date:20150925

[Freesurfer] high area.pial values

2015-09-25 Thread Andrews, Derek

Dear FreeSurfer Support Team

First of all, I must thank you for your excellent software!

I have been looking at distributions of various free surfer features 
(histograms of the vertex wise measures).  I have noticed some high values 
among the pial and white matter surfaces, these values range from 20-85.  
Again, this in only in a handful of vertices (out of millions of measures). I 
am wondering what could account for such a high value?

Thank you for your help in clarifying this.

Best, Derek




Derek Sayre Andrews, MSc
PhD Candidate

Department of Forensic and Neurodevelopmental Sciences &

The Sackler Institute for Translational Neurodevelopment
Institute of Psychiatry, Psychology & Neuroscience, King's College London

Telephone: +44 (0)20 7848 5701
Email: derek.andr...@kcl.ac.uk

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Re: [Freesurfer] Longitudinal Two Stage Model using mri_glmfit

2015-09-25 Thread Martin Reuter


Hi Bronwyn,

yes --stack-spc was needed.

About your questions:
1. there is a section in the help text about Cortex Labels (scroll up). 
If you run qcache (where the subject data is mapped to a common 
template, e.g. fsaverage), you can specify --isec-labels < output> to do 
three things: a) it takes the cortex label from each subject and maps it 
to fsaverage (or whatever target you specified in --qcache) and 
intersects the labels there. b) it uses this intersected label for 
smoothing to ensure that no outside-cortex values get smoothed and 
averaged anywhere, and c) it writes out this intersected label .
 This is the recommended approach, but you may have difficulties as 
some subjects can have pretty ugly cortex masks and when intersecting 
all you may get something with holes. So inspect the intersected label. 
The if it has many holes in important regions, you should probably 
check, edit or remove the subjects that are responsible.
2. It should not differ (much), but it is numerically more stable if you 
use time-from-baseline.
3. --generic-time can be used in cases such as test-retest data, where 
you want just 1 and 2 for the two time points in all subjects. (the time 
delta is always 1 between neighboring time points).


Best, Martin

On 09/24/2015 11:26 PM, Bronwyn Overs wrote:

Hi Martin,

Sorry i have just realised that I need to add the --stack-spc flag to 
my long_mris_slopes command to get the stacked file for my glm 
analysis. I now have three other questions about long_mris_slopes:
1. When you run --isec-lables with the flag --meas thickness, is the 
output file specific to the thickness, or is it just related to the 
subject surface in general.
2. For my --time flag, will the output measures (e.g. spc) differ if I 
use years between scans (e.g. 0, 2) vs age at each scan (e.g. 14, 16)?

2. What is the flag --generic-time used for?

Kind regards,

Bronwyn Overs
Research Assistant

Neuroscience Research Australia

Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
*M* 0411 308 769 *T* +61 2 9399 1883

neura.edu.au 

Follow @neuraustralia on twitter 
Follow NeuRA on facebook 
Subscribe to 
the NeuRA Magazine 


On 25/09/2015 10:55 am, Bronwyn Overs wrote:

Hi Martin,

I wanted to ask about getting the stacked SPC values for use with 
mri_glmfit. I ran the following long_mri_slopes command but cannot 
identify which if any is the stacked spc mgh file:


long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas thickness 
--hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label 
--time years --qcache fsaverage --sd $SUBJECTS_DIR


Do I need to run another command to produced a stacked spc file for 
use with glm_fit?


Kind regards,

Bronwyn Overs
Research Assistant

Neuroscience Research Australia

Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
*M* 0411 308 769 *T* +61 2 9399 1883

neura.edu.au 

Follow @neuraustralia on twitter 
Follow NeuRA on facebook 
Subscribe to 
the NeuRA Magazine 


On 23/09/2015 12:15 am, Martin Reuter wrote:

Hi Bronwyn,

yes that is possible, you would pass the SPC values stack as y. See

https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel

for an example (that one uses percent change with respect to 
baseline, pc1, but you can do the same with symmetrized percent 
change (spc)).


Best, Martin

On 09/22/2015 03:13 AM, Bronwyn Overs wrote:

Dear freesurfer mailing list,

Is it possible to run a longitudinal two stage model from the 
command line using mri_glmift, instead of using the qdec gui? If 
so, what --y would you pass to use the preprocessed spc values?

