[Freesurfer] significant of long_mris_slopes

[lanbo Wang]

Dear freesurfer group,

Hi!
I used long_stats_slopes and code to process my longitudinal data:
long_stats_slopes --qdec sub_qdec_long.dat --stats lh.aparc.stats --meas
thickness --sd $SUBJECTS_DIR --do-rate --generic-time --stack-rate
thickness.lh.aparc-rate.stack.txt
mri_glmfit --osgm --glmdir thickness.lh.aparc-rate --table
thickness.lh.aparc-rate.stack.txt
I got results sig.table.dat in folder of 'thickness.lh.aparc-rate'. I want
to ask what's meaning of this results. Is it the significant results or
just directly result?

All best,
Lanbo Wang


sig.table.dat
Description: Binary data
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[Freesurfer] Questions about BA template

[lanbo Wang]

Dear experts,

I have questions about BA template:
1. What's different between BA and BA.thresh?
2. I want to check the size of each structure of BA and BA.thresh template.
How can I got it?

Thank you in advance.

All best,
Lanbo Wang
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[Freesurfer] Question about Xhemi

[lanbo Wang]

Dear Freesurfer experts,

When I try run mris_apply_reg according to Xhemi:
"the error is lh.map.mgh does not exist or is not readable by you"
lh.map.mgh is made by which step?

Thank you in advance.

best,
Lanbo
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[Freesurfer] mris_apply_reg

[lanbo Wang]

Dear Freesurfer experts,

I try run this code according to Xhemi：
mris_apply_reg --src-label label/rh.V1_exvivo.thresh.label --trg
rh-on-lh.V1_exvivo.thresh.label \
--streg xhemi/surf/lh.fsaverage_sym.sphere.reg surf/lh.fsaverage_sym.sphere.reg

However, error shows: Option --src-label unknown. And also
mris_apply_reg --help didn't show how to correctly use -label.

What's the correctly code.

Thanks for your advices.

Best,

Lanbo
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Re: [Freesurfer] mris_apply_reg

[lanbo Wang]

Dear Mohamad,

You're right, after I use version 6.0, it works. Thanks for your help.

best,
Lanbo


On Fri, Nov 3, 2017 at 3:12 PM, Alshikho, Mohamad J. <
malshi...@mgh.harvard.edu> wrote:

> Hi Lanbo,
>
> You need Freesurfer 6 to run this command. The flag --src-label is not
> part of FS5.3
>
>
>
> Best,
>
> M_
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@
> nmr.mgh.harvard.edu] *On Behalf Of *lanbo Wang
> *Sent:* Friday, November 3, 2017 11:49 AM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* [Freesurfer] mris_apply_reg
>
>
>
> Dear Freesurfer experts,
>
> I try run this code according to Xhemi：
> mris_apply_reg --src-label label/rh.V1_exvivo.thresh.label --trg 
> rh-on-lh.V1_exvivo.thresh.label \
>
> --streg xhemi/surf/lh.fsaverage_sym.sphere.reg 
> surf/lh.fsaverage_sym.sphere.reg
>
> However, error shows: Option --src-label unknown. And also mris_apply_reg 
> --help didn't show how to correctly use -label.
>
> What's the correctly code.
>
> Thanks for your advices.
>
> Best,
>
> Lanbo
>
>
>
>
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Re: [Freesurfer] Question about Xhemi

[lanbo Wang]

Dear Douglas,

The comman line and terminal output show is this:
[mtobia@localhost subjects_results_symptom]$ mris_apply_reg --src
lh.map.mgh --trg lh.map.lh.fsaverage_sym.mgh \
> --streg $SUBJECTS_DIR/s02_base/surf/lh.fsaverage_sym.sphere.reg
$FREESURFER_HOME/subjects/fsaverage_sym/surf/lh.sphere.reg
ERROR: lh.map.mgh does not exist or is not readable by you

And also I have other 2 questions:
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?
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?

Thanks for your patient and help.

All best,
Lanbo Wang


On Sun, Nov 5, 2017 at 1:27 PM, Douglas Greve 
wrote:

> Can you send the command line you are using and the full terminal output?
>
> On 11/2/17 3:09 PM, lanbo Wang wrote:
>
> Dear Freesurfer experts,
>
> When I try run mris_apply_reg according to Xhemi:
> "the error is lh.map.mgh does not exist or is not readable by you"
> lh.map.mgh is made by which step?
>
> Thank you in advance.
>
> best,
> Lanbo
>
>
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>
>
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> is
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> e-mail
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[Freesurfer] hemisphere analysis

[lanbo Wang]

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?
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?

Thanks for your patient and help.

