Thank you very much Doug. You are so awsome :)
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
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: Monday, November 14, 2016 at 1:00 PM
From: "Douglas N 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 N Greve" <gr...@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Fw: Re: surface based analysis for subcortical structures
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" <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 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.ander...@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" <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
>>
>>
>> _______________________________________________ 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
>
--
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
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" <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 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.ander...@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" <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
>>
>>
>> _______________________________________________ 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
>
--
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
_______________________________________________ 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.
