Re: [Freesurfer] one group in RepeatedMeasuresAnova or Paird Analysis

2017-03-08 Thread Livia Liu
Re: [Freesurfer] one group in RepeatedMeasuresAnova or PairdAnalysis

Dear Douglas Greve,
Thank you for your reply. I'm very sorry that I can't directly reply on the
web, so I had to be sent a new email.

I still have a question for your answer “ Note that for the paired-diff,
you need to subtract tp1 from tp2 manually and pass the result to
mri_glmfit.”  Would you please describe some more detail for me? And in the
paired analysis, if I have no covariates, what the mean.mtx should be?

I'm terribly sorry, and thanks again.
Livia Liu


2017-03-07 20:54 GMT+08:00 刘丽 :

> Dear FS Experts,
>
> I have one group to compare the difference between their preoperative and
> postoperative after one month. I followed http://surfer.nmr.mgh.harvard.
> edu/fswiki/FsTutorial/LongitudinalTutorial to process data. I run these
> command in number 2.* Longitudinal Image Processing*:
>
> 1. recon-all –s sub01_MR1 –all / recon-all –s sub01_MR2 –all
>
> 2. recon-all -base sub01 -tp sub01_MR1 -tp sub01_MR2 –all
>
> 3. recon-all -long sub01_MR1 sub01 –all / recon-all -long sub01_MR2 sub01
> –all
>
> I am confused about choosing which kind of analysis in the page
> http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalStatistics And I
> tried http://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova
>
> The “rmanova.fsgd”:
>
> GroupDescriptorFile 1
>
> Class sub01
>
> Class sub02
>
> …
>
> VariablesTP1-vs-TP2
>
> Input sub01_MR1 sub01   1
>
> Input sub01_MR2 sub01   -1
>
> Input sub02_MR1 sub02   1
>
> Input sub02_MR2 sub02   -1
>
> …
>
> “tp1-va-tp2.mtx”:  0 0 … 1
>
> And I look in one mail in the list, say “one group to use Paird Analysis
> easier”.  http://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis
>
> “pairs.fsgd”:
>
> GroupDescriptorFile 1
>
> Class Main
>
> Input sub04_MR1 Main
>
> Input sub04_MR2 Main
>
> Input sub05_MR1 Main
>
> Input sub05_MR2 Main
>
> …
>
> “paird-diff.fsgd” :
>
> GroupDescriptorFile 1
>
> Class Main
>
> Variables Age
>
> Input sub04pair   Main 24
>
> Input sub05pair   Main 27
>
> …
>
> “mean.mtx”: 1 0
>
> My question:
>
> 1. Are the above several files I set up correct??There are inconsistent
> results in them… So which one should I choose??
>
> 2. I found the increase or decrease a subjects had a great influence on
> the analysis result, how to filter the participants??
>
> Looking forward to reply, and thanks very much!
>
> Kind regards,
>
> Livia
>
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[Freesurfer] Two group two time longitudinal analysis

2017-05-03 Thread Livia Liu
Dear FS experts,
I have two group and two times to do longitudinal cross analysis.
I looked your answer in
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg45870.html
and
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg52032.html
Sorry, I can’t understand what you said” you can either subtract the two
time points and then do a regular group analysis”
" subtract tp1 from tp2 manually and pass the result to mri_glmfit."

How to subtract the two time manually and how to do then ? Would you
please tell me more details?

And in my analysis, if I use the paired analysis, how to design
paired.fsgd and paired-diff.fsgd?

In http://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis  I am sorry
to only see how to do in one group.



Looking forward to reply, and thanks very much.

Kind regards,

Livia
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Re: [Freesurfer] Two group two time longitudinal analysis

2017-05-21 Thread Livia Liu
Dear Martin,
Thank you for your reply. I used a paired analysis to do "two groups two
times data of the longitudinal analysis".

But unfortunately, I did not make the results, and I use “mri_glmfit-sim”
to find 0 vertices in mask.

My files are as follows.

