Dr. Douglas,
I try #3 method, when I run mri_glmfit, get error.
The code I used:
[mtobia@localhost lh.lh-rh.thickness]$ mri_glmfit --y
lh.lh-rh.thickness.sm10.mgh --glmdir
glm.lh.lh-rh.thickness.sm10 --osgm --surf fsaverage_sym lh
Reading source surface
/HD4/subjects_results_symptom//fsaverage_sym/surf/lh.white
Number of vertices 163842
Number of faces 327680
Total area 61972.710938
AvgVtxArea 0.378247
AvgVtxDist 0.693419
StdVtxDist 0.190498
$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
cwd /HD4/subjects_results_symptom/lh.lh-rh.thickness
cmdline mri_glmfit --y lh.lh-rh.thickness.sm10.mgh --glmdir
glm.lh.lh-rh.thickness.sm10 --osgm --surf fsaverage_sym lh
sysname Linux
hostname localhost.localdomain
machine x86_64
user mtobia
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 1
y
/HD4/subjects_results_symptom/lh.lh-rh.thickness/lh.lh-rh.th
<http://lh.lh-rh.th>ickness.sm10.mgh
logyflag 0
usedti 0
labelmask
/HD4/subjects_results_symptom//fsaverage_sym/label/lh.cortex.label
maskinv 0
glmdir glm.lh.lh-rh.thickness.sm10
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory glm.lh.lh-rh.thickness.sm10
Loading y from
/HD4/subjects_results_symptom/lh.lh-rh.thickness/lh.lh-rh.th
<http://lh.lh-rh.th>ickness.sm10.mgh
Saving design matrix to glm.lh.lh-rh.thickness.sm10/Xg.dat
Normalized matrix condition is 1
Matrix condition is 1
Found 146902 points in label.
Pruning voxels by thr: 0.000000
Found 146902 voxels in mask
Saving mask to glm.lh.lh-rh.thickness.sm10/mask.mgh
Reshaping mriglm->mask...
search space = 79288.081914
DOF = 0
ERROR: DOF = 0
The code I used before this one is
How can I resolve this problem.
Thanks,
Lanbo
On Tue, Nov 7, 2017 at 6:10 PM, Douglas N Greve
<gr...@nmr.mgh.harvard.edu
<mailto:gr...@nmr.mgh.harvard.edu>> wrote:
which code. I gave 3 options below, which one did you use?
On 11/07/2017 02:43 PM, lanbo Wang wrote:
> I try to use this code to compare left and right
hemisphere by paired
> t-test and add age as covariate.
>
> Thanks,
> Lanbo
>
> On Tue, Nov 7, 2017 at 11:40 AM, Douglas N Greve
> <gr...@nmr.mgh.harvard.edu
<mailto:gr...@nmr.mgh.harvard.edu>
<mailto:gr...@nmr.mgh.harvard.edu
<mailto:gr...@nmr.mgh.harvard.edu>>> wrote:
>
> which method are you trying to implement? If #3,
then you need to run
> mris_preproc separately for each subject, and then
run that fscalc
> command
>
>
> On 11/07/2017 11:33 AM, lanbo Wang wrote:
> > Hi Douglas,
> >
> > Thanks for your reply.
> > I created the fsgd file as you show me, and run
code like this. Am I
> > right?
> > 1.
> > mris_preproc --fsgd Subject.xhemi.dat \
> > --target fsaverage_sym --hemi lh \
> > --xhemi --paired-diff \
> > --srcsurfreg fsaverage_sym.sphere.reg \
> > --meas thickness \
> > --out lh.lh-rh.thickness.age.sm00.mg
<http://lh.lh-rh.thickness.age.sm00.mg>h \
> > --s subj_02_1 --s subj_04_1 --s subj_05_1 --s
subj_06_1 --s
> > subj_08_1 --s subj_09_1 --s subj_10_1 --s
subj_11_1 --s
> subj_12_1
> > --s subj_13_1 --s subj_14_1 --s subj_15_1 --s
subj_16_1 --s
> > subj_17_1 --s subj_18_1 --s subj_20_1 --s
subj_21_1 --s
> subj_22_1
> > --s subj_24_1 --s subj_25_1 --s subj_26_1 --s
subj_27_1 --s
> > subj_29_1 --s subj_32_1
> >
> > 2.
> > mri_glmfit --y lh.lh-rh.thickness.age.sm10.mg
<http://lh.lh-rh.thickness.age.sm10.mg>h --glmdir
> > glm.lh.lh-rh.thickness.age.sm10 \
> > --fsgd Subject.xhemi.dat \
> > --C Avg-thickness-age-Cor.mtx \
> > --surf fsaverage_sym lh
> >
> > Attachment is fsgd and Avg-thickness-age-cor.mtx.
> >
> > All best,
> > Lanbo Wang
> >
> >
> > On Tue, Nov 7, 2017 at 10:18 AM, Bruce Fischl
> > <fis...@nmr.mgh.harvard.edu
<mailto:fis...@nmr.mgh.harvard.edu>
<mailto:fis...@nmr.mgh.harvard.edu
<mailto:fis...@nmr.mgh.harvard.edu>>
> <mailto:fis...@nmr.mgh.harvard.edu
<mailto:fis...@nmr.mgh.harvard.edu>
> <mailto:fis...@nmr.mgh.harvard.edu
<mailto:fis...@nmr.mgh.harvard.edu>>>> wrote:
> >
> > Hi Danny
> >
> > you need to give us more information if you
want us to help you.
