Re: [Freesurfer] Tksurfer + Histogram

[Saurabh Thakur]

Thanks for reply bruce.

I got my mistake.Actually i am learning Cortical thickness using
freesurfer.In which ROI5.nii n *TT_avg152T1.nii*. image is required which i
took from our own data set,but didnt have thickness file for surface to
surface mapping.Now i will do recon all on my data set to get complete
information.Thanks again for your advice.

cheers
Saurabh Thakur,






On Wed, Mar 26, 2014 at 5:59 PM, Bruce Fischl wrote:

> Hi Saurabh
>
> I'm not sure I understand. This is the purpose of recon-all - to generate
> morphomological models, including the thickness estimates in lh.thickness.
> Is that would you mean? BTW: I wouldn't look at thickness in the
> hippocampus, the results will be unreliable due to all the internal
> structure in the hippocampus that is not well-resolved at current
> resolutions.
>
> cheers
> Bruce
>
>
> On Wed, 26 Mar 2014, Saurabh Thakur wrote:
>
>  Hello Bruce,
>>
>> I am referring to link
>>
>> http://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness
>>
>> to calculate the cortical thickness of particular area such as Left
>> hippocampus for our own data set.
>>
>> But i am looking for forward to generate lh.thickness file in freesurfer
>> for
>> own data set which can be used as overlay. (Used for surface to surface
>> overlay)
>>
>> Can u suggest how to generate lh.thickness file for my own data using
>> freesurfer...?
>>
>> Thanks in advanced.
>>
>> cheers
>> Saurabh Thakur,
>>
>>
>>
>>
>>
>>
>> On Tue, Mar 11, 2014 at 10:28 PM, Bruce Fischl <
>> fis...@nmr.mgh.harvard.edu>
>> wrote:
>>   try configure->functional overlay or something like that after
>>   loading the thickness into a functional overlay
>>   On Tue, 11 Mar 2014, Saurabh Thakur wrote:
>>
>> I am referring one paper.
>> It mentioned about the freesurfer and cortical
>> thickness they hv got in
>> tksurfer.
>>
>> I m just want to know how to get that done in
>> tksurfer.
>>
>> I hv attached that paper for the reference.
>>
>> cheers
>> Saurabh Thakur,
>>
>>
>>
>>
>>
>>
>> On Tue, Mar 11, 2014 at 7:14 AM, Bruce Fischl
>> 
>> wrote:
>>   what is it that you want to histogram? If the
>> thickness,
>>   tksurfer will do
>>   this for you if you load it as an overlay. Or
>> you can read it
>>   into matlab
>>   and show it there
>>
>>   On Tue, 11 Mar 2014, Saurabh Thakur
>>   wrote:
>>
>>   > Hello Freesurfer Expert,
>>   >
>>   > Can anyone help me with histogram plotting
>> of different
>>   surfaces in
>>   > tksurfer.
>>   >
>>   > I looking to calculate the thickness of
>> cortex.
>>   >
>>   > Thanks in advance,
>>   >
>>   >
>>   > Saurabh Thakur,
>>   >
>>   >
>>   >
>>   >
>>   >
>>   >
>> ___
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Re: [Freesurfer] MNI CONVERSION PROBLEM

[Douglas Greve]

What is your vol2vol command line?


On 3/26/14 3:58 PM, Gabriel Gonzalez Escamilla wrote:

Dear FS experts,


I've been dealing with the conversion to MNI152 of some volumetric 
labels of my subjects extracted with mris_extract_label in FS v.5.1 
but, I've been unable to succeed.



I've tried bbregister and mni152reg commands, both of them give me an 
example to check at the registrations using tktegister2, when I use it 
everything seems to be OK, but when I do apply with mri_vol2vol any of 
the matrices to the volumetric masks, they appear to be rotated, I 
don't know how is it possible or how to fix it.



Any help will be really appreciated.


Many thanks in advanced,
Gabriel


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[Freesurfer] Surface area issue in longitudinal studies

[Paul Mazaika]

We are using Freesurfer v5.3 with the recent Jacobian area correction, but 
there may be a subtle bug that affects longitudinal studies. In a pediatric 
population, we see area growth on top of gyrii, and area loss in the base of 
sulci. This effect may be a true morphological change, but it may be due to an 
approximation error of a curved area by planar surfaces in regions of high 
curvature. Is there a command or script to compute an "adjusted area" on a 
vertex-wise basis? For every vertex, I would like to compute something like:
Adjusted area = Area*(1 + G*d^2*k^2)
where Area is the v5.3 area, G is a constant, d is the local vertex spacing, 
and k is the local mean curvature.

