something is wrong with the mask (the terminal output says that there are no voxels in the mask)
On 1/30/18 11:51 AM, miracle ozzoude wrote:
---------- Forwarded message ---------- From: *miracle ozzoude* <miracooloz@gmail.com mailto:miracooloz@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 mailto: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 ADEX76.0000
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 faces327680
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
sysnameDarwin
hostname opennet-33-172.uhnres.utoronto.ca http://opennet-33-172.uhnres.utoronto.ca
machinex86_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
usedti0
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=0F=0atindex 0 0 0seed=1517221145
age
maxvox sig=0F=0atindex 0 0 0seed=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 ADEX76.0000
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 faces327680
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
sysnameDarwin
hostname opennet-33-172.uhnres.utoronto.ca http://opennet-33-172.uhnres.utoronto.ca
machinex86_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
usedti0
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=0F=0atindex 0 0 0seed=1517884366
age
maxvox sig=0F=0atindex 0 0 0seed=1517884366
mri_glmfit done
On Wed, Jan 24, 2018 at 2:59 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@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 > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto: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>> > > <mailto: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>> > > <mailto: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>> > <mailto: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>> > >> <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>> > >> <mailto: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>> > >> <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>> > <mailto: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>> > > <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>> > > <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> > <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>> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://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> > <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> > <http://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/> > <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> <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> > 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>
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