[Freesurfer] Problems viewing significant clusters on qdec display

[Vikas Bandalli]

Dear Freesurfers,

I have come across a problem with viewing the significant clusters on qdec
display tab.
When a particular query is selected after analyzing for a selected design
there are multiple clusters of varying size which appear. This query when
run  (corrected) with Monte carlo simulation (at particular  selected
threshold ex;- 1.3 ),the display tab shows an inflated image with
significant cluster at selected threshold and also there is an output in
the terminal as well which gives data about the size,number of vertices etc
of the output cluster
Please correct me if I am following the procedure for multiple comparisons
wrongly or going wrong in any part of analysis and correction for multiple
comparisons.

However I have observed that sometimes,even though there is an output in
the terminal (sometimes the cluster having almost as 1900-200 vtxs),there
is no display of the cluster on the inflated image on the display tab.
I dont know why this is happening,But I have seen this to be the case in a
number of situations.

I would also be interested to know if there is any other alternate method
for viewing clusters.Since the clusters on display images are absolute
necessity for all reporting purposes .
I hope to hear from you soon.

Regards ,
Vikas Bandalli Raju
-- 
Vikas B. R.
Medical student
Bangalore Medical College and Research Institute (BMCRI),
Bangalore,India,
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[Freesurfer] Significant clusters from mri_glmfit

[sabin khadka]

Hi all,
I used FDR correction method to correct for multiple comparison after 
mri_glmfit. And I have a cluster covering multiple regions. I want to extract 
the thickness, surface area, lgi values for local maxima (or, multiple regions 
covered by the big significant cluster). I see it is not straightforward as 
when monte-carlo cluster correction is applied. Can anyone suggest me if there 
is a work around for this apart from manually creating a ROI masks and 
extracting values?

Thanks for help! Cheers,
Sabin Khadka___
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[Freesurfer] Post-doc opening in Neuroinformatics

[Gregory Book]

The Olin Neuropsychiatry Research Center has an opening for a post-doc
specializing in neuroinformatics, big-data analysis, and machine learning.
The Olin Center is the neuropsychiatric research center within Hartford
Hospital’s Institute of Living campus, in Hartford, CT. We house a Siemens
Skyra 3T whole-body MRI, multiple EEG, TMS, and eye tracking systems, an
internal historical database of nearly 13,000 MRI sessions, and a 400-core
Linux compute cluster. The candidate will contribute to the development of
neuroimaging databases in support of multiple NIH funded projects and with
several primary investigators on large scale analyses. The candidate will
contribute to the development of the Neuroinformatics Database (
http://github.com/gbook/nidb) to archive data, automate data analysis using
new and existing pipelines, and publish journal articles on their own
research. MS degree in engineering, science, neuroscience, or psychology is
required, PhD preferred. Candidate is expected to have experience in SQL
programming and at least one programming language. Proficiency in multiple
programming languages such as Perl, C, C++, Javascript, PHP, Matlab, and
Python is highly desirable. Contact Greg Book at gregory.b...@hhchealth.org
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[Freesurfer] Using customized stats code for mass-univariate approach in freesurfer for structural data

[Chung, Yoonho]

Hi - If I would like to try to perform mass-univariate statistics at the vertex 
level (thickness, area, vol at each vertex) without using the mri_glmfit, is 
this order a sound step (in general) for mapping stats parameter of choice 
(p-val or t s  or weights for example) to the surface?


1. Use mris_preproc and surf2surf to get the data to common space and smooth.

2. Load the data to matlab using fs_read_Y() or MRIread

3. Perform stats at each vertex using stats toolbox to apply modeling approach 
of your choice (e.g., machine learning, linear mixed model etc.)

4. Extract P-values (or other parameters) for each vertex for the variable of 
primary interest

5. Use MRIwrite to create mgh file

6. Perform multiple comparison using freesurfer functions (e.g., FDR or monte 
carlo sim)

7. view corrected maps using tksufer?


