you can use mri_concat to concatenate all the ces.nii.gz files for a single
subject into a single file, then run your glm
On 1/25/20 12:15 PM, Rami Hamati wrote:
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Sorry if my question was unclear. We would like to analyze each run separately
to observe if there is any habituation between runs of our task. Is there a way
to concatenate each run separately?
Message: 15
Date: Fri, 24 Jan 2020 15:36:36 +0000
From: "Greve, Douglas N.,Ph.D."
<[email protected]<mailto:[email protected]>>
Subject: Re: [Freesurfer] help: fs-fast group level analysis per run
To: "[email protected]<mailto:[email protected]>"
<[email protected]<mailto:[email protected]>>
Message-ID:
<[email protected]<mailto:[email protected]>>
Content-Type: text/plain; charset="utf-8"
The run-wise functionality was added after selxavg was written as a way to help
debug. If you want all the runs in your group analysis, why not turn off the
run-wise flag?
On 1/22/2020 4:40 PM, Rami Hamati wrote:
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Hello freesurfers,
I'm attempting to run second-level analysis on separate runs of a brain scan,
that were generated by selxavg3-sess -run-wise (pr001, pr002, pr003, pr004) as
described in selxavg3-sess --help.
But, when attempting to concatenate the data using isxconcat-sess, (as
described here:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/FsFastGroupLevel )
there is no similar -run-wise function. I've searched the list and no similar
errors have been reported.. I am wondering if there is a command or workaround
for this. Thank you very much!
--
Rami Hamati, MSc.
Royal's Institute of Mental Health Research
Molecular Imaging Laboratory (MIL)
1145 Carling Ave, Ottawa, ON K1Z 7K4
[email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>>
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Message: 16
Date: Fri, 24 Jan 2020 11:11:55 -0500
From: Graduate Imaging
<[email protected]<mailto:[email protected]>>
Subject: Re: [Freesurfer] FreeSurfer analyses in MatLab
To: Freesurfer support list
<[email protected]<mailto:[email protected]>>
Message-ID:
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On Fri, Jan 24, 2020 at 10:32 AM Greve, Douglas N.,Ph.D. <
[email protected]<mailto:[email protected]>> wrote:
>
>
> On 1/22/2020 2:13 PM, Graduate Imaging wrote:
>
> External Email - Use Caution
>
>
> On Tue, Jan 21, 2020 at 10:40 AM Greve, Douglas N.,Ph.D. <
> [email protected]<mailto:[email protected]>> wrote:
>
>>
>>
>> On 1/17/2020 10:39 AM, Graduate Imaging wrote:
>>
>> External Email - Use Caution
>>
>>> Hello,
>>>
>>> I recently ran a vertex wise analysis on two different projects the
>>> first had three groups with three co-variates that looked at if group
>>> membership was associated with brain volume. The second project had two
>>> groups with three co-variates looking at psychiatric x BMI interaction
>>> effect on brain volume. I'm interested in running ROI analyses in matlab to
>>> ensure the same matrices were used.
>>>
>>> To run the ROI analyses I'm going to important the design matrix from
>>> the vertex wise analysis and use the fast_glmfit and fast_fratio commands
>>> as shown below:
>>> X = load('Xg.dat');
>>> C = load('C.dat');
>>> y = load('ROI.dat'); text file containing participant ROI values from
>>> the DKT atlas.
>>> [beta rvar] = fast_glmfit(y,X);
>>> [F pvalues] = fast_fratio(beta,X,rvar,C
>>>
>>> My first question is the beta values that are calculated from
>>> fast_glmfit are unstandardized is there anyway way to have it compute
>>> standardized values?
>>>
>>> I think this is how you would compute that
>>> betastddev = sqrt(rvar*diag(inv(X'*X)));
>>> betastandard = beta./betastddev;
>>>
>> When I try running this in Matlab I get the Error using *** incorrect
>> dimensions for matrix multiplication message.
>>
>> That means that the number of items in y (ie, number of subjects in
>> ROI.dat) is different than the number of rows in X (number of subjects in
>> the fsgd). What are the sizes of y and X?
>>
> That's what I suspected as well however, X = 102x12 and Y= 102x5. I ran
> [betastddev = sqrt(rvar*diag(inv(X'*X))); betastandard = beta./betastddev]
> after running successfully running [[beta rvar] = fast_glmfit(Y,X); [F
> pvalues] = fast_fratio(beta,X,rvar,C)] so its odd that the the dimensions
> wouldn't be matching.