Thank you,
Paul K. Mazaika
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[Freesurfer] recon error

[Xiaomin Yue]

Hi, 
I got this error while running recon:  'imgreg_4dfp 
/opt/freesurfer-530/average/711-2C_as_mni_average_305 
/opt/freesurfer-530/average/711-2B_as_mni_average_305_mask talsrcimg_g11 none 
talsrcimg_to_711-2C_as_mni_average_305_t4 1283' failed! status=254ERROR: 
mpr2mni305 execution aborted
Xiaomin
From: yu...@hotmail.com
To: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] fsfast question
Date: Wed, 26 Mar 2014 17:03:48 -0400





Thanks very much,  i will try it.
Xiaomin
From: cschwie...@mail.rockefeller.edu
Date: Wed, 26 Mar 2014 14:56:26 -0400
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] fsfast question

you could try to run mkanalysis-sess with -notask and your nuisance regressors 
specified as -nuisreg, then run selxavg3-sess with -no-con-ok and -svres to 
save the residuals. 
maybe that solves your problem? 


caspar


2014-03-26 14:38 GMT-04:00 Douglas N Greve :


No, sorry

On 03/26/2014 01:54 PM, Xiaomin Yue wrote:

> I like to regress out the linear drift, mean, and head motion

> generated by the motion correction step of fsfast from the raw time

> course only.  Is it possible using fsfast?

>

> Xiaomin

>

> > Date: Wed, 26 Mar 2014 11:28:57 -0400

> > From: gr...@nmr.mgh.harvard.edu

> > To: freesurfer@nmr.mgh.harvard.edu

> > Subject: Re: [Freesurfer] fsfast question

> >

> >

> > Sorry, I don't follow what you are asking. FSFAST does not do any drift

> > removal from the raw data, all of that is in the design matrix

> > doug

> >

> > On 03/26/2014 10:45 AM, Xiaomin Yue wrote:

> > > Hi,

> > >

> > > The analysis necessary to my study is to run some analysis on the raw

> > > time course data. Before working on the raw time course data, it is

> > > necessary to remove linear drifting, mean, and head motion. Can I

> > > just specify those parameters without having conditions in the steps

> > > of generating design matrix? If so, what command should be used?

> > >

> > > Thanks,

> > > Xiaomin Yue

> > >

> > >

> > > ___

> > > Freesurfer mailing list

> > > 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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> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

> >

> >

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> 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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> > but does not contain patient information, please contact the sender

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> > dispose of the e-mail.

> >

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>

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Re: [Freesurfer] fsfast question

[Xiaomin Yue]

Thanks very much,  i will try it.
Xiaomin
From: cschwie...@mail.rockefeller.edu
Date: Wed, 26 Mar 2014 14:56:26 -0400
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] fsfast question

you could try to run mkanalysis-sess with -notask and your nuisance regressors 
specified as -nuisreg, then run selxavg3-sess with -no-con-ok and -svres to 
save the residuals. 
maybe that solves your problem? 


caspar


2014-03-26 14:38 GMT-04:00 Douglas N Greve :


No, sorry

On 03/26/2014 01:54 PM, Xiaomin Yue wrote:

> I like to regress out the linear drift, mean, and head motion

> generated by the motion correction step of fsfast from the raw time

> course only.  Is it possible using fsfast?

>

> Xiaomin

>

> > Date: Wed, 26 Mar 2014 11:28:57 -0400

> > From: gr...@nmr.mgh.harvard.edu

> > To: freesurfer@nmr.mgh.harvard.edu

> > Subject: Re: [Freesurfer] fsfast question

> >

> >

> > Sorry, I don't follow what you are asking. FSFAST does not do any drift

> > removal from the raw data, all of that is in the design matrix

> > doug

> >

> > On 03/26/2014 10:45 AM, Xiaomin Yue wrote:

> > > Hi,

> > >

> > > The analysis necessary to my study is to run some analysis on the raw

> > > time course data. Before working on the raw time course data, it is

> > > necessary to remove linear drifting, mean, and head motion. Can I

> > > just specify those parameters without having conditions in the steps

> > > of generating design matrix? If so, what command should be used?

> > >

> > > Thanks,

> > > Xiaomin Yue

> > >

> > >

> > > ___

> > > Freesurfer mailing list

> > > 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/

> >

> > ___

> > 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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Phone Number: 617-724-2358

Fax: 617-726-7422



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[Freesurfer] MNI CONVERSION PROBLEM

[Gabriel Gonzalez Escamilla]

Dear FS experts,


I've been dealing with the conversion to MNI152 of some volumetric labels of my 
subjects extracted with mris_extract_label in FS v.5.1 but, I've been unable to 
succeed.


I've tried bbregister and mni152reg commands, both of them give me an example 
to check at the registrations using tktegister2, when I use it everything seems 
to be OK, but when I do apply with mri_vol2vol any of the matrices to the 
volumetric masks, they appear to be rotated, I don't know how is it possible or 
how to fix it.


Any help will be really appreciated.


Many thanks in advanced,
Gabriel 
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Re: [Freesurfer] fsfast question

[Caspar M. Schwiedrzik]

you could try to run mkanalysis-sess with -notask and your nuisance
regressors specified as -nuisreg, then run selxavg3-sess with -no-con-ok
and -svres to save the residuals.
maybe that solves your problem?
caspar


2014-03-26 14:38 GMT-04:00 Douglas N Greve :

> No, sorry
> On 03/26/2014 01:54 PM, Xiaomin Yue wrote:
> > I like to regress out the linear drift, mean, and head motion
> > generated by the motion correction step of fsfast from the raw time
> > course only.  Is it possible using fsfast?
> >
> > Xiaomin
> >
> > > Date: Wed, 26 Mar 2014