Any steps I should consider adding or avoid?

Thank you!

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[Freesurfer] Intensity stats file for new ROI

[Sabrina Yu]

Hello,

I have created my own subcortical ROI in freesurfer (saved as .label file), and 
am trying to generate an intensity stats file for this ROI. Reading the mailing 
list, I think that the best way to do this is to:

1) mri_label2vol to convert my ROI to a volume file

2) mri_label_volume to generate stats on this volume


I was able to achieve the first step, but am unable to generate a stats file 
with intensity info for the volume. This is the command I tried to use:

cd /freesurfer/subjects//mri

mri_label_volume -s  stroke_area.mgz label 1


Any help would be much appreciated! Thank you in advance.


Sabrina
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Re: [Freesurfer] Intensity stats file for new ROI

[Bruce Fischl]

Hi Sabrina

if you have drawn the label in freeview you can use mri_label_vals to 
generate a file of the value of each voxel in the label in whatever 
volume you specify. You can then do whatever you want with them (e.g. fit 
a Gaussian to it, etc...)


Bruce
On Tue, 24 May 2016, Sabrina Yu wrote:



Hello, 


I have created my own subcortical ROI in freesurfer (saved as .label file),
and am trying to generate an intensity stats file for this ROI. Reading the
mailing list, I think that the best way to do this is to: 

1) mri_label2vol to convert my ROI to a volume file

2) mri_label_volume to generate stats on this volume


I was able to achieve the first step, but am unable to generate a stats file
with intensity info for the volume. This is the command I tried to use:

cd /freesurfer/subjects//mri

mri_label_volume -s  stroke_area.mgz label 1


Any help would be much appreciated! Thank you in advance. 


Sabrina 


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[Freesurfer] Design Matrix Creation

[Timothy Hendrickson]

Freesurfer Support,

I'd like to create a design matrix for a group analysis outside of the DODS
and DOSS models. I understand that in order to do this the -X flag must be
used. However, I have been unable to find examples of how to do this.

I am hoping to reveal a difference in thickness or gyrification amongst a
clinical population. The data set contains two factors: diagnosis, and
study site and one covariate: age. Diagnosis has two levels: controls, and
patients. Study site has four levels, one level for each location the data
has been collected from.

What I would ideally like to do is:

1) Take into account offset differences amongst diagnosis and study site.

2) Allowing a difference in age slope amongst the diagnosis levels

3) Modeling the age slope as the same for the study site levels

My FSGD file is designed as follows

Class SITE 1-Control
Class SITE 1-PATIENT
Class SITE 2-Control
Class SITE 2-PATIENT
Class SITE 3-Control
Class SITE 3-PATIENT
Class SITE 4-Control
Class SITE 4-PATIENT
Variables age_at_scan

study site levels = 1,2,3 and 4
diagnosis levels = PATIENT and Control
age_at_scan = covariate age

Any advice would be greatly appreciated.

Respectfully,

Tim

-- 
Timothy Hendrickson
Department of Psychiatry
University of Minnesota
Mobile: 507-259-3434 (texts okay)
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Re: [Freesurfer] LME MATLAB, X matrix error

[Martin Reuter]

Dear Han,

if controls have only 1 time point, you cannot compare/analyse any 
measurement of change across the groups (such as atrophy rates). You can 
only do a cross sectional analysis at baseline.
For patients you could separately look at atrophy rates (if they differ 
from zero, which should be true for any type of group - so that alone is 
not very exciting).

Usually there is only one time column with time-from-baseline for example

me1 0 ...
me2 1.2 ...
me 3 1.8 ...
you1 0 ..
you2 0.9 ...
he1 0
she1 0
she2 1.1
and so on (this could be in years). There can be differently many rows 
per subject, depending on the number of time points. Single time point 
subjects, can be mixed in and will help to estimate cross subject 
variances, but they won't really help much with estimates of 
longitudinal changes. Having a full group with only a single time point 
does not make sense in a longitudinal design.