Fsgd 1: (pairs.fsgd)

GroupDescriptorFile 1

Class Sub

Class Con

Input sub01_MR1 Sub

Input sub01_MR2 Sub

Input con01_MR1 Con

Input con01_MR2 Con

...

Fsgd 2: (paired-diff.fsgd)

GroupDescriptorFile 1

Class Sub

Class Con

Input sub01pair Sub

Input con01pair Con

...

mean.mtx: 1 -1


Are they correct in my Paired analysis? And I am trying LME now.


However, I see other people in the mailing list of the questions and
replys, I realize that I may be wrong.

My two groups of two time are the experimental group (bs) and the placebo
group (placebo).

I want to do “the crossover analysis” Just like:(postbs-prebs) -
(postplacebo-preplacebo)
Should not I use longitudinal analysis for these two groups? What kind of
analysis do I need to do?
Please tell me where I should look in the wiki.

Looking forward to reply, and thanks very much.

Kind regards,

Livia
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[Freesurfer] LME correction in longitudinal analysis

2017-06-05 Thread Livia Liu
Dear FS experts,

I are analysing longitudinal data - the difference between 2 groups (1
and 2) with 2 time points for each group (0, 1 --all the same time
interval: a month).

I followed  http://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels

and with Jorge's early reply in
http://www.mail-achive.com/freesurfer@nmr.mgh.harvard.edu/msg25750.html

(1)qdec.table.dat

fsid fsid-base time group

sub04_MR1 sub04 0 1

sub04_MR2 sub04 1 1

sub05_MR1 sub05 0 1

sub05_MR1 sub05 1 1

...

con01_MR1 con01 0 2

con01_MR1 con01 1 2

con01_MR1 con01 0 2

con01_MR1 con01 1 2

...

(2) mris_preproc --qdec-long qdec.table.dat --target fsaverage --hemi
lh --meas thickness --out lh.thickness.mgh

 mri_surf2surf --hemi lh --s fsaverage --sval lh.thickness.mgh --tval
lh.thickness_sm10.mgh --fwhm-trg 10 --cortex  --noreshape

(3) [Y,mri] = fs_read_Y('lh.thickness_sm10.mgh');

lhsphere=fs_read_surf('$FsDir/freesurfer/subjects/fsaverage/surf/lh.sphere');

lhcortex=fs_read_label('$FsDir/freesurfer/subjects/fsaverage/surf/lh.cortex.label');

(4)Qdec = fReadQdec('qdec.table.dat');

   Qdec = rmQdecCol(Qdec,1);

   sID = Qdec(2:end,1);

   Qdec = rmQdecCol(Qdec,1);

   M = Qdec2num(Qdec);

  [M,Y,ni] = sortData(M,1,Y,sID);

   X = [ones(length(M),1) M M(:,1).*M(:,2)];

But when I followed wiki,code[M,Y,ni]first,  matrix X will be four columns:

   1-A column of 1s(intercept term)

   2-The time covariate (0s and 1s)

   3-The group covariate (2s and 1s,but in my table group 1 in the
first, I think maybe it upside down?So I used the code X before
code[M,Y,ni],then it will be 1s and 2s)

   4-The group and time interaction (It is also affected by the third
column to change).

Is my use correct here? I think it will be influn

(5)Then I used voxel-wise mixed model analysis following Jorge's reply.

lhstats = lme_mass_fit_vw(X,[1],Y,ni,lhcortex);

CM.C = [0 0 0 1];

F_lhstats = lme_mass_F(lhstats,CM);

(6)fs_write_fstats(F_stats,mri,'sig.mgh','sig');

How to do correction about the result 'sig.mgh'?

May I use lme_mass_FDR or lme_mass_FDR2? How to do?

And if I can have a file including clusters' massage like summary file?

I can't do a mri_glmfit-sim or mc-z in QDEC, and FDR in QDEC, maybe
the t-value to high,there are nothing left.