All best,
Lanbo Wang
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Re: [Freesurfer] hemisphere analysis

[lanbo Wang]

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 
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> 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
>>   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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>>   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/
>>
>> ___
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>> Freesurfer@nmr.mgh.harvard.edu
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Re: [Freesurfer] hemisphere analysis

[lanbo Wang]

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 
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
> > 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
> > 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>
> >   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

Re: [Freesurfer] hemisphere analysis

[lanbo Wang]

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 faces327680
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: 0.00
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 
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
> > 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.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
> > > 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) pr

Re: [Freesurfer] hemisphere analysis

[lanbo Wang]

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 
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 faces327680
> 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: 0.00
> 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  > 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
>> > 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 \
&

Re: [Freesurfer] hemisphere analysis

[lanbo Wang]

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 
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  > 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 faces327680
>> 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
>> 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.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: 0.00
>> 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> 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,
>>> &

Re: [Freesurfer] hemisphere analysis

[lanbo Wang]

Can I use data processed by other tool like FSL, or I can only use DTI
image after Freesurfer processing?

On Fri, Nov 10, 2017 at 3:07 PM, Douglas Greve 
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 
> 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 <
>> gr...@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 faces327680
>>> 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
>>> 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.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: 0.00
>>> Found 146902 voxels in mask
>>> Saving mask to glm.lh.lh-rh.thickness.sm10/mask.mgh
>>> Reshaping mriglm->mask...
>>> search space 

[Freesurfer] dmrirc.tutorial problem

[lanbo Wang]

Dear experts,

I try to run trac-all -bedp -c dmrirc.tutorial, but error shows like this,
then stop:
INFO: SUBJECTS_DIR is /HD4/DTI
INFO: Diffusion root is HD4/DTI
Actual FREESURFER_HOME /HD2/freesurfer
WARN: Running bedbostx locally - this might take a while
WARN: It is recommended to run this step on a cluster
bedpostx_mgh -n 2 HD4/DTI/DBK08/dmri
WARN: Running bedbostx locally - this might take a while
WARN: It is recommended to run this step on a cluster
bedpostx_mgh -n 2 HD4/DTI/DBK08.2nd/dmri
WARN: Running bedbostx locally - this might take a while
WARN: It is recommended to run this step on a cluster
bedpostx_mgh -n 2 HD4/DTI/DBK08.3rd/dmri
WARN: Running bedbostx locally - this might take a while
WARN: It is recommended to run this step on a cluster
bedpostx_mgh -n 2 HD4/DTI/DBK08.4th/dmri
[mtobia@localhost DTI]$ trac-all -bedp -c dmrirc.tutorial
INFO: SUBJECTS_DIR is /HD4/DTI
INFO: Diffusion root is HD4/DTI
Actual FREESURFER_HOME /HD2/freesurfer
WARN: Running bedbostx locally - this might take a while
WARN: It is recommended to run this step on a cluster
bedpostx_mgh -n 2 HD4/DTI/DBK08/dmri
WARN: Running bedbostx locally - this might take a while
WARN: It is recommended to run this step on a cluster
bedpostx_mgh -n 2 HD4/DTI/DBK08.2nd/dmri
WARN: Running bedbostx locally - this might take a while
WARN: It is recommended to run this step on a cluster
bedpostx_mgh -n 2 HD4/DTI/DBK08.3rd/dmri
WARN: Running bedbostx locally - this might take a while
WARN: It is recommended to run this step on a cluster
bedpostx_mgh -n 2 HD4/DTI/DBK08.4th/dmri


Thanks for your patient and help.

All best,
Lanbo Wang


dmrirc.tutorial
Description: Binary data
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[Freesurfer] Question about compare left and right hemi of longitudinal data

[lanbo Wang]

Hi, all experts.
I want to compare changes rate between left and right hemisphere of
longitudinal data, How should I do that, how to combine xhemi with two
stage or LME?

Best,
Lanbo
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[Freesurfer] Question about LME modle

[lanbo Wang]

Dear all freesurfer experts,

Hi,

When use lme_lowessPlot, the plot shows black and green two lines. What the
meaning of two line?