Best, Martin


On 05/21/2016 06:42 PM, Hanbyul Cho wrote:

Dear Martin Reuter,

Thank you for your reply.

Our patients have several time points, but controls have only 1 time 
points,

so when I coded the patients group =1, controls groups = 0 ,
the 2. time  and  3. time2 column were same as 5. 4.X time 6. 4.X 
time2 column.

and 8. 7. X time and 9. 8. X time2 were all zeros.

And then, how about this X matrix (Subjects N X 5)?

1. Intercept (all '1')
2. 4.X time (from baseline time point)
3. 4.X time2
4. age
5. extra values for covariate

is it a vallid matrix for test the effects of group X time2 ?


Thank you,

Han.

On Sat, May 21, 2016 at 3:13 PM, Martin Reuter 
mailto:mreu...@nmr.mgh.harvard.edu>> wrote:


Hi Han,
Try to find a local statistician to help you with your analysis.
About your matrix: rows need to be number of all time points from
all subject. Time 2 should probably not be there. Also columns 7-9
need to be dropped (they are just the negative of the rows before).

Best Martin

On May 21, 2016 3:32 PM, Hanbyul Cho mailto:hanbyul.h@gmail.com>> wrote:

Dear FreeSurfer Team,

I processed in MATLAB for Linear Mixed Effects Models Analysis
with this X matrix:

X matrix is 'Subjects N X 11', 11 columns are as follow,

1. Intercept (all '1')
2. time (from baseline time point)
3. time2
4. Patients group = 1, Control = 0
5. 4.X time
6. 4.X time2
7. Patients group = 0, Control = 1
8. 7. X time
9. 8. X time2
10. age
11. extra values for covariate


1.
When I process this command,
[lhTh01,lhRe01] = lme_mass_fit_EMinit(X,[1],Y,ni,lhcortex,3,4)
The MATLAB windows print the warning alarm repeatedly.
" Warning: Matrix is close to singular or badly scaled.
Results may be inaccurate."
Is this X matrix something wrong?


2.
After complete   'lme_mass_fit_EMinit' process with the
warning, I tried the next command,
[lhRgs01,lhRgMeans01] = lme_mass_RgGrow(lhsphere, lhRe01,
lhTh01,lhcortex,2,95);
This command took a long time to process, and it caused
the whole stop MATLAB works.
Is it also because of the X matrix...?


Could you let me know the solution for the X matrix problems ?

Best Wishes,

Han


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--
Martin Reuter, PhD
Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
Web  : http://reuter.mit.edu

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[Freesurfer] mris_preproc - srcsubjreg

[Makaretz, Sara Johanna]

Hi Doug, I¹m curious why the newer mris_preproc does not use sphere.reg as
the default srcsurfreg when the target is not fsaverage - see below

Thanks for any info! (not urgent)


On 2016-5-24, 11:30, "Z K"  wrote:

