The cache is not set up for volume-based analysis. There are two options: 1. use gaussian random fields (--grf instead of --cache). If you want to use this option, let me know as I have recently made some changes to it that make it more accurate
2. use permutation (--perm 5000 1.3 pos). This method is probably better given the problems in the Eklund, 2016, PNAS paper doug On 10/20/2016 09:20 PM, John Anderson wrote: > 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" <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 > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > 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. > > > _______________________________________________ > 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 gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