--

Kind regards,

Bronwyn Overs
Research Assistant

Neuroscience Research Australia

Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
*M* 0411 308 769 *T* +61 2 9399 1883

neura.edu.au 

Follow @neuraustralia on twitter 
Follow NeuRA on facebook 
Subscribe 
to the NeuRA Magazine 





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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

[Freesurfer] The range of value of the area file

2015-09-25 Thread chenhf_uestc

Dear Freesurfer experts,

I read the raw area file and the area resampled to the fsaverage space and 
found several interesting things.

raw58l = read_curv('E:\fs_result\NC058\surf\lh.area'); % the range of the area 
value is [-0.0471 6.2118]
raw58r = read_curv('E:\fs_result\NC058\surf\rh.area'); % the range of the area 
value is [0 6.8963]
raw59l = read_curv('E:\fs_result\NC059\surf\lh.area'); % the range of the area 
value is [-0.3347 5.4892]
raw59r = read_curv('E:\fs_result\NC059\surf\rh.area'); % the range of the area 
value is [-1818 5.4269]

The first question, what is the unit of the area file in the surf folder (such 
as lh.area), mm2? Why the minimal value of the area can be less than zero?

Subsequently, I perform further experiments, reading the resampled area file.

resamp_58l = load_mgh('E:\fs_result\NC058\surf\lh.area.fsaverage.mgh'); % the 
range of the area value is [-0.0118 7.4073]
resamp_58r = load_mgh('E:\fs_result\NC058\surf\rh.area.fsaverage.mgh'); % the 
range of the area value is [0 19.0191]
resamp_59l = load_mgh('E:\fs_result\NC059\surf\lh.area.fsaverage.mgh'); % the 
range of the area value is [-0.3937 9.9084]
resamp_59r = load_mgh('E:\fs_result\NC059\surf\rh.area.fsaverage.mgh'); % the 
range of the area value is -0.0909 8.2306[]

The second question, why the value of some area file change a lot? For example, 
the maximum value of raw58r is 6.8963, but 19.0191 of resampled one.

Next, 
resamp_smooth5_58l = 
load_mgh('E:\fs_result\NC058\surf\lh.area.fwhm5.fsaverage.mgh');  % the range 
of the area value is [0 1.7293]
resamp_smooth5_58r = 
load_mgh('E:\fs_result\NC058\surf\rh.area.fwhm5.fsaverage.mgh');  % the range 
of the area value is [0 2.1877]
resamp_smooth5_59l = 
load_mgh('E:\fs_result\NC059\surf\lh.area.fwhm5.fsaverage.mgh');  % the range 
of the area value is [0 1.2875]
resamp_smooth5_59r = 
load_mgh('E:\fs_result\NC059\surf\rh.area.fwhm5.fsaverage.mgh');  % the range 
of the area value is [0 1.3542]

The third question, why all the minimal values after smooth was zero? Why all 
the maximal values after smooth reduce a lot? 

Finally, 
resamp_smooth25_58l = 
load_mgh('E:\fs_result\NC058\surf\lh.area.fwhm25.fsaverage.mgh');  % the range 
of the area value is [0 1.2014]
resamp_smooth25_58r = 
load_mgh('E:\fs_result\NC058\surf\rh.area.fwhm25.fsaverage.mgh');  % the range 
of the area value is [0 1.2611]
resamp_smooth25_59l = 
load_mgh('E:\fs_result\NC059\surf\lh.area.fwhm25.fsaverage.mgh');  % the range 
of the area value is [0 0.9730]
resamp_smooth25_59r = 
load_mgh('E:\fs_result\NC059\surf\rh.area.fwhm25.fsaverage.mgh');  % the range 
of the area value is [0 1.0119]

The final question, why all the maximal values  of fwhm25 smooth are less than 
the values  of fwhm5 smooth?

How can I get the area value in the recon-all analyses? The cortical thickness 
is the distance betwwen the white matter and the pial, but what is the 
procedures the area value obtained? 

Any help would be greatly appreciately!

Best,
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Re: [Freesurfer] different layer ROI

2015-09-25 Thread Yun Wang

But the question is how to sample different layer surface ’s functional data in 
one or multiple ROI.

Thanks!

