Can you upload the glmfit folders and the glmfit input (--y file) to our
filedrop?
https://gate.nmr.mgh.harvard.edu/filedrop2/
On 2/1/18 7:46 PM, miracle ozzoude wrote:
Hello Doug,
I have attached a screen shot of the mask.mgh for both right and left
hemispheres. Everything looks yellow. I followed the paired t-test
tutorial on the wiki page (included my scripts, fsgd files, and matrix
in email thread). How do i go about fixing it? Thanks you
Best,
Paul
On Tue, Jan 30, 2018 at 9:57 PM, Douglas Greve
<gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote:
that usually means that something has gone wrong with the
analysis. Do the maps look ok? In particular, look at the mask
On 1/20/18 1:56 PM, miracle ozzoude wrote:
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>> 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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