Thank you,
Lanbo
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Re: [Freesurfer] Question about compare left and right hemi of longitudinal data

[lanbo Wang]

Thanks for replying me. But I still have two questions.
Firstly, when I try xhemi on pre-possessed longitudinal data, it showed
error like this:
Performing left-right swap of labels
TR=2300.00, TE=2.98, TI=900.00, flip angle=9.00
i_ras = (-1, 3.72529e-08, 3.35276e-08)
j_ras = (-2.6077e-08, -3.72529e-09, -1)
k_ras = (-1.78814e-07, 1, 6.98492e-10)
writing to /HD4/symptom_test//subj_02_1.long.s02_base/xhemi/mri/aparc+
aseg.mgz...
Wed Dec 20 17:46:35 EST 2017
recon-all -sb subj_02_1.long.s02_base/xhemi -talairach

ERROR: Are you trying to run or re-run a longitudinal time point?
   If so, please specify the following parameters:

   \' -long   \'

   where  is the time point id (SAME as cross sectional
   ID) and  is the ID created in the -base run.
   The directory .long. will be created
   automatically or used for output, if it already exists.

Secondly, how I can get the change rate after construct left -right
registration.

Thanks,
Lanbo

On Fri, Dec 22, 2017 at 5:40 AM, Martin Reuter 
wrote:

> Hi Lanbo,
>
> you could look at longitudinal changes of the left-right difference in
> volume per ROI. Or do you mean on the cortical thickness map (I have never
> done that, but probably works similarly, construct left -right
> registration, compute difference, then run the LME on that).
>
> Best, Martin
>
> Am 17.12.2017 um 17:54 schrieb lanbo Wang:
>
> Hi, all experts.
> I want to compare changes rate between left and right hemisphere of
> longitudinal data, How should I do that, how to combine xhemi with two
> stage or LME?
>
> Best,
> Lanbo
>
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://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
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/usr/local/freesurfer/bin/xhemireg
--s subj_02_1.long.s02_base
$Id: xhemireg,v 1.12.4.3 2012/05/02 21:28:58 greve Exp $
Wed Dec 20 17:46:00 EST 2017
Linux localhost.localdomain 3.10.0-693.5.2.el7.x86_64 #1 SMP Fri Oct 20 20:32:50 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
/HD4/symptom_test/subj_02_1.long.s02_base
setenv SUBJECTS_DIR /HD4/symptom_test/ 
Wed Dec 20 17:46:00 EST 2017
Wed Dec 20 17:46:00 EST 2017
mri_vol2vol --mov mri/orig.mgz --targ mri/orig.mgz --reg /HD4/symptom_test//subj_02_1.long.s02_base/xhemi/lrrev.register.dat --o /HD4/symptom_test//subj_02_1.long.s02_base/xhemi/mri/orig.mgz --keep-precision --no-save-reg

Matrix from regfile:
-1.000   0.000   0.000   1.000;
 0.000   1.000   0.000   0.000;
 0.000   0.000   1.000   0.000;
 0.000   0.000   0.000   1.000;

movvol mri/orig.mgz
targvol mri/orig.mgz
outvol /HD4/symptom_test//subj_02_1.long.s02_base/xhemi/mri/orig.mgz
regfile /HD4/symptom_test//subj_02_1.long.s02_base/xhemi/lrrev.register.dat
invert 0
tal0
talres 2
regheader 0
noresample 0
interp  trilinear (1)
precision  uchar (0)
Gdiag_no  -1
Synth  0
SynthSeed  1514107653

Final tkRAS-to-tkRAS Matrix is:
-1.000   0.000   0.000   1.000;
 0.000   1.000   0.000   0.000;
 0.000   0.000   1.000   0.000;
 0.000   0.000   0.000   1.000;


Vox2Vox Matrix is:
-1.000   0.000   0.000   255.000;
 0.000   1.000   0.000   0.000;
 0.000   0.000   1.000   0.000;
 0.000   0.000   0.000   1.000;

Resampling
Output registration matrix is identity

mri_vol2vol done
mri_vol2vol --mov mri/T1.mgz --targ mri/T1.mgz --reg /HD4/symptom_test//subj_02_1.long.s02_base/xhemi/lrrev.register.dat --o /HD4/symptom_test//subj_02_1.long.s02_base/xhemi/mri/T1.mgz --keep-precision --no-save-reg

Matrix from regfile:
-1.000   0.000   0.000   1.000;
 0.000   1.000   0.000   0.000;
 0.000   0.000   1.000   0.000;
 0.000   0.000   0.000   1.000;

movvol mri/T1.mgz
targvol mri/T1.mgz
outvol /HD4/symptom_test//subj_02_1.long.s02_base/xhemi/mri/T1.mgz
regfile /HD4/symptom_test//subj_02_1.long.s02_base/xhemi/lrrev.register.dat
invert 0
tal0
talres 2
regheader 0
noresample 0
interp  trilinear (1)
precision  uchar (0)
Gdiag_no  -1
Synth  0
SynthSeed  1514410525

