Thank you very much Doug,
The codes worked very well. I was using the wrong command to correct the data.
My command was 
mri_glmfit-sim --glmdir subc.glmdir --cache 1.3 pos --cwp 0.05 --3spaces
 
and for subcortical structures it must be 
mri_glmfit-sim --glmdir subc.glmdir --grf 3 pos --cwpvalthresh .0166
All the bests,
John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419
 
 
Sent: Thursday, October 20, 2016 at 9:20 PM
From: "John Anderson" <j.anderson@publicist.com>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] surface based analysis for subcortical structures
Dear Doug,
Thank you very much for this detailed explaination. I highly appreciate your help
Kindly I have the following question:
The command mri_vol2vol ran smoothly without any errors
The command mri_mask output the following :
 
mri_mask suvr.tal2mm.nii $FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz suvr.tal2mm.subc.nii 
freadFloat: fread failed
DoAbs = 0
Writing masked volume to suvr.tal2mm.subc.nii...done.
 
Should I worry about this error ?
 
 
I ignored this error and I continued the following steps. They went fine but when I correct for multiple comparisons using the command "mri_glmfit-sim" I get the following:
 
 
mri_glmfit-sim --glmdir subc.glmdir --cache 1.3 pos --cwp 0.05 --3spaces
cmdline mri_glmfit --y all.pet.tal2mm.subc.sm5.nii --fsgd fsgd.dat --C 2G0C.mtx --glmdir subc.glmdir
log file is subc.glmdir/cache.mri_glmfit-sim.log
cd /analyses/pet_scan/SBM/sm
/usr/local/freesurfer/stable5_3_0/bin/mri_glmfit-sim
--glmdir subc.glmdir --cache 1.3 pos --cwp 0.05 --3spaces
$Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $
Thu Oct 20 21:10:31 EDT 2016
Linux sven 2.6.32-642.3.1.el6.x86_64 #1 SMP Tue Jul 12 18:30:56 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
malshikh
setenv SUBJECTS_DIR /analyses/recons
FREESURFER_HOME /usr/local/freesurfer/stable5_3_0
Original mri_glmfit command line:
cmdline mri_glmfit --y all.pet.tal2mm.subc.sm5.nii --fsgd fsgd.dat --C 2G0C.mtx --glmdir subc.glmdir
DoSim = 0
UseCache = 1
DoPoll = 0
DoPBSubmit = 0
DoBackground = 0
DiagCluster = 0
gd2mtx = dods
fwhm = 10.682767
ERROR: cannot find /usr/local/freesurfer/stable5_3_0/average/mult-comp-cor///cortex/fwhm11/pos/th13/mc-z.csd
 
I smoothed just fwhm = 1
 
Kindly how can I troubleshoo? thank you for any advice
 
Bests,
John 
 
Sent: Thursday, October 20, 2016 at 12:16 PM
From: "Douglas N Greve" <greve@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] surface based analysis for subcortical structures

After spmregister, you can run

mri_vol2vol --mov pet.nii --reg reg.dat --tal --talres 2 --talxfm
talairach.xfm --nearest --no-save-reg --o pet.tal2mm.nii

# mask out the cortical structures

mri_mask pet.tal2mm.nii
$FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz
pet.tal2mm.subc.nii

# Concatenate all subjects together

mri_concat s1/pet.tal2mm.subc.nii s2/pet.tal2mm.subc.nii ... --o
all.pet.tal2mm.subc.nii --prune

# smooth

mri_fwhm --i all.pet.tal2mm.subc.nii --mask
$FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz --fwhm X
--smooth-only --o all.pet.tal2mm.subc.smoothed.nii

mri_glmfit --y all.pet.tal2mm.subc.smoothed.nii --fsgd fsgd.txt--C
2gc0.mtx --glmdir subc.glmdir



On 10/19/2016 05:09 PM, John Anderson wrote:
> Dear experts,
> I ran surface based analysis using PET maps. As the following:
> spmregister --s subj --mov pet.nii --reg reg.dat --out pet_t1.mgh
> mris_preproc --target fsaverage --hemi lh --iv subj1/ubject1_pet.nii subject1/pet/pet_2_T1_register.dat ..... --projfrac 0.5 --out lh.mgh
> mri_surf2surf --hemi lh --s fsaverage --fwhm 6 --cortex --sval lh.mgh --tval lh.sm6.mgh
> mri_glmfit--y lh.sm6.mgh--fsgd fsgd.txt--C 2gc0.mtx --surf fsaverage lh --cortex --glmdir lh.glmdir//
> then mri_glmfit-sim to correct for multiple comparison.
> I want to study the subcortical regions and map it on MNI305. How can
> I resume tha analysis for subcortical structures?
> Thank you for any help!
> Bests,
> John
>
>
> _______________________________________________
> 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
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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