>Good question, and I dont know the answer. mris_preproc is Dougs baby so
>I suggest just posting this question to the list with "mris_preproc" in
>the subject, and I bet he will give you the answer.
>
>-Zeke
>
>On 05/23/2016 10:31 PM, Makaretz, Sara Johanna wrote:
>> Hi Zeke,
>>
>> I am running some surface glms where targ is a patient surface. The help
>> says --target TargetSubject (requires ?h.TargetSubject.sphere.reg), and
>> I was getting errors because dev-default mris_preproc wanted
>> mri_surf2surf to have srcsurfreg =
>> $SUBJECTS_DIR/$srcsubject/surf/$h.$TARGSUBJ.sphere.reg
>>
>> But mris_preproc in 5.3 let me do target = patient surface with no extra
>> surf reg files or extra flags to get mri_surf2surf to use srcsurfreg =
>> $SUBJECTS_DIR/$srcsubject/surf/$h.sphere.reg
>>
>> I had been running this with 5.3:
>> mris_preproc\
>>  --target $TARGSUBJ\
>>  --hemi lh\
>>  --meas thickness\
>>  --fsgd file.fsgd\
>>  --out lh.output.mgh
>>
>> And I was about to email freesurfer@nmr but "for fun" tried adding
>> --surfreg sphere.reg which got mris_surf2surf to use the right reg
>> files. So now I'm selfishly trying to figure this out - do you know what
>> prompted the switch from sphere.reg "opt-out" to sphere.reg "opt-in"?
>> Aka why sphere.reg is non-default when the target is non-fsaverage? Did
>> that make sense? I know there must be some reason, so I really want to
>> know a bit more so I can stay sane when old scripts break.
>>
>> Thanks for any info! Sorry to bother you!
>> Sara
>>
>>
>>
>>
>>
>>
>> Outputs from the FS-dev one:
>>
>> $Id: mris_preproc,v 1.76 2015/12/09 20:02:53 zkaufman Exp $
>> 
>> Src lh $TARGSUBJ.sphere.reg
>> Trg lh sphere.reg
>> 
>> mri_surf2surf --srcsubject $SRCSUBJ --srchemi lh --srcsurfreg
>> $TARGSUBJ.sphere.reg --trgsubject $TARGSUBJ --trghemi lh --trgsurfreg
>> sphere.reg --etcetcetc
>> 
>> ERROR can't find $SUBJECTS_DIR/$SRCSUBJ/surf/$TARGSUBJ.sphere.reg
>> because I never made it
>>
>>
>>
>> Outputs from the FS-dev one with fsaverage as the targ subj:
>>
>> $Id: mris_preproc,v 1.76 2015/12/09 20:02:53 zkaufman Exp $
>> 
>> Src lh sphere.reg
>> Trg lh sphere.reg
>> 
>> mri_surf2surf --srcsubject $SRCSUBJ --srchemi lh --srcsurfreg sphere.reg
>> --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --etcetcetc
>> 
>> mris_preproc finds everything, runs no problem
>>
>>
>>
>> Outputs from the FS-5.3 one:
>>
>> $Id: mris_preproc,v 1.59.2.4 2012/12/06 16:06:52 mreuter Exp $
>> 
>> Src lh sphere.reg
>> Trg lh sphere.reg
>> 
>> mri_surf2surf --srcsubject $SRCSUBJ --srchemi lh --srcsurfreg sphere.reg
>> --trgsubject $TARGSUBJ --trghemi lh --trgsurfreg sphere.reg --etcetcetc
>> 
>> mris_preproc exits with no errors because everything exists
>>
>>
>>
>>


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Re: [Freesurfer] Using customized stats code for mass-univariate approach in freesurfer for structural data

[Martin Reuter]

Hi Yoonho,

the steps look good. Take a look at
https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels
which basically describes exactly these steps for the case of linear 
mixed effects models. Note that we have dedicated code for that as part 
of FreeSurfer (see also the references explaining why this code is 
great, e.g. "Spatiotemporal Linear  Neuroimage 2013")


Also, you can do a more powerful 2stage FDR correction using 
lme_mass_FDR2 in matlab directly (best to combine hemisphers for that, 
see wiki).


cheers, Martin


On 05/24/2016 01:55 PM, Chung, Yoonho wrote:


Hi - If I would like to try to perform mass-univariate statistics at 
the vertex level (thickness, area, vol at each vertex) without using 
the mri_glmfit, is this order a sound step (in general) for mapping 
stats parameter of choice (p-val or t s  or weights for example) to 
the surface?



1. Use mris_preproc and surf2surf to get the data to common space and 
smooth.


2. Load the data to matlab using fs_read_Y() or MRIread

3. Perform stats at each vertex using stats toolbox to apply modeling 
approach of your choice (e.g., machine learning, linear mixed model etc.)