Final tkRAS-to-tkRAS Matrix is:
-1.000   0.000   0.000   1.000;
 0.000   1.000   0.000   0.000;
 0.000   0.000   1.000   0.000;
 0.000   0.000   0.000   1.000;


Vox2Vox Matrix is:
-1.000   0.000   0.000   255.000;
 0.000   1.000   0.000   0.000;
 0.000   0.000   1.000   0.000

[Freesurfer] Question about combine longitudinal analysis and xhemi

[lanbo Wang]

​
 xhemireg.lh.log

​Thanks for replying me. But I still have two questions.
Firstly, when I try xhemi on pre-possessed longitudinal data, it showed
error like this:
Performing left-right swap of labels
TR=2300.00, TE=2.98, TI=900.00, flip angle=9.00
i_ras = (-1, 3.72529e-08, 3.35276e-08)
j_ras = (-2.6077e-08, -3.72529e-09, -1)
k_ras = (-1.78814e-07, 1, 6.98492e-10)
writing to /HD4/symptom_test//subj_02_1.long.s02_base/xhemi/mri/aparc+a
seg.mgz...
Wed Dec 20 17:46:35 EST 2017
recon-all -sb subj_02_1.long.s02_base/xhemi -talairach

ERROR: Are you trying to run or re-run a longitudinal time point?
   If so, please specify the following parameters:

   \' -long   \'

   where  is the time point id (SAME as cross sectional
   ID) and  is the ID created in the -base run.
   The directory .long. will be created
   automatically or used for output, if it already exists.

Secondly, how I can get the change rate after construct left -right
registration.

Thanks,
Lanbo
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Re: [Freesurfer] Question about compare left and right hemi of longitudinal data

[lanbo Wang]

Hi Martin,

I didn't try to run recon-all, I try to run flipped.
The code I used is:
foreach subject (subj_27_2.long.s27_base)
foreach?   surfreg --s $subject --t fsaverage_sym --lh
foreach?   surfreg --s $subject --t fsaverage_sym --lh --xhemi
foreach? end


Thanks,
Lanbo

On Tue, Jan 16, 2018 at 4:46 AM, Martin Reuter 
wrote:

> Hi Lanbo,
>
> what is the exact command you use for this? The problem is that the script
> or your command does not pass the right flags to recon all. Whenever
> recon-all is supposed to work on a longitudinal directory it needs to know
> the base and the long so the recon all command needs to show
>
> -long subj_02_1 s02_base
>
> as part of its arguments. So either adjust your command line, or if the
> recon-all call is performed from within another script, we need to change
> that script (add a -long flag so that the script performs the correct
> recon-all call in those cases when working on a longitudinal time point).
>
> Once you have the left right difference (define on one of the
> hemispheres), you can treat it similar as a thickness map and run it
> through the Matlab LME code. https://surfer.nmr.mgh.harvard.edu/fswiki/
> LinearMixedEffectsModels
>
>
> Best, Martin
>
> Am 27.12.2017 um 16:11 schrieb lanbo Wang:
>
> Thanks for replying me. But I still have two questions.
> Firstly, when I try xhemi on pre-possessed longitudinal data, it showed
> error like this:
> Performing left-right swap of labels
> TR=2300.00, TE=2.98, TI=900.00, flip angle=9.00
> i_ras = (-1, 3.72529e-08, 3.35276e-08)
> j_ras = (-2.6077e-08, -3.72529e-09, -1)
> k_ras = (-1.78814e-07, 1, 6.98492e-10)
> writing to /HD4/symptom_test//subj_02_1.long.s02_base/xhemi/mri/aparc+a
> seg.mgz...
> Wed Dec 20 17:46:35 EST 2017
> recon-all -sb subj_02_1.long.s02_base/xhemi -talairach
>
> ERROR: Are you trying to run or re-run a longitudinal time point?
>If so, please specify the following parameters:
>
>\' -long   \'
>
>where  is the time point id (SAME as cross sectional
>ID) and  is the ID created in the -base run.
>The directory .long. will be created
>automatically or used for output, if it already exists.
>
> Secondly, how I can get the change rate after construct left -right
> registration.
>
> Thanks,
> Lanbo
>
> On Fri, Dec 22, 2017 at 5:40 AM, Martin Reuter <
> mreu...@nmr.mgh.harvard.edu> wrote:
>
>> Hi Lanbo,
>>
>> you could look at longitudinal changes of the left-right difference in
>> volume per ROI. Or do you mean on the cortical thickness map (I have never
>> done that, but probably works similarly, construct left -right
>> registration, compute difference, then run the LME on that).
>>
>> Best, Martin
>>
>> Am 17.12.2017 um 17:54 schrieb lanbo Wang:
>>
>> Hi, all experts.
>> I want to compare changes rate between left and right hemisphere of
>> longitudinal data, How should I do that, how to combine xhemi with two
>> stage or LME?
>>
>> Best,
>> Lanbo
>>
>>
>> ___
>> Freesurfer mailing 
>> listfreesur...@nmr.mgh.harvard.eduhttps://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 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> ___
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> 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
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> e

[Freesurfer] Linear Mixed Effect Modle

[lanbo Wang]

Hi, all experts.