Yun


> On Sep 25, 2015, at 10:59, Bruce Fischl  wrote:
> 
> you want to extract the time series from an fMRI volume in say "deep" and 
> "superficial" V1? If so, then I think what you want is 3 intermediate 
> surfaces between white and pial, then sample using surfaces 1 and 3 (but not 
> 2, which would be the boundary between the top half and the bottom half).
> 
> cheers
> Bruce
> 
> On Fri, 25 Sep 2015, Yun Wang wrote:
> 
>> Hi All,
>> 
>> I have two questions:
>> 
>> 1   I have used mris_expand to get additional two layer surface between 
>> white and pial surface. what I want to do next : using label such as V1 as 
>> ROI, then get different layer ROI in V1. How can I get it?
>> 
>> 2 After I get layers’ ROI, I want to extract the time series . Anyone have 
>> idea?
>> 
>> 
>> Thanks!
>> 
>> Yun Wang
>> ___
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Re: [Freesurfer] high area.pial values

2015-09-25 Thread Bruce Fischl

are they only high on the pial and not on the white? I would have guessed 
that they would be high on both, and further that it is due to the topology 
correction and the quirks of the way we retesselate. One easy way to find 
out if this is true is if the vertex index is near the end of the list 
(i.e. close to the total number of vertices, since the vertices added 
during the correction are at the end of the array)


cheers
Bruce

On Fri, 25 Sep 2015, Andrews, Derek wrote:


Dear FreeSurfer Support Team

First of all, I must thank you for your excellent software! 

I have been looking at distributions of various free surfer features
(histograms of the vertex wise measures).  I have noticed some high values
among the pial and white matter surfaces, these values range from 20-85.
 Again, this in only in a handful of vertices (out of millions of measures).
I am wondering what could account for such a high value? 

Thank you for your help in clarifying this. 

Best, Derek 




Derek Sayre Andrews, MSc
PhD Candidate

Department of Forensic and Neurodevelopmental Sciences & 

The Sackler Institute for Translational Neurodevelopment
Institute of Psychiatry, Psychology & Neuroscience, King's College London

Telephone: +44 (0)20 7848 5701
Email: derek.andr...@kcl.ac.uk 



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Re: [Freesurfer] different layer ROI

2015-09-25 Thread Bruce Fischl

you want to extract the time series from an fMRI volume in say "deep" and 
"superficial" V1? If so, then I think what you want is 3 intermediate 
surfaces between white and pial, then sample using surfaces 1 and 3 (but 
not 2, which would be the boundary between the top half and the bottom 
half).


cheers
Bruce

On Fri, 25 Sep 2015, Yun Wang wrote:


Hi All,

I have two questions:

1   I have used mris_expand to get additional two layer surface between 
white and pial surface. what I want to do next : using label such as V1 as ROI, 
then get different layer ROI in V1. How can I get it?

2 After I get layers’ ROI, I want to extract the time series . Anyone have idea?


Thanks!

Yun Wang
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Re: [Freesurfer] different layer ROI

2015-09-25 Thread Bruce Fischl

Hi Yun

just specify the surface you want in mri_vol2surf to generate a time series
per-vertex on each surface, then you can average each of those within the
V1 ROI if you want.

cheers
Bruce

On Fri, 25 Sep 2015, Yun Wang wrote:

But the question is how to sample different layer surface ’s functional data in
one or multiple ROI.

Thanks!

Yun

On Sep 25, 2015, at 10:59, Bruce Fischl wrote:

you want to extract the time series from an fMRI volume in say "deep" and
"superficial" V1? If so, then I think what you want is 3 intermediate surfaces between
white and pial, then sample using surfaces 1 and 3 (but not 2, which would be the boundary between
the top half and the bottom half).

cheers
Bruce

On Fri, 25 Sep 2015, Yun Wang wrote:

Hi All,

I have two questions:

1 I have used mris_expand to get additional two layer surface between
white and pial surface. what I want to do next : using label such as V1 as ROI,
then get different layer ROI in V1. How can I get it?

2 After I get layers’ ROI, I want to extract the time series . Anyone have idea?

Thanks!

Yun Wang
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Re: [Freesurfer] different layer ROI

2015-09-25 Thread Yun Wang

Oh, so after I get the different layers’ functional data,  using which function 
to extract V1 ROI value ? I am not so familiar with freesurfer, excuse me with 
my ignorance. 