4. Extract P-values (or other parameters) for each vertex for the 
variable of primary interest


5. Use MRIwrite to create mgh file

6. Perform multiple comparison using freesurfer functions (e.g., 
FDR or monte carlo sim)


7. view corrected maps using tksufer?


Any steps I should consider adding or avoid?

Thank you!




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Martin Reuter, PhD
Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
Web  : http://reuter.mit.edu

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[Freesurfer] White matter segmentation

[Mahmoudi, Fariborz]

Dear All,

I want to segment white matter into 131xx and 141xx label series. I used 
aparc.a2009s but it just gave me cortex labels (111xx and 121xx). Can  anyone 
guide me how could I do this?

Regards,
Fari



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Re: [Freesurfer] Using customized stats code for mass-univariate approach in freesurfer for structural data

[Douglas N Greve]

That looks fine. If you are going to use the monte carlo sim, then 
you'll need an estimate of the FWHM. In mri_glmfit, we get that by 
running mris_fwhm on the residuals. So, assuming that your analysis has 
residuals, then you should save those out too.

On 05/24/2016 01:55 PM, Chung, Yoonho wrote:
>
> Hi - If I would like to try to perform mass-univariate statistics at 
> the vertex level (thickness, area, vol at each vertex) without using 
> the mri_glmfit, is this order a sound step (in general) for mapping 
> stats parameter of choice (p-val or t s  or weights for example) to 
> the surface?
>
>
> 1. Use mris_preproc and surf2surf to get the data to common space and 
> smooth.
>
> 2. Load the data to matlab using fs_read_Y() or MRIread
>
> 3. Perform stats at each vertex using stats toolbox to apply modeling 
> approach of your choice (e.g., machine learning, linear mixed model etc.)
>
> 4. Extract P-values (or other parameters) for each vertex for the 
> variable of primary interest
>
> 5. Use MRIwrite to create mgh file
>
> 6. Perform multiple comparison using freesurfer functions (e.g., 
> FDR or monte carlo sim)
>
> 7. view corrected maps using tksufer?
>
>
> Any steps I should consider adding or avoid?
>
> Thank you!
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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-- 
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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
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Re: [Freesurfer] Design Matrix Creation

[Douglas N Greve]

You'll need a regressor for each of the 8 classes you describe below. 
You can use mri_glmfit to generate this (Xg.dat file)
You'll need two more regressors for age, one for each diagnosis. If a 
subject (ie, row) is a control then the two values will be AGE 0. If the 
subject of the row is a patient, then the two values will be 0 AGE. You 
can then set up a Controls-Patients age (ie, interaction between dx and 
age) contrast like
[0 0 0 0 0 0 0 0 1 -1]



On 05/24/2016 02:30 PM, Timothy Hendrickson wrote:
>
> Freesurfer Support,
>
> I'd like to create a design matrix for a group analysis outside of the 
> DODS and DOSS models. I understand that in order to do this the -X 
> flag must be used. However, I have been unable to find examples of how 
> to do this.
>
> I am hoping to reveal a difference in thickness or gyrification 
> amongst a clinical population. The data set contains two factors: 
> diagnosis, and study site and one covariate: age. Diagnosis has two 
> levels: controls, and patients. Study site has four levels, one level 
> for each location the data has been collected from.
>
> What I would ideally like to do is:
>
> 1) Take into account offset differences amongst diagnosis and study site.
>
> 2) Allowing a difference in age slope amongst the diagnosis levels
>
> 3) Modeling the age slope as the same for the study site levels
>
> My FSGD file is designed as follows
>
> Class SITE 1-Control
> Class SITE 1-PATIENT
> Class SITE 2-Control
> Class SITE 2-PATIENT
> Class SITE 3-Control
> Class SITE 3-PATIENT
> Class SITE 4-Control
> Class SITE 4-PATIENT
> Variables age_at_scan
>
> study site levels = 1,2,3 and 4
> diagnosis levels = PATIENT and Control
> age_at_scan = covariate age
>
> Any advice would be greatly appreciated.
>
> Respectfully,
>
> Tim
>
> -- 
> Timothy Hendrickson
> Department of Psychiatry
> University of Minnesota
> Mobile: 507-259-3434  (texts okay)
>
>
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] White matter segmentation