When I try to use LME model. There is a code "mris_preproc --qdec-long
qdec.table.dat --target fsaverage --hemi lh --meas thickness --out
lh.thickness.mgh" in LME tutorials website under *"b)Mass-univariate". *
When I ran it, error happened:
"""
[mtobia@localhost PD]$ mris_preproc --qdec-long $SUBJECTS_DIR/sub_long.dat
--target fsaverage --hemi lh --meas thickness --out lh.thickness.long.mgh
nsubjects = 80
ERROR: cannot find /HD4/PD/Patients_Symptom//.long.
"""
And I already check the file name, The folder name match
.long..
What should I do now?
Thanks for your help.

Best,
Lanbo


sub_long.dat
Description: Binary data
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Re: [Freesurfer] Linear Mixed Effect Modle

[lanbo Wang]

Hi,

I used 5.3 version. And it worked after I deleted empty line.
And it works when I use 6.0 version.

Thanks for your help!

Best,
Lanbo

On Mon, Jan 22, 2018 at 10:16 AM, Diers, Kersten /DZNE <
kersten.di...@dzne.de> wrote:

> Hi,
>
> do you happen to use Freesurfer version 5.3 or maybe earlier?
>
> It seems to me that in the 5.3 version empty lines in the qdec-long
> file (sub_long.dat in your case) were not skipped by the mris_preproc
> script, hence the 'nsubjects = 80' message although there are only 79
> "subjects" (time-points, to be precise) in your sub_long.dat file.
>
> This does not occur anymore in the 6.0 version.
>
> I suppose the problem can be solved by removing the trailing empty line
> in your sub_long.dat file.
>
> Please let us know if you are using a newer version than 5.3, since
> then we need to look for something else.
>
> Best regards,
>
> Kersten
>
>
>
> -Original Message-
> From: lanbo Wang 
> Reply-to: Freesurfer support list 
> To: Freesurfer support list 
> Subject: [Freesurfer] Linear Mixed Effect Modle
> Date: Sat, 20 Jan 2018 21:00:44 +0100
>
> Hi, all experts.
>
> When I try to use LME model. There is a code "mris_preproc --qdec-long
> qdec.table.dat --target fsaverage --hemi lh --meas thickness --out
> lh.thickness.mgh" in LME tutorials website under "b)Mass-univariate".
> When I ran it, error happened:
> """
> [mtobia@localhost PD]$ mris_preproc --qdec-long
> $SUBJECTS_DIR/sub_long.dat --target fsaverage --hemi lh --meas
> thickness --out lh.thickness.long.mgh
> nsubjects = 80
> ERROR: cannot find /HD4/PD/Patients_Symptom//.long.
> """
> And I already check the file name, The folder name match
> .long..
> What should I do now?
> Thanks for your help.
>
> Best,
> Lanbo
>
> ___
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>
>
> 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
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> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
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Re: [Freesurfer] Question about compare left and right hemi of longitudinal data

[lanbo Wang]

The problem is that the surfreg command is failing.

Thanks,
Lanbo

On Thu, Jan 18, 2018 at 5:14 PM, Douglas Greve 
wrote:

> Is the problem that the surfreg command is failing or that you don't know
> how to apply LME?
>
> On 1/17/18 9:55 AM, lanbo Wang wrote:
>
> Hi Martin,
>
> I didn't try to run recon-all, I try to run flipped.
> The code I used is:
> foreach subject (subj_27_2.long.s27_base)
> foreach?   surfreg --s $subject --t fsaverage_sym --lh
> foreach?   surfreg --s $subject --t fsaverage_sym --lh --xhemi
> foreach? end
>
>
> Thanks,
> Lanbo
>
> On Tue, Jan 16, 2018 at 4:46 AM, Martin Reuter <
> mreu...@nmr.mgh.harvard.edu> wrote:
>
>> Hi Lanbo,
>>
>> what is the exact command you use for this? The problem is that the
>> script or your command does not pass the right flags to recon all. Whenever
>> recon-all is supposed to work on a longitudinal directory it needs to know
>> the base and the long so the recon all command needs to show
>>
>> -long subj_02_1 s02_base
>>
>> as part of its arguments. So either adjust your command line, or if the
>> recon-all call is performed from within another script, we need to change
>> that script (add a -long flag so that the script performs the correct
>> recon-all call in those cases when working on a longitudinal time point).
>>
>> Once you have the left right difference (define on one of the
>> hemispheres), you can treat it similar as a thickness map and run it
>> through the Matlab LME code. https://surfer.nmr.mgh.harvard
>> .edu/fswiki/LinearMixedEffectsModels
>>
>>
>> Best, Martin
>>
>> Am 27.12.2017 um 16:11 schrieb lanbo Wang:
>>
>> Thanks for replying me. But I still have two questions.
>> Firstly, when I try xhemi on pre-possessed longitudinal data, it showed
>> error like this:
>> Performing left-right swap of labels
>> TR=2300.00, TE=2.98, TI=900.00, flip angle=9.00
>> i_ras = (-1, 3.72529e-08, 3.35276e-08)
>> j_ras = (-2.6077e-08, -3.72529e-09, -1)
>> k_ras = (-1.78814e-07, 1, 6.98492e-10)
>> writing to /HD4/symptom_test//subj_02_1.long.s02_base/xhemi/mri/aparc+a
>> seg.mgz...
>> Wed Dec 20 17:46:35 EST 2017
>> recon-all -sb subj_02_1.long.s02_base/xhemi -talairach
>>
>> ERROR: Are you trying to run or re-run a longitudinal time point?
>>If so, please specify the following parameters:
>>
>>\' -long   \'
>>
>>where  is the time point id (SAME as cross sectional
>>ID) and  is the ID created in the -base run.
>>The directory .long. will be created
>>automatically or used for output, if it already exists.
>>
>> Secondly, how I can get the change rate after construct left -right
>> registration.
>>
>> Thanks,
>> Lanbo
>>
>> On Fri, Dec 22, 2017 at 5:40 AM, Martin Reuter <
>> mreu...@nmr.mgh.harvard.edu> wrote:
>>
>>> Hi Lanbo,
>>>
>>> you could look at longitudinal changes of the left-right difference in
>>> volume per ROI. Or do you mean on the cortical thickness map (I have never
>>> done that, but probably works similarly, construct left -right
>>> registration, compute difference, then run the LME on that).
>>>
>>> Best, Martin
>>>
>>> Am 17.12.2017 um 17:54 schrieb lanbo Wang:
>>>
>>> Hi, all experts.
>>> I want to compare changes rate between left and right hemisphere of
>>> longitudinal data, How should I do that, how to combine xhemi with two
>>> stage or LME?
>>>
>>> Best,
>>> Lanbo
>>>
>>>
>>> ___
>>> Freesurfer mailing 
>>> listfreesur...@nmr.mgh.harvard.eduhttps://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
>>&

[Freesurfer] LME univariate data

[lanbo Wang]

Dear Experts,

Hi,
There is no example detail on website of LME tutorial. I have some question
about it.
Could you send me the table of ADNI univariate example data?


Thanks,
Lanbo
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Re: [Freesurfer] LME univariate data

[lanbo Wang]

Dear Kersten,

Thanks, I find it. And I have other questions:
1. The intercepts all set as one, so in this model it doesn't separate
different subjects, or can say no individual subject change rate?
2. Should we set age according to different timepoint, or just use baseline
age?

Thanks,
Lanbo

On Tue, Mar 13, 2018 at 3:34 PM, Diers, Kersten /DZNE  wrote:

> Hello Lanbo,
>
> the univariate example data can actually be downloaded from the LME
> tutorial website:
>
> Search for: "An optional sample dataset which can be used to become
> familiar with the LME Matlab tools can be found here". The linked
> tar.gz archive contains two folders, one for the univariate and one for
> the mass-univariate example data.
>
> Best regards,
>
> Kersten
>
> On Di, 2018-03-13 at 13:38 +0100, lanbo Wang wrote:
> > Dear Experts,
> >
> > Hi,
> > There is no example detail on website of LME tutorial. I have some
> > question about it.
> > Could you send me the table of ADNI univariate example data?
> >
> >
> > Thanks,
> > Lanbo
>
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Re: [Freesurfer] LME univariate data

[lanbo Wang]

Dear Kersten,

Thanks a lot, it's really help. I have another question, after I got
results that two group have significant, then how could I get direction?