> On Sep 25, 2015, at 11:45, Bruce Fischl  wrote:
> 
> projdist would be 0 since you want to sample right on the surface location. I 
> don't think you need a mask
> On Fri, 25 Sep 2015, Yun Wang wrote:
> 
>> Thanks! Again I want to make sure when using mri_vol2surf for my case
>> the options
>> 
>> —surf   :  my layer surface  ?
>> —projdist : how should I use this?
>> —mask:the label that I want use V1?
>> 
>> 
>> 
>> 
>>> On Sep 25, 2015, at 11:18, Bruce Fischl  wrote:
>>> 
>>> Hi Yun
>>> 
>>> just specify the surface you want in mri_vol2surf to generate a time series 
>>> per-vertex on each surface, then you can average each of those within the 
>>> V1 ROI if you want.
>>> 
>>> cheers
>>> Bruce
>>> 
>>> 
>>> 
>>> On Fri, 25 Sep 2015, Yun Wang wrote:
>>> 
 But the question is how to sample different layer surface ’s functional 
 data in one or multiple ROI.
 
 Thanks!
 
 Yun
 
 
> On Sep 25, 2015, at 10:59, Bruce Fischl  
> wrote:
> 
> you want to extract the time series from an fMRI volume in say "deep" and 
> "superficial" V1? If so, then I think what you want is 3 intermediate 
> surfaces between white and pial, then sample using surfaces 1 and 3 (but 
> not 2, which would be the boundary between the top half and the bottom 
> half).
> 
> cheers
> Bruce
> 
> On Fri, 25 Sep 2015, Yun Wang wrote:
> 
>> Hi All,
>> 
>> I have two questions:
>> 
>> 1   I have used mris_expand to get additional two layer surface 
>> between white and pial surface. what I want to do next : using label 
>> such as V1 as ROI, then get different layer ROI in V1. How can I get it?
>> 
>> 2 After I get layers’ ROI, I want to extract the time series . Anyone 
>> have idea?
>> 
>> 
>> Thanks!
>> 
>> Yun Wang
>> ___
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>> 
>> 
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> is
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> e-mail
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 ___
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 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 
 
>>> ___
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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
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>>> properly
>>> dispose of the e-mail.
>> 
>> 
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>> 
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Re: [Freesurfer] different layer ROI

2015-09-25 Thread Yun Wang

Thanks! Again I want to make sure when using mri_vol2surf for my case 
the options
 
—surf   :  my layer surface  ?
—projdist : how should I use this?
—mask:the label that I want use V1? 




> On Sep 25, 2015, at 11:18, Bruce Fischl  wrote:
> 
> Hi Yun
> 
> just specify the surface you want in mri_vol2surf to generate a time series 
> per-vertex on each surface, then you can average each of those within the V1 
> ROI if you want.
> 
> cheers
> Bruce
> 
> 
> 
> On Fri, 25 Sep 2015, Yun Wang wrote:
> 
>> But the question is how to sample different layer surface ’s functional data 
>> in one or multiple ROI.
>> 
>> Thanks!
>> 
>> Yun
>> 
>> 
>>> On Sep 25, 2015, at 10:59, Bruce Fischl  wrote:
>>> 
>>> you want to extract the time series from an fMRI volume in say "deep" and 
>>> "superficial" V1? If so, then I think what you want is 3 intermediate 
>>> surfaces between white and pial, then sample using surfaces 1 and 3 (but 
>>> not 2, which would be the boundary between the top half and the bottom 
>>> half).
>>> 
>>> cheers
>>> Bruce
>>> 
>>> On Fri, 25 Sep 2015, Yun Wang wrote:
>>> 
 Hi All,
 
 I have two questions:
 
 1   I have used mris_expand to get additional two layer surface 
 between white and pial surface. what I want to do next : using label such 
 as V1 as ROI, then get different layer ROI in V1. How can I get it?
 
 2 After I get layers’ ROI, I want to extract the time series . Anyone have 
 idea?
 
 
 Thanks!
 
 Yun Wang
 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 
 
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>> 
>>> 
>>> The information in this e-mail is intended only for the person to whom it is
>>> addressed. If you believe this e-mail was sent to you in error and the 
>>> e-mail
>>> contains patient information, please contact the Partners Compliance 
>>> HelpLine at
>>> http://www.partners.org/complianceline . If the e-mail was sent to you in 
>>> error
>>> but does not contain patient information, please contact the sender and 
>>> properly
>>> dispose of the e-mail.
>> 
>> 
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>> 
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Re: [Freesurfer] different layer ROI

2015-09-25 Thread Bruce Fischl

projdist would be 0 since you want to sample right on the surface
location. I don't think you need a mask

On Fri, 25 Sep 2015, Yun Wang wrote:

Thanks! Again I want to make sure when using mri_vol2surf for my case
the options

—surf : my layer surface ?
—projdist : how should I use this?
—mask:the label that I want use V1?