[Douglas N Greve]

see
http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg47157.html


On 05/24/2016 05:44 PM, Mahmoudi, Fariborz wrote:
>
> Dear All,
>
> I want to segment white matter into 131xx and 141xx label series. I 
> used aparc.a2009s but it just gave me cortex labels (111xx and 121xx). 
> Can  anyone guide me how could I do this?
>
> Regards,
>
> Fari
>
>
> 
>
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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] Group Analysis: Two Groups and Two Covariates.

[Hanbyul Cho]

Dear Douglas N Greve,

Today, I tested the previous group analysis on other computer, and saw the
same error massage.

I attached the tested fsgd and mtx files.

command:
mri_glmfit --y 052416_lh.Pa_Co_G2V2_dods_sm15.mgh --fsgd
052416_PA_CO_G2V2.fsgd dods --glmdir 052416_lh.Pa_Co_G2V2_dods_sm15.glmdir
--cortex --surf fsaverage lh --C 052416_contrast.mtx

Thank you,

Best wishes,

Han





On Mon, May 23, 2016 at 12:56 PM, Douglas N Greve  wrote:

> If you seek help with this problem, make sure to send:
>1. Your command line:
>  mri_glmfit --y lh.**G2V2.dods_sm15.mgh --fsgd **.fsgd dods --C
> **G2V2.mtx --surf fsaverage lh --cortex --glmdir lh.**G2V2.dods_sm15.glmdir
>2. The FSGD file (if using one)
>3. And the design matrix above
>
> On 05/21/2016 04:57 PM, Hanbyul Cho wrote:
> > Dear FreeSurfer Team,
> >
> > I processed the Group analysis by FreeSurfer 5.3.0
> >
> > Our data has two groups (Patient, Control) and two covariate values
> > (age, extra value)
> > mtx, contrast is 1 -1 0 0 0 0
> > The mris_preproc, and mri_surf2surf command were completed without error.
> >
> > mris_preproc --fsgd **G2V2.fsgd --target fsaverage --hemi lh --meas
> > thickness --out lh.**G2V2.dods.mgh
> > mri_surf2surf --hemi lh --s fsaverage --sval lh.**G2V2.dods.mgh --fwhm
> > 15 --cortex --tval lh.**G2V2.dods_sm15.mgh
> > mri_glmfit --y lh.**G2V2.dods_sm15.mgh --fsgd **.fsgd dods --C
> > **G2V2.mtx --surf fsaverage lh --cortex --glmdir
> > lh.**G2V2.dods_sm15.glmdir
> >
> > After mri_glmfit command, I saw the error message.
> >
> > =
> > ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08
> > 
> > Possible problem with experimental design:
> > Check for duplicate entries and/or lack of range of
> > continuous variables within a class.
> > If you seek help with this problem, make sure to send:
> >   1. Your command line:
> > mri_glmfit --y lh.**G2V2.dods_sm15.mgh --fsgd **.fsgd dods --C
> > **G2V2.mtx --surf fsaverage lh --cortex --glmdir
> > lh.**G2V2.dods_sm15.glmdir
> >   2. The FSGD file (if using one)
> >   3. And the design matrix above
> > =
> >
> > I think our fsgd and mtx compositions are equal to the g2v2.fsgd which
> > FreeSurfer wiki example.
> > (https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G2V)
> >
> > In this situation, how can I correct my fsgd or mtx files? Is there
> > any other command option?
> >
> > Best Regards,
> >
> > Han
> >
> >
> > ___
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>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
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052416_contrast.mtx
Description: Binary data


052416_PA_CO_G2V2.fsgd
Description: Binary data
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