1001_2 1001_2.long.1001 1003 1003_1 1003_1.long.1003 1003_2 1003_2.long.1003 1005 1005_1 1005_1.long.1005 1005_2 1005_2.long.1005 1008 1008_1 1008_1.long.1008 1008_2 1008_2.long.1008 1013 1013_1 1013_1.long.1013 1013_2 1013_2.long.1013 1014 1014_1 1014_1.long.1014 1014_2 1014_2.long.1014 gdfReadHeader: reading paired_diff.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 Age 76 3.70328 Class Means of each Continuous Variable 1 ADEX 76.0000 INFO: gd2mtx_method is doss Reading source surface /Users/carm/Documents/Cas/ ADEX/freesurfer/Preliminary_Analysis_Jan9_2018/fsaverage/surf/lh.white Number of vertices 163842 Number of faces 327680 Total area 65416.648438 AvgVtxArea 0.399267 AvgVtxDist 0.721953 StdVtxDist 0.195470 $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /Users/carm/Documents/Cas/ADEX/freesurfer/Preliminary_Analysis_Jan9_2018 cmdline mri_glmfit --y lh.paired.diff.thickness.10.mgh --fsgd paired_diff.fsgd doss --C mean.mtx --C age.mtx --surf fsaverage lh --cortex --glmdir lh.paired.diff.glmdir sysname Darwin hostname opennet-33-172.uhnres.utoronto.ca machine x86_64 user carm FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /Users/carm/Documents/Cas/ADEX/freesurfer/Preliminary_ Analysis_Jan9_2018/lh.paired.diff.thickness.10.mgh logyflag 0 usedti 0 FSGD paired_diff.fsgd labelmask /Users/carm/Documents/Cas/ADEX/freesurfer/Preliminary_ Analysis_Jan9_2018/fsaverage/label/lh.cortex.label maskinv 0 glmdir lh.paired.diff.glmdir IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory lh.paired.diff.glmdir Loading y from /Users/carm/Documents/Cas/ADEX/freesurfer/Preliminary_ Analysis_Jan9_2018/lh.paired.diff.thickness.10.mgh INFO: gd2mtx_method is doss Saving design matrix to lh.paired.diff.glmdir/Xg.dat Normalized matrix condition is 1686.7 Matrix condition is 2.46289e+06 Found 149955 points in label. Pruning voxels by thr: 0.000000 Found 0 voxels in mask Saving mask to lh.paired.diff.glmdir/mask.mgh Reshaping mriglm->mask... search space = 0.000000 DOF = 5 Starting fit and test Fit completed in 8.33333e-05 minutes Computing spatial AR1 on surface WARNING: ar1 = nan <= 0. Setting fwhm to 0. Residual: ar1mn=nan, ar1std=nan, gstd=0.000000, fwhm=0.000000 Writing results mean maxvox sig=0 F=0 at index 0 0 0 seed=1517221145 age maxvox sig=0 F=0 at index 0 0 0 seed=1517221145 mri_glmfit done gdfReadHeader: reading paired_diff.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 Age 76 3.70328 Class Means of each Continuous Variable 1 ADEX 76.0000 INFO: gd2mtx_method is doss Reading source surface /Users/carm/Documents/Cas/ ADEX/freesurfer/Preliminary_Analysis_Jan9_2018/fsaverage/surf/rh.white Number of vertices 163842 Number of faces 327680 Total area 65020.765625 AvgVtxArea 0.396850 AvgVtxDist 0.717994 StdVtxDist 0.193566 $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /Users/carm/Documents/Cas/ADEX/freesurfer/Preliminary_Analysis_Jan9_2018 cmdline mri_glmfit --y rh.paired.diff.thickness.10.mgh --fsgd paired_diff.fsgd doss --C mean.mtx --C age.mtx --surf fsaverage rh --cortex --glmdir rh.paired.diff.glmdir sysname Darwin hostname opennet-33-172.uhnres.utoronto.ca machine x86_64 user carm FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /Users/carm/Documents/Cas/ADEX/freesurfer/Preliminary_ Analysis_Jan9_2018/rh.paired.diff.thickness.10.mgh logyflag 0 usedti 0 FSGD paired_diff.fsgd labelmask /Users/carm/Documents/Cas/ADEX/freesurfer/Preliminary_ Analysis_Jan9_2018/fsaverage/label/rh.cortex.label maskinv 0 glmdir rh.paired.diff.glmdir IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory rh.paired.diff.glmdir Loading y from /Users/carm/Documents/Cas/ADEX/freesurfer/Preliminary_ Analysis_Jan9_2018/rh.paired.diff.thickness.10.mgh INFO: gd2mtx_method is doss Saving design matrix to rh.paired.diff.glmdir/Xg.dat Normalized matrix condition is 1686.7 Matrix condition is 2.46289e+06 Found 149926 points in label. Pruning voxels by thr: 0.000000 Found 0 voxels in mask Saving mask to rh.paired.diff.glmdir/mask.mgh Reshaping mriglm->mask... search space = 0.000000 DOF = 5 Starting fit and test Fit completed in 0.0001 minutes Computing spatial AR1 on surface WARNING: ar1 = nan <= 0. Setting fwhm to 0. Residual: ar1mn=nan, ar1std=nan, gstd=0.000000, fwhm=0.000000 Writing results mean maxvox sig=0 F=0 at index 0 0 0 seed=1517884366 age maxvox sig=0 F=0 at index 0 0 0 seed=1517884366 mri_glmfit done On Wed, Jan 24, 2018 at 2:59 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > 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 > > <gr...@nmr.mgh.harvard.edu <mailto:gr...@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* <miracoo...@gmail.com <mailto: > miracoo...@gmail.com> > > > <mailto:miracoo...@gmail.com <mailto:miracoo...@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 > > > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > > <mailto:gr...@nmr.mgh.harvard.edu > > <mailto:gr...@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. 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> > > > <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 > > <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 > > gr...@nmr.mgh.harvard.edu <mailto:gr...@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:freesur...@nmr.mgh.har > vard.edu> > > 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 > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@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 >
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