Please give me some help.Thank you very much, and looking forward to your reply!
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Re: [Freesurfer] LME correction in longitudinal analysis

2017-06-05 Thread Livia Liu
Dear FS experts,
I want to add some in my early mail.
If the contrast CM.C= [0 0 0 1] is designed for the interaction effect(time
and group).
How to design contrasts to do the main effect about the time and group?
CM.C=[0 1 0 1] and CM.C=[0 0 1 1]? Or other?
I wonder I may be wrong in designing matrix X in early mail.
Please help me.Looking forward to reply, and thanks very much.
Kind regards,
Livia
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Re: [Freesurfer] LME correction in longitudinal analysis

2017-06-06 Thread Livia Liu
Dear Martin,
Thank you very much for your quick reply.

I use voxel-wise mixed model analysis, and I see different design:


lhstats = lme_mass_fit_vw(X,[1],Y,ni,lhcortex);Summary: Algorithm
did not converge at 0 percent of the total number of locations.

lhstats = lme_mass_fit_vw(X,[1 2],Y,ni,lhcortex);Summary:
Algorithm did not converge at 9.231.. percent of...


What the meaning and difference between [1] [1 2] or other?


In the end of the page
https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels

It use Region-wise linear mixed-effects estimation:lme_mass_fit_Rgw ,
then do FDR.


Sorry, I can not make sure how to do FDR in my result.Please tell me
some details.

And should I try this Region-wise model in my analysis?


My purpose is to compare cortical thickness changes in patient group
after treatment and  placebo group in 2 time points.

Then You say in the second mail:(if longitudinal slopes = atrophy
rates, differ across groups),I am so sorry that I can't understand.

If I get the interaction result, how to explain?

I wonder I must get the main effect about the time or group to measure
what cause the interaction.

 Could you please give me some direction? Looking forward to reply,
and thanks very much.


Kind regards,
Livia
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Re: [Freesurfer] LME correction in longitudinal analysis

2017-06-14 Thread Livia Liu
Dear Martin,

Thank you very much again for your reply. I did better with your help, but
I am really sorry that I still have some questions.



1. I found there are positive and negative regions in the result “sig.mgh”
map. I wonder “lme_mass_F” is a kind of F analysis or T analysis in fact.
How to get the F value or T value? I can only get P value.



2. And I tried to use the cmd “mri_surfcluster” to generate the set of
detected clusters and their anatomical coordinates like the file
"...sig.cluster.summary" in GLM analysis. Unfortunately,I failed to get the
correct command. Could you tell me right way?


3. I load sig.mgh file and save ROIs’ label file in qdec tool, then I use
the cmd "mri_label2label" and "mris_anatomical_stats" to get the value of
thickness. For area and volume, can I get in the same way? In the stats:#
ColHeaders StructName NumVert SurfArea GrayVol ThickAvg ThickStd MeanCurv
GausCurv FoldInd CurvInd

lh.1.label 25 19 51   3.044 0.237 0.105 0.068
0 0

I think that the “SurfArea” is the value of area, “GrayVol” is the value of
volume.In my other GLM analysis, I found that cortical surface area or
volume is not an integer in the file “…y.ocn.dat”.Is it right way to get
the ROI value?


4.If there are any way to convert the file “lh.thickness”"lh.area" or
"lh.volume" in every subject to the format “nii” which can be used in SPM. I
want to do a same analysis in SPM to compare my result.

I use the cmd: mri_surf2vol --surfval $SUBJECTS_DIR/sub01/surf/lh.thickness
--hemi lh --fillribbon --subject fsaverage --template
$SUBJECTS_DIR/fsaverage/mri/orig --o lh.thickness01.nii

then I use the cmd: tkregister2 --mov $SUBJECTS_DIR/fsaverage/mri/orig.mgz
--noedit --s fsaverage --regheader --reg $SUBJECTS_DIR/register.dat

But in the terminal output: A volume registration file must be supplied.

I don’t know how to get the volume registration file. I failed to get the
correct cmd by searching in mail-list. Please give me some help.

I am sorry again to bring you a lot of questions.  Thank you very much, and
looking forward to reply.