On Sep 25, 2015, at 11:18, Bruce Fischl wrote:

Hi Yun

just specify the surface you want in mri_vol2surf to generate a time series
per-vertex on each surface, then you can average each of those within the V1
ROI if you want.

cheers
Bruce

On Fri, 25 Sep 2015, Yun Wang wrote:

But the question is how to sample different layer surface ’s functional data in
one or multiple ROI.

Thanks!

Yun

On Sep 25, 2015, at 10:59, Bruce Fischl wrote:

cheers
Bruce

On Fri, 25 Sep 2015, Yun Wang wrote:

Hi All,

I have two questions:

2 After I get layers’ ROI, I want to extract the time series . Anyone have idea?

Thanks!

Yun Wang
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[Freesurfer] 3_group_comparison

2015-09-25 Thread Dusan Hirjak

Dear Freesurfer experts, 
I am trying to compare 3 groups (aut, sch, ges) according to thickness, area 
and LGI at once (omnibus test). 
I did run the following command: 
mris_preproc --fsgd NSS_3_GR.fsgd \ --cache-in thickness.fwhm15.fsaverage \ 
--target fsaverage --hemi lh \ --out lh.NSS_3_GR.thickness.15.mgh
This step did work properly:-)

Now, Im trying to run the following command, but it does not work:
mri_glmfit \ --y lh.NSS_3_GR.thickness.15.mgh \ --fsgd NSS_3_GR.fsgd dods\ --C 
contrasts.mtx \ --surf fsaverage lh \ --cortex \ --glmdir NSS_3_GR.glmdir
I got this message: "ERROR: Option  --y unknown"
What am I doing wrong? 
Thank you for your help! 

Best regards 

Dusan ___
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[Freesurfer] postdoc - UT Houston - neuroimaging of mood disorders {Disarmed}

2015-09-25 Thread Benson Mwangi

Kindly forward this advert to the list members.


Many thanks





We are looking for a postdoc to work on neuroimaging of mood disorders.
The focus of the work in our lab is on structural MRI, MRS and DTI
studies.  There are also projects where we are looking into imaging
genetics, as well as linking neurcognitive findings to the neuroanatomical
MRI data.

A psychologist, biomedical engineer or computer science person with prior
experience in image analyses and ability to write manuscripts in English
would be a good fit.


Please email your CV to Professor Soares with an explanation of your
background and interests.



Thanks.





Jair C. Soares, M.D., Ph.D.
Professor and Chairman
Director, UTHealth Center of Excellence on Mood Disorders
Department of Psychiatry and Behavioral Sciences
UTHealth Medical School
1941 East Road, #3210
Houston, TX 77054
Phone: (713)486-2507
FAX: (713)486-2553
email: jair.c.soa...@uth.tmc.edu
http://utpsychiatry.org/

http://utmoodcenter.org/

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Re: [Freesurfer] .mgh file not load into surfstats

2015-09-25 Thread Myriam Oliver

Hi Bruce!
Thank you for your response. Sorry about the incomplete information,

I need the average surface of each participant, so for me it will be great
to use the output already generated for freesurfer. However, it is not read
by surfstats. So, one solution was to change to .mgh format to .obj

The solution two can be use the lh.white which surfstats reads and change
the matrix dimensions so I can compare all subjects. This is the command I
use for each subject to change the matrix dimensions:

mri_surf2surf --s ' subjectid ' --hemi lh --sval-tal-xyz white --tval
talairach.white --tval-xyz --trgsubject ' subjectid

%Average surface

left_files = SurfStatListDir([cd filesep 'lh.white.transform'], []);
right_files = SurfStatListDir([cd filesep 'rh.white.transform'], []);
f = [left_files, right_files];
avsurf = SurfStatAvSurf(f);

The error is:
Error using + Matrix dimensions must agree.
Error in SurfStatAvSurf (line 36)
surf.coord=fun(surf.coord,double(s.coord));

Thank you!