>
> Also when using fast_glmfit and fast_fratio via Matlab for ROI analyses
> what are the appropriate papers to cite? In the Matlab files in fsfast
> there is reference to Worsley, K.J. and Friston, K.J. Analysis of fMRI
> Time-Series Revisited - Again. Neuroimage 2, 173-181, 1995. Would this be
> the correct citation?
>
> The GLM is so old I would not know what to cite. If you feel you need to
> cite something, that Worsley paper is fine.
>
Thanks. For DODS looking at an interaction term for the previously
mentioned 2 group 4 co-variate analysis it produces the beta weights for
each of the 10 regressors. Am I correct is assuming the way the analysis
works is that it creates interaction terms for the class with each of the
co-variates? If so the analysis could be summarized by Y = B0 + B1*X1 +
B2*X2 + B3*X3 + B4X4 + B5X5 + B6*X1*X2 + B7*X1*X3 + B8*X1*X4 + B9*X1*X5 +
e. Where X1= Class, X2= BMI, X3=ICV, X4= Age and X5=sex (I've since
incorporated this to be apart of class but want to continue with this
example). If that is the case to get an overall interaction term I should
be able to manually create these interaction terms and put them into a
matrix then for the contrast just regress out all of the effects except for
the BMI*class (B6*X1*X2). However, when I do this the p value is not the
same (far more significant) than using the DODS analysis with the 0 0 1 -1
0 0... contrast.
>
>>> My second question is when I ran the ROI analyses looking at the
>>> diagnosis x BMI interaction effect it outputs an array of beta values for
>>> each regressor. In addition to each groups beta value (for BMI) I'm
>>> interested in the beta value of the interaction (ie diagnosis x BMI). I was
>>> wondering how do i go about obtaining this? Would I have to create a new
>>> matrix with the interaction term included in it?
>>>
>>> If so would the analysis essentially be one group with the diagnosis x
>>> BMI interaction term plus the three co-variates?
>>>
>>> If you are using an FSGD file and have used DODS, then you can create an
>>> interaction contrast. Send me your fsgd file if you want further help
>>>
>> Yes I was using DODS approach for this analysis, I've attached my FSGD
>> file to this email.
>>
>>
>> You have 2 groups and 4 coviariates so 10 regressors. The dx BMI
>> interaction would need a contrast matrix
>> 0 0 1 -1 0 0 ... the rest 0s
>> BTW, sex should not be a covariate. You really need to have four groups,
>> P-male, P-female, HC-male, and HC-female (which would change the contrast
>> above)
>> Also, I would normalize the age and ICV
>>
>> Thanks for the correction I'll update my matrix accordingly to four
> groups and normalize the variables! The contrast matrix I ran was actually
> the same you suggested however it pastes an array of beta values for each
> 10 regressors. However, I was interested in obtaining a beta value that
> represents the interaction.
>
>>
>>> _______________________________________________
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>>
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Message: 17
Date: Fri, 24 Jan 2020 15:39:10 +0000
From: "Greve, Douglas N.,Ph.D."
<[email protected]<mailto:[email protected]>>
Subject: Re: [Freesurfer] Troubleshooting FLAIR Images
To: "[email protected]<mailto:[email protected]>"
<[email protected]<mailto:[email protected]>>
Message-ID:
<[email protected]<mailto:[email protected]>>
Content-Type: text/plain; charset="windows-1252"
The error that you have there is probably an incorrectly fixed defect and
should be fixed by editing the wm.mgz (ie, probably not control points for
now). There are no edits specifically for FLAIR (which will only affect the
pial surface -- here the white surface is off)
On 1/23/2020 2:34 PM, Swanson,Clayton wrote:
External Email - Use Caution
Hi FreeSurfer Developers,
After looking through the archives my question still remains. I am wondering if
the same rules apply for editing/correcting FLAIR images as it does for T1
images. For example, can I add control points to the WM.mgz then re-run
recon-all using the command recon-all - s <subject> -autorecon2-cp -autorecon3.
For visualization I have attached a screenshot of what I am attempting to
correct.
Thank you for your help,
Clayton
[cid:[email protected]<mailto:cid%[email protected]>]
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End of Freesurfer Digest, Vol 191, Issue 36
*******************************************
--
Rami Hamati, MSc.
Royal's Institute of Mental Health Research
Molecular Imaging Laboratory (MIL)
1145 Carling Ave, Ottawa, ON K1Z 7K4
[email protected]<mailto:[email protected]>
[email protected]<mailto:[email protected]>
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