Kind regards,

Livia
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Re: [Freesurfer] LME correction in longitudinal analysis

2017-06-19 Thread Livia Liu
Dear Martin,


 Thank you so much for all the help that you had given me.


Kind regards,

Livia
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[Freesurfer] cluster analysis in longitudinal analysis

2017-06-19 Thread Livia Liu
Dear FS experts,

I are analysing longitudinal data - the difference of the cortical
thickness, surface area and volume between 2 groups (1 and 0) with 2 time
points for each group (0, 1 --all the same time interval: a month).

I followed the page
http://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels in wiki.
According to experts' advice in the mail-list, I used voxel-wise mixed
model “lhstats = lme_mass_fit_vw(X,[1],Y,ni,lhcortex)” to do analysis. And
I got the result “sig.mgh” (Freesurfer significance map -log10(p-value)).


1. I loaded the “sig.mgh” to do the FDR correction in the qdec tool. When I
press the button of ‘set using FDR ’, the threshold value changes. But the
minimum value in the color bar is a little bit small than the value in the
table. I used the value in the color bar to get the correction result.

Q: Can I do FDR correction like this? And could you give me some more
advices about the correction? And how to do other multiple comparison
correction like Monte Carlo simulation in longitudinal analysis?


2.To get more infotmation about the cluster, I used the cmd
“mri_surfcluster --in sig.mgh --subject fsaverage --surf inflated --hemi lh
–thmin *( minimum value in above FDR correction) --sign abs –annot aparc
–-sum  lh.t.cluster.summary” to generate the set of detected clusters and
their anatomical coordinates.

Q: I want to know if I use the correct command?


3.I saved clusters’ label file manually in qdec tool. Then I use the cmd
"mri_label2label" and "mris_anatomical_stats" to get the value of
thickness. Just like the page:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI

For area and volume, can I get in the same way? For example, in the stats:#
ColHeaders StructName NumVert SurfArea GrayVol ThickAvg ThickStd MeanCurv
GausCurv FoldInd CurvInd

 lh.1.label 25 19 51   3.044 0.237 0.105 0.068
0  0

I think that the “SurfArea” is the value of area, “GrayVol” is the value of
volume. I wonder that it may be wrong way. In my other GLM analysis, I
found that cortical surface area or volume is not an integer in the file
“…y.ocn.dat”.

Q:Is it right way to get the cluster value? What methods do you recommend
to extract the cluster’s mask and the value within the cluster?


Thank you very much, and looking forward to reply.


Kind regards,

Livia
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[Freesurfer] How FDR was used to correct for multiple comparisons

2018-04-16 Thread Livia Liu
Dear FS experts,



I'd like to know that how FDR was used to correct for multiple comparisons.
I do FDR correction in two way in FreeSurfer.



1, Do the FDR correction in the qdec tool. And the page of “False Discovery
Rate” in the page “Multiple-Comparisons Correction in Qdec” was lost.

2, Use “lme_mass_FDR.m” to do the FDR correction in LME model, which was
based on Tom's FDR.m in the github, however the page was also lost.



Would help to provide more details as to how FDR in the two way was used to
correct for multiple comparisons?


Thank you very much, and looking forward to reply.


Kind regards,

Livia
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Re: [Freesurfer] How FDR was used to correct for multiple comparisons

2018-04-16 Thread Livia Liu
Dear Douglas,


Thank you for your reply. I run “mri_fdr –help” to get docs that include
some information for how to use this command. However, I still don’t know
how FDR was used to correct for multiple comparisons.


This question is an opinion given by one reviewer, and I really don’t know
how to reply.

For the description "To correct for multiple comparisons, the thresholds of
the P maps were set to yield an expected false discovery rate (FDR) of
0.05." The reviewer said “Would help to provide more details as to how FDR
was used to correct for multiple?”


Would you please give me some help to response the question?  Thank you
very much.