> > Please include the command you ran and the
entire screen output.
> >
> > cheers
> > Bruce
> >
> >
> > On Tue, 7 Nov 2017, Danny Deng wrote:
> >
> > Dear FDs,
> > I encountered an odd situation:
> >
> > My free surfer will always shut down
when I run command.
> >
> > My MacOS version is 10.12.6 (16G29)
processor: 1.6 GHz Intel
> > Core i5
> >
> > I don’t know if the compatibility is
fine with my download
> > version (MacOS Lion OS X 10.7 (64b
> > intel)Stable v6.0.0)
> >
> > Please kindly suggest.
> >
> > Thanks ver much
> >
> > Best Regards,Danny Deng
> >
> >
> > On Nov 7, 2017, at 7:14 AM,
Douglas N Greve
> > <gr...@nmr.mgh.harvard.edu
<mailto:gr...@nmr.mgh.harvard.edu>
> <mailto:gr...@nmr.mgh.harvard.edu
<mailto:gr...@nmr.mgh.harvard.edu>>
> <mailto:gr...@nmr.mgh.harvard.edu
<mailto:gr...@nmr.mgh.harvard.edu>
<mailto:gr...@nmr.mgh.harvard.edu
<mailto:gr...@nmr.mgh.harvard.edu>>>>
> > wrote:
> >
> >
> >
> > On 11/06/2017 12:03 PM, lanbo Wang wrote:
> > Dear experts,
> >
> > I have two questions about hemisphere analysis:
> >
> > 1) When I run left-right hemisphere paired t-test,
> can I
> > add age as
> > covariate? If use fsgd to add covariate, to this
> paired
> > t-test
> > analysis, how to make the fsgd table?
> >
> > use this one-group, one-covariate example
> >
https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V
<https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V>
>
<https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V
<https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V>>
> >
<https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V
<https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V>
>
<https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V
<https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V>>>
> > 2) I want to reorganize the hemisphere from
> left-right to
> > symptom-nosymptom according to body symptom side
> record
> > and compare
> > different between symptom hemisphere and nosymptom
> > hemisphere. Can I
> > use freesurfer to do it?
> >
> > Yes, though it is a little tricky with
multiple ways, each
> > complicated
> > in its own way.
> > 1. Create your own design matrix. You
can use the one
> created by
> > mri_glmfit to start. Assuming you want
> > symptomHemi-nosymptomHemi, then,
> > in each subject whose symptomHemi is rh,
multiply its
> line in
> > the design
> > matrix by -1. Then pass this design
matrix to mri_glmfit
> with --X
> > instead of passing an FSGD file.
> > 2. Load the output of mris_preproc into
matlab, eg, y =
> > MRIread('y.mgh');, then change the sign as in
#1 above, eg,
> > y.vol(:,:,:,10) = -y.vol(:,:,:,10); and so on
for each
> applicable
> > subject. Then save the data with
MRIwrite(y,'new.y.mgh');,
> > then run
> > mri_glmfit as normal with the new file.
> > 3. Run mris_preproc for each subject
separately to
> generate an
> > lh.lh-rh.thickness.sm00.subject10.mgh file.
Then change the
> > sign as in
> > #1 above with
> > fscalc
lh.lh-rh.thickness.sm00.subject10.mgh mul -1 -o
> > lh.lh-rh.thickness.sm00.subject10.mgh
> > Then run mri_concat to concatenate all
the subjects together
> > in the same
> > order as they are listed in the FSGD
file, then use this
> stack
> > as input
> > the mri_glmfit
> >
> >
> > Thanks for your patient and help.
> >
> > All best,
> > Lanbo Wang
> >
> >
> > _______________________________________________
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> >
> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > gr...@nmr.mgh.harvard.edu
<mailto:gr...@nmr.mgh.harvard.edu>
<mailto:gr...@nmr.mgh.harvard.edu
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<mailto:gr...@nmr.mgh.harvard.edu>>>
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<tel:617-724-2358 <tel:617-724-2358>>
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<tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422
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> >
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<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>
> >
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<https://gate.nmr.mgh.harvard.edu/filedrop2>>
> >
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<https://gate.nmr.mgh.harvard.edu/filedrop2>
> <https://gate.nmr.mgh.harvard.edu/filedrop2
<https://gate.nmr.mgh.harvard.edu/filedrop2>>>
> >
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>
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>
> >
>
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> >
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>
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<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>>
> >
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<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>
>
<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>>>
> >
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<mailto:Freesurfer@nmr.mgh.harvard.edu>>
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> <mailto:Freesurfer@nmr.mgh.harvard.edu
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> >
> >
> > The information in this e-mail is
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> person
> > to whom it is
> > addressed. If you believe this e-mail was sent
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> error
> > and the e-mail
> > contains patient information, please
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> > Compliance HelpLine at
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> >
> >
> > The information in this e-mail is intended
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> 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
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> > Compliance HelpLine at
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>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
<mailto:gr...@nmr.mgh.harvard.edu>
<mailto:gr...@nmr.mgh.harvard.edu
<mailto:gr...@nmr.mgh.harvard.edu>>
> Phone Number: 617-724-2358 <tel:617-724-2358>
<tel:617-724-2358 <tel:617-724-2358>>
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<tel:617-726-7422 <tel:617-726-7422>>
>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
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