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
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 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
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
oops, sorry,
download these files
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_glmfit-sim
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_volcluster
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_surfcluster
Copy them into $FREESURFER_HOME/bin (after making a backup of the previous files).
Edit mri_glmfit-sim to remove
source $FREESURFER_HOME/sources.csh
then hopefully everything should work
doug
On 11/04/2016 06:11 AM, John Anderson wrote:
Hi Doug, I want to use GRF. Will you be willing to share the new versions of the programs? Your help is highly appreciated. Thanks! Jon *on:* Friday, October 28, 2016 at 11:53 AM *From:* "Douglas Greve" greve@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 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 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_______________________________________________ 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 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
Hi, I just found a bug in mri_glmfit-sim in regards to GRF on volume-based data. I put a fixed version at the same location. Please use the new version
On 11/04/2016 10:25 AM, Douglas N Greve wrote:
oops, sorry,
download these files
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_glmfit-sim
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_volcluster
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_surfcluster
Copy them into $FREESURFER_HOME/bin (after making a backup of the previous files).
Edit mri_glmfit-sim to remove
source $FREESURFER_HOME/sources.csh
then hopefully everything should work
doug
On 11/04/2016 06:11 AM, John Anderson wrote:
Hi Doug, I want to use GRF. Will you be willing to share the new versions of the programs? Your help is highly appreciated. Thanks! Jon *on:* Friday, October 28, 2016 at 11:53 AM *From:* "Douglas Greve" greve@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 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, NH03755 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 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://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_______________________________________________ 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 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
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" 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
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
freesurfer@nmr.mgh.harvard.edu
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Douglas Greve -
Douglas N Greve
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John Anderson