Kind regards,

Livia


2018-04-17 0:40 GMT+08:00 Douglas N. Greve :

> You can also use mri_fdr Run  it with --help to get docs
>
>
> On 04/16/2018 10:23 AM, Livia Liu wrote:
> >
> > Dear FS experts,
> >
> > I'd like to know that how FDR was used to correct for multiple
> > comparisons. I do FDR correction in two way in FreeSurfer.
> >
> > 1, Do the FDR correction in the qdec tool. And the page of “False
> > Discovery Rate” in the page “Multiple-Comparisons Correction in Qdec”
> > was lost.
> >
> > 2, Use “lme_mass_FDR.m” to do the FDR correction in LME model, which
> > was based on Tom's FDR.m in the github, however the page was also lost.
> >
> > Would help to provide more details as to how FDR in the two way was
> > used to correct for multiple comparisons?
> >
> >
> > Thank you very much, and looking forward to reply.
> >
> > Kind regards,
> >
> > Livia
> >
> >
> >
> >
> > ___
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Re: [Freesurfer] How FDR was used to correct for multiple comparisons

2018-04-18 Thread Livia Liu
Dear Douglas,

Thank you for your reply. I read the related FDR paper given in the
“mri_fdr –help”.

Please tell me if the FDR correction in FreeSurfer do like the below.

For the V vertices being tested, the general procedure is as follows:

(1) Select a desired FDR bound q between 0 and 1. This is the maximum FDR
that the researcher is willing to tolerate on average and we select q=0.05.

(2) Order the P values from smallest to largest: P(1) ≤P(2) ≤• •≤P(v). Let
v(i) be the vertex corresponding to P value P(i).

(3) Let r be the largest i for which: P(i) ≤i/V*q/c(V), where c(V) is a
predetermined constant.

(4) Declare the voxels v(1), . . . ,v(r) active, or in other words,
threshold the image of test statistics at the value corresponding to the P
value P(r).



If I response like this, is it right?



Thank you very much, and looking forward to reply.



Kind regards,

Livia

2018-04-18 0:41 GMT+08:00 Douglas Greve :

> You should read the FDR paper for more detail. But the FDR is the number
> of false positives relative to the total number of positives. The way it is
> interpreted is that when you look at an image, 5% of the voxels above
> threshold are false. You don't know which 5%. If the 5% came out of a big
> blob, probably you would not change your conclusion about that blob. If
> there were a few single voxels that were above threshold, you probably
> don't want to write your paper around it.
>
> On 4/16/18 11:42 PM, Livia Liu wrote:
>
> Dear Douglas,
>
>
> Thank you for your reply. I run “mri_fdr –help” to get docs that include
> some information for how to use this command. However, I still don’t know
> how FDR was used to correct for multiple comparisons.
>
>
> This question is an opinion given by one reviewer, and I really don’t know
> how to reply.
>
> For the description "To correct for multiple comparisons, the thresholds
> of the P maps were set to yield an expected false discovery rate (FDR) of
> 0.05." The reviewer said “Would help to provide more details as to how FDR
> was used to correct for multiple?”
>
>
> Would you please give me some help to response the question?  Thank you
> very much.
>
>
> Kind regards,
>
> Livia
>
> 2018-04-17 0:40 GMT+08:00 Douglas N. Greve :
>
>> You can also use mri_fdr Run  it with --help to get docs
>>
>>
>> On 04/16/2018 10:23 AM, Livia Liu wrote:
>> >
>> > Dear FS experts,
>> >
>> > I'd like to know that how FDR was used to correct for multiple
>> > comparisons. I do FDR correction in two way in FreeSurfer.
>> >
>> > 1, Do the FDR correction in the qdec tool. And the page of “False
>> > Discovery Rate” in the page “Multiple-Comparisons Correction in Qdec”
>> > was lost.
>> >
>> > 2, Use “lme_mass_FDR.m” to do the FDR correction in LME model, which
>> > was based on Tom's FDR.m in the github, however the page was also lost.
>> >
>> > Would help to provide more details as to how FDR in the two way was
>> > used to correct for multiple comparisons?
>> >
>> >
>> > Thank you very much, and looking forward to reply.
>> >
>> > Kind regards,
>> >
>> > Livia
>> >
>> >
>> >
>> >
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