Hi Doug,
Yes! Thank you for the offer to share the script.
Actually I want to run surface based analysis for sub cortical structres
I tried the command
mri_glmfit-sim --glmdir subc.glmdir --cache 1.3 pos --cwp 0.05 --3spaces
mri_glmfit-sim --glmdir subc.glmdir --cache 1.3 pos --cwp 0.05 --3spaces
But it failed (I don't know why!) and this is the reason why I want to use "mri_glmfit-sim --glmdir subc.glmdir --grf 3 pos --cwpvalthresh .0166"
Bests,
John
John
Sent: Friday, October 28, 2016 at 11:53 AM
From: "Douglas Greve" <gr...@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Fw: Re: surface based analysis for subcortical structures
From: "Douglas Greve" <gr...@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Fw: Re: surface based analysis for subcortical structures
If you want to use GRF, then I should get you new versions of some of the programs as the volume-based GRF used the Friston 1994 algorithm that was not as accurate as the Worsley 1996 algorithm. I just updated my code last week (better late than never:). But in the end, you probably want to use permutation if your group analysis allows it.
On 10/23/16 10:25 AM, John Anderson wrote:
Thank you very much Doug,The codes worked very well. I was using the wrong command to correct the data.My command wasmri_glmfit-sim --glmdir subc.glmdir --cache 1.3 pos --cwp 0.05 --3spacesand for subcortical structures it must bemri_glmfit-sim --glmdir subc.glmdir --grf 3 pos --cwpvalthresh .0166All 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) 646-1419Sent: Thursday, October 20, 2016 at 9:20 PM
From: "John Anderson" <j.ander...@publicist.com>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] surface based analysis for subcortical structuresDear Doug,Thank you very much for this detailed explaination. I highly appreciate your helpKindly I have the following question:The command mri_vol2vol ran smoothly without any errorsThe command mri_mask output the following :mri_mask suvr.tal2mm.nii $FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz suvr.tal2mm.subc.nii
freadFloat: fread failed
DoAbs = 0
Writing masked volume to suvr.tal2mm.subc.nii...done.Should I worry about this error ?I ignored this error and I continued the following steps. They went fine but when I correct for multiple comparisons using the command "mri_glmfit-sim" I get the following:mri_glmfit-sim --glmdir subc.glmdir --cache 1.3 pos --cwp 0.05 --3spaces
cmdline mri_glmfit --y all.pet.tal2mm.subc.sm5.nii --fsgd fsgd.dat --C 2G0C.mtx --glmdir subc.glmdir
log file is subc.glmdir/cache.mri_glmfit-sim.logcd /analyses/pet_scan/SBM/sm
/usr/local/freesurfer/stable5_3_0/bin/mri_glmfit-sim
--glmdir subc.glmdir --cache 1.3 pos --cwp 0.05 --3spaces$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_0Original mri_glmfit command line:
cmdline mri_glmfit --y all.pet.tal2mm.subc.sm5.nii --fsgd fsgd.dat --C 2G0C.mtx --glmdir subc.glmdirDoSim = 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 = 1Kindly how can I troubleshoo? thank you for any adviceBests,
JohnSent: Thursday, October 20, 2016 at 12:16 PM
From: "Douglas N Greve" <gr...@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
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
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_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 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 . 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.