Thanks,
Lanbo

On Tue, Mar 13, 2018 at 5:40 PM, Diers, Kersten /DZNE  wrote:

> Hello,
>
> On Di, 2018-03-13 at 21:48 +0100, lanbo Wang wrote:
> > Dear Kersten,
> >
> > Thanks, I find it. And I have other questions:
> > 1. The intercepts all set as one, so in this model it doesn't
> > separate different subjects, or can say no individual subject change
> > rate?
>
> If I understood correctly, the question is whether or not we can get
> estimates for individual slopes across time?
>
> If so, then yes, that's possible - but I'd have to run an analysis
> myself and look up how to do it exactly - I'll get back on this.
>
> > 2. Should we set age according to different timepoint, or just use
> > baseline age?
>
> It's better to use age at baseline.
>
> One of the nice things of the LME is that it can separate the cross-
> sectional effect of age (at baseline) and the longitudinal effect of
> aging (=effect of time). So the aging effect is already incorporated
> within the 'time since baseline' variable, which of course should also
> be present in the model.
>
> Since it is difficult to estimate and interpret effects that are very
> redundant (such as time vs age at each timepoint), it's better to just
> use age at baseline for the other regressor.
>
> Best regards,
>
> Kersten
>
> > Thanks,
> > Lanbo
> >
> > On Tue, Mar 13, 2018 at 3:34 PM, Diers, Kersten /DZNE  > dzne.de<mailto:kersten.di...@dzne.de>> wrote:
> > Hello Lanbo,
> >
> > the univariate example data can actually be downloaded from the LME
> > tutorial website:
> >
> > Search for: "An optional sample dataset which can be used to become
> > familiar with the LME Matlab tools can be found here". The linked
> > tar.gz archive contains two folders, one for the univariate and one
> > for
> > the mass-univariate example data.
> >
> > Best regards,
> >
> > Kersten
> >
> > On Di, 2018-03-13 at 13:38 +0100, lanbo Wang wrote:
> > >
> > > Dear Experts,
> > >
> > > Hi,
> > > There is no example detail on website of LME tutorial. I have some
> > > question about it.
> > > Could you send me the table of ADNI univariate example data?
> > >
> > >
> > > Thanks,
> > > Lanbo
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu<mailto: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.
> >
> >
>
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Re: [Freesurfer] LME univariate data

[lanbo Wang]

Dear Kersten,

I have a question about LME model. After I acquired p value, could I know
which group is bigger?

Thanks,
Lanbo

On Fri, Mar 16, 2018 at 12:13 AM, lanbo Wang  wrote:

> Dear Kersten,
>
> Thanks a lot, it's really help. I have another question, after I got
> results that two group have significant, then how could I get direction?
>
> Thanks,
> Lanbo
>
> On Tue, Mar 13, 2018 at 5:40 PM, Diers, Kersten /DZNE <
> kersten.di...@dzne.de> wrote:
>
>> Hello,
>>
>> On Di, 2018-03-13 at 21:48 +0100, lanbo Wang wrote:
>> > Dear Kersten,
>> >
>> > Thanks, I find it. And I have other questions:
>> > 1. The intercepts all set as one, so in this model it doesn't
>> > separate different subjects, or can say no individual subject change
>> > rate?
>>
>> If I understood correctly, the question is whether or not we can get
>> estimates for individual slopes across time?
>>
>> If so, then yes, that's possible - but I'd have to run an analysis
>> myself and look up how to do it exactly - I'll get back on this.
>>
>> > 2. Should we set age according to different timepoint, or just use
>> > baseline age?
>>
>> It's better to use age at baseline.
>>
>> One of the nice things of the LME is that it can separate the cross-
>> sectional effect of age (at baseline) and the longitudinal effect of
>> aging (=effect of time). So the aging effect is already incorporated
>> within the 'time since baseline' variable, which of course should also
>> be present in the model.
>>
>> Since it is difficult to estimate and interpret effects that are very
>> redundant (such as time vs age at each timepoint), it's better to just
>> use age at baseline for the other regressor.
>>
>> Best regards,
>>
>> Kersten
>>
>> > Thanks,
>> > Lanbo
>> >
>> > On Tue, Mar 13, 2018 at 3:34 PM, Diers, Kersten /DZNE > > dzne.de<mailto:kersten.di...@dzne.de>> wrote:
>> > Hello Lanbo,
>> >
>> > the univariate example data can actually be downloaded from the LME
>> > tutorial website:
>> >
>> > Search for: "An optional sample dataset which can be used to become
>> > familiar with the LME Matlab tools can be found here". The linked
>> > tar.gz archive contains two folders, one for the univariate and one
>> > for
>> > the mass-univariate example data.
>> >
>> > Best regards,
>> >
>> > Kersten
>> >
>> > On Di, 2018-03-13 at 13:38 +0100, lanbo Wang wrote:
>> > >
>> > > Dear Experts,
>> > >
>> > > Hi,
>> > > There is no example detail on website of LME tutorial. I have some
>> > > question about it.
>> > > Could you send me the table of ADNI univariate example data?
>> > >
>> > >
>> > > Thanks,
>> > > Lanbo
>> > ___
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu<mailto: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
>>
>
>
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Re: [Freesurfer] LME univariate data