2015-09-24 15:50 GMT-04:00 Bruce Fischl :

> when you say "it does not work either', what do you mean? Please remember
> to send us the entire screen output of commands you are asking about
> On Thu,
> 24 Sep 2015, Myriam Oliver wrote:
>
> > Dear Freesurfers,
> >
> > I wanted to ask you if you know how can I convert a .mgh file to a .obj
> > file.
> >
> > I want to run surfstats (specifically SurfStatReadSurf ) but it does not
> > read .mgh files (i.e, the surface file; lh.w-g.pct.mgh.fsaverage.mgh).
> > Although, it reads the lh.white, but I need the average, as otherwise I
> have
> > an error of matrix dimension between subjects.
> >
> > I try using the lh.white and changing the matrix dimensions through:
> > mri_surf2surf --s ' subjectid ' --hemi lh --sval-tal-xyz white --tval
> > talairach.white --tval-xyz --trgsubject ' subjectid
> >
> > But it does not work either.
> >
> > Any help about how can I use the .mgh file in surfstats?
> >
> > Thanks!
> >
> >
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>
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> addressed. If you believe this e-mail was sent to you in error and the
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> HelpLine at
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> dispose of the e-mail.
>
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-- 

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Re: [Freesurfer] .mgh file not load into surfstats

2015-09-25 Thread Bruce Fischl

Hi Myriam

sorry, I don't know SurfStat at all so I don't really understand the error. 
Can you run mris_info on your transformed surfaces and confirm that they 
have the same number of vertices? If you are transforming .mgh files note 
that they are *NOT* surfaces, but scalar fields over the surface. They can 
be transformed with mri_surf2surf, but you wouldn't use --tval-xyz  and 
such.

cheers
Bruce

On Fri, 25 Sep 2015, Myriam Oliver 
wrote:

Hi Bruce!
Thank you for your response. Sorry about the incomplete information,

I need the average surface of each participant, so for me it will be great
to use the output already generated for freesurfer. However, it is not read
by surfstats. So, one solution was to change to .mgh format to .obj

The solution two can be use the lh.white which surfstats reads and change
the matrix dimensions so I can compare all subjects. This is the command I
use for each subject to change the matrix dimensions:

mri_surf2surf --s ' subjectid ' --hemi lh --sval-tal-xyz white --tval
talairach.white --tval-xyz --trgsubject ' subjectid

%Average surface

left_files = SurfStatListDir([cd filesep 'lh.white.transform'], []);
right_files = SurfStatListDir([cd filesep 'rh.white.transform'], []);
f = [left_files, right_files];
avsurf = SurfStatAvSurf(f);

The error is:
Error using + Matrix dimensions must agree.
Error in SurfStatAvSurf (line 36)
    surf.coord=fun(surf.coord,double(s.coord));

Thank you!

2015-09-24 15:50 GMT-04:00 Bruce Fischl :
  when you say "it does not work either', what do you mean? Please
  remember
  to send us the entire screen output of commands you are asking
  about
  On Thu,
  24 Sep 2015, Myriam Oliver wrote:

  > Dear Freesurfers,
  >
  > I wanted to ask you if you know how can I convert a .mgh file
  to a .obj
  > file.
  >
  > I want to run surfstats (specifically SurfStatReadSurf ) but
  it does not
  > read .mgh files (i.e, the surface file;
  lh.w-g.pct.mgh.fsaverage.mgh).
  > Although, it reads the lh.white, but I need the average, as
  otherwise I have
  > an error of matrix dimension between subjects.
  >
  > I try using the lh.white and changing the matrix dimensions
  through:
  > mri_surf2surf --s ' subjectid ' --hemi lh --sval-tal-xyz white
  --tval
  > talairach.white --tval-xyz --trgsubject ' subjectid
  >
  > But it does not work either.
  >
  > Any help about how can I use the .mgh file in surfstats?
  >
  > Thanks!
  >
  >
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--
Myriam

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[Freesurfer] dt_recon

2015-09-25 Thread Alshikho, Mohamad J.

