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
>     >>
>     >>
>     >>
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>     --
>     Douglas N. Greve, Ph.D.
>     MGH-NMR Center
>     greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
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