[lanbo Wang]

Dear Kersten,

Thanks for reply. I have new question.
When I set model use total_i_vol_stats = lme_fit_FS(X,[1 2],Y(:,2),ni)
and total_i_vol_stats = lme_fit_FS(X,[1],Y(:,2),ni).
But Bhat of two models' year have a lot different, for example, with 2 is
1.2422 without 2 is -0.5737. The direction has already changed. I feel
confuse about this. Looking for your reply.

Thanks,
Lanbo


On Wed, Mar 28, 2018 at 2:05 PM, Diers, Kersten /DZNE  wrote:

> Hi
>
> sorry for the delayed response, I was not able to reply during the last
> week.
>
> You are right that the F-test provided in the LME toolbox initially
> does not provide information about the direction of the effects.
>
> You could do the following:
>
> First, it is always useful to plot the data to get a first impression.
> However, if the statistical model also contains additional covariates,
> this plot does not completely reflect the effects as estimated by the
> model. So this may not give a complete picture.
>
> A second option is to take a look at the sign of the estimated beta
> values, which also reflect the direction of the effects. These beta
> values are stored in the output of the 'lme_fit_FS' script, e.g.
> 'total_hipp_vol_stats.Bhat' in the tutorial example. For proper
> interpretation, you'd need to relate the beta values and their
> corresponding columns of the design matrix, and also take your
> contrasts of interest into account. So this is somewhat complicated.
>
> As an alternative, the LME toolbox also provides so-called "signed p-
> values". Note that these are not p-values in the conventional sense. A
> signed p-value is the sign (-1 or +1) of the scalar product of a row of
> the contrast matrix and the vector of the estimated betas, and it can
> give information about the direction of a specific effect.
>
> These signed p-values can be accessed from the output of the 'lme_F'
> script, see e.g. the 'F_C.sgn' variable for the tutorial example.
>
> There will be as many signed p-values as there are rows in the contrast
> matrix, so each signed p-value corresponds to one row of the contrast
> matrix.
>
> The interpretation of this signed p-value depends on how the contrast
> was formulated:
>
> In a hypothetical example (different from and simpler than the tutorial
> example), suppose that one row of a contrast matrix starts like
>
> 0 1 -1 ...
>
> and the entries correspond to group1, group2, group3, ..., then a
> positive signed p-value will in this particular case indicate that the
> difference 'group2 minus group3' is greater than zero, which means that
> group2 has greater values than group3. On the other hand, a negative
> signed p-value will in this particular case indicate that the
> difference 'group2 minus group3' is less than zero, and hence group3
> must have greater values than group2.
>
> However, also consider the equally valid alternative that a row of a
> contrast matrix starts like
>
> 0 -1 1 ...
>
> and the entries again correspond to group1, group2, group3, ..., then a
> positive signed p-value will in this particular case indicate that the
> difference 'group3 minus group2' is greater than zero, which means that
> group3 has greater values than group2. On the other hand, a negative
> signed p-value will in this particular case indicate that the
> difference 'group3 minus group2' is less than zero, and hence group2
> must have greater values than group3.
>
> So the second interpretation is just the opposite as the first one.
> This illustrates that careful attention needs to be paid to the
> formulation of the contrasts. Also, it's best if the interpretation
> gained from the signed p-values agrees with the interpretation of a
> simple plot of the data.
>
> To summarize, if we are testing for simple group differences, the F-
> test only provides a single p-value, which indicates if there is at
> least one significant difference among the several groups. To get an
> idea which groups actually differ, and in which direction, one needs to
> take a closer look, for example at those effects that are reflected in
> the rows of the contrast matrix; for this, one option is to use the
> signed p-values as described above.
>
> Hope this helps,
>
> Kersten
>
> On Di, 2018-03-27 at 15:31 +0200, lanbo Wang wrote:
> > Dear Kersten,
> >
> > I have a question about LME model. After I acquired p value, could I
> > know which group is bigger?
> >
> > Thanks,
> > Lanbo
> >
> > On Fri, Mar 16, 2018 at 12:13 AM, lanbo Wang  > to:drram...@gmail.com>> wrote:
> > Dear Kersten,
> >
> > Thanks a lot, it&