Hi Doug and Bruce,
After running the command :
dt_recon --i 6-1025.dcm --s M87102113 --o dti dt_recon --i f.nii --b f.bvals 
f.bvecs --s M87102113 --o dti  <<< source:   Freesurfer wiki>>>

I need to generate the final statistics ( FA for every parcellate and segment 
in aseg and wmparc atlases) using the command "mri_segstats"

In order to do so I need to move "fa.nii" to anatomical space using the command:

mri_vol2vol -mov fa.nii -lta register.lta -fstarg -o fa.anat.mgh
  <<< source:   Freesurfer wiki>>>


My questions are about the file "register.lta" :

1.   What is the difference between this file and the file "register.dat" ( 
which I can see it as an output of  the command " bbregister" in the final 
analysis using the command "dt_recon")

2.   How can I generate the file " register.lta"?

3.   Can I feed the file " register.dat" instead of the file " 
register.lta" into the command "mri_vol2vol "  (in order to move the ''fa.nii" 
to anatomical space). If so which flag I should use instead of the flag "--lta" 
in the command mri_vol2vol?

Many thanks
Mohamad
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Re: [Freesurfer] .mgh file not load into surfstats

2015-09-25 Thread chenhf_uestc

Hi, Myriam

Actually, you do not need to convert a .mgh file to a .obj file, just use the 
SurfStatReadData function rather than SurfStatReadSurf. In addition, you can 
use load_mgh or MRIread function (Matlab function) in Freesurfer to read the 
mgh file.

For the error "using + Matrix dimensions must agree", I guess that the 
recon-all analyses were conducted in the subject native space, and the number 
of vertices in left/right hemi is different. You should first resample your 
data to the standard space (here, it's fsaverage space).

Hope these helps.

Best,
Feng

发件人：Myriam Oliver 
发送时间：2015-09-25 20:46
主题：Re: [Freesurfer] .mgh file not load into surfstats
收件人："Freesurfer support list"
抄送：

Hi Bruce!

Thank you for your response. Sorry about the incomplete information,

I need the average surface of each participant, so for me it will be great to 
use the output already generated for freesurfer. However, it is not read by 
surfstats. So, one solution was to change to .mgh format to .obj

The solution two can be use the lh.white which surfstats reads and change the 
matrix dimensions so I can compare all subjects. This is the command I use for 
each subject to change the matrix dimensions:

mri_surf2surf --s ' subjectid ' --hemi lh --sval-tal-xyz white --tval 
talairach.white --tval-xyz --trgsubject ' subjectid

%Average surface

left_files = SurfStatListDir([cd filesep 'lh.white.transform'], []);
right_files = SurfStatListDir([cd filesep 'rh.white.transform'], []);

f = [left_files, right_files];

avsurf = SurfStatAvSurf(f);

The error is:

Error using + Matrix dimensions must agree.

Error in SurfStatAvSurf (line 36)

surf.coord=fun(surf.coord,double(s.coord));

Thank you!

2015-09-24 15:50 GMT-04:00 Bruce Fischl :

when you say "it does not work either', what do you mean? Please remember
to send us the entire screen output of commands you are asking about
On Thu,

24 Sep 2015, Myriam Oliver wrote:

> Dear Freesurfers,
>
> I wanted to ask you if you know how can I convert a .mgh file to a .obj
> file.
>
> I want to run surfstats (specifically SurfStatReadSurf ) but it does not
> read .mgh files (i.e, the surface file; lh.w-g.pct.mgh.fsaverage.mgh).
> Although, it reads the lh.white, but I need the average, as otherwise I have
> an error of matrix dimension between subjects.
>
> I try using the lh.white and changing the matrix dimensions through:
> mri_surf2surf --s ' subjectid ' --hemi lh --sval-tal-xyz white --tval
> talairach.white --tval-xyz --trgsubject ' subjectid
>
> But it does not work either.
>
> Any help about how can I use the .mgh file in surfstats?
>
> Thanks!
>
>

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[Freesurfer] high area.pial values

Re: [Freesurfer] Longitudinal Two Stage Model using mri_glmfit

[Freesurfer] The range of value of the area file

Re: [Freesurfer] different layer ROI

Re: [Freesurfer] high area.pial values

Re: [Freesurfer] different layer ROI

Re: [Freesurfer] different layer ROI

Re: [Freesurfer] different layer ROI

Re: [Freesurfer] different layer ROI

Re: [Freesurfer] different layer ROI

[Freesurfer] 3_group_comparison

[Freesurfer] postdoc - UT Houston - neuroimaging of mood disorders {Disarmed}

Re: [Freesurfer] .mgh file not load into surfstats

Re: [Freesurfer] .mgh file not load into surfstats

[Freesurfer] dt_recon

Re: [Freesurfer] .mgh file not load into surfstats

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