On Mon, Jan 22, 2018 at 11:57 AM, Douglas N Greve <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>>
> 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>>
>
>
> 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>> 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>).
>> 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
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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