On Fri, Nov 10, 2017 at 3:07 PM, Douglas Greve <greve@nmr.mgh.harvard.edu> wrote:

Yes
On 11/10/17 2:45 PM, lanbo Wang wrote:
Thank you very much, it's work.
I have another question, this is for structural imaging. Can I use those steps for fmri or DTI imaging?
On Fri, Nov 10, 2017 at 1:08 PM, Douglas Greve <greve@nmr.mgh.harvard.edu> wrote:
Don't use --conjunct, just mri_concat file1 file2 ... file N --o output
On 11/10/17 12:56 PM, lanbo Wang wrote:
I firstly did mris_preproc separately. Secondly used fscalc to reverse left symptom subjects. Thirdly used mri_concat --conjunct to combine all the subjects together.

The code is:
1.mris_preproc --target fsaverage_sym --hemi lh \
--xhemi --paired-diff \
--srcsurfreg fsaverage_sym.sphere.reg \
--meas thickness \
--out lh.lh-rh.thickness.sm00.s02.mgh \
--s subj_02_1
2. fscalc lh.lh-rh.thickness.sm00.s09.mgh mul -1 -o lh.lh-rh.thickness.sm00.s09.mgh
3.mri_concat --conjunct --i lh.lh-rh.thickness.sm00.s02.mgh lh.lh-rh.thickness.sm00.s03.mgh lh.lh-rh.thickness.sm00.s04.mgh lh.lh-rh.thickness.sm00.s05.mgh lh.lh-rh.thickness.sm00.s06.mgh lh.lh-rh.thickness.sm00.s08.mgh lh.lh-rh.thickness.sm00.s09.mgh lh.lh-rh.thickness.sm00.s10.mgh lh.lh-rh.thickness.sm00.s11.mgh lh.lh-rh.thickness.sm00.s12.mgh lh.lh-rh.thickness.sm00.s13.mgh lh.lh-rh.thickness.sm00.s14.mgh lh.lh-rh.thickness.sm00.s15.mgh lh.lh-rh.thickness.sm00.s16.mgh lh.lh-rh.thickness.sm00.s17.mgh lh.lh-rh.thickness.sm00.s18.mgh lh.lh-rh.thickness.sm00.s19.mgh lh.lh-rh.thickness.sm00.s20.mgh lh.lh-rh.thickness.sm00.s21.mgh lh.lh-rh.thickness.sm00.s22.mgh lh.lh-rh.thickness.sm00.s24.mgh lh.lh-rh.thickness.sm00.s25.mgh lh.lh-rh.thickness.sm00.s26.mgh lh.lh-rh.thickness.sm00.s27.mgh lh.lh-rh.thickness.sm00.s29.mgh lh.lh-rh.thickness.sm00.s32.mgh --o lh.lh-rh.thickness.sm00.mgh
4.smooth
5.mri_glmfit --y lh.lh-rh.thickness.sm10.mgh --glmdir glm.lh.lh-rh.thickness.sm10 --osgm --surf fsaverage_sym lh
On Fri, Nov 10, 2017 at 11:17 AM, Douglas Greve <greve@nmr.mgh.harvard.edu> wrote:
Do you only have one subject in your input file? You need to run mris_preproc separately for each subject, create a different file for each, then mri_concat the files together
On 11/9/17 6:20 PM, lanbo Wang wrote:
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.thickness.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.thickness.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 <greve@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

> <greve@nmr.mgh.harvard.edu <mailto:greve@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.mgh \
> > --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.mgh --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
> > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>

> <mailto:fischl@nmr.mgh.harvard.edu
> <mailto:fischl@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
> > <greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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>>
> >    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
> >
> >
> >    _______________________________________________
> >    Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>

> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
> >
> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>
> > Phone Number: 617-724-2358 <tel:617-724-2358>
> <tel:617-724-2358 <tel:617-724-2358>>
> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422
> <tel:617-726-7422>>
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>
> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> <https://gate.nmr.mgh.harvard.edu/filedrop2>
> > <https://gate.nmr.mgh.harvard.edu/filedrop2
> <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>
> >
>   <http://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/
> <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/>>
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <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
> <http://www.partners.org/complianceline>
> > <http://www.partners.org/complianceline
> <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
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >

>   <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <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
> <http://www.partners.org/complianceline>
> > <http://www.partners.org/complianceline
> <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
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> Phone Number: 617-724-2358 <tel:617-724-2358>
> Fax: 617-726-7422 <tel:617-726-7422>
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> <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/
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <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

--
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
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
_______________________________________________
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
_______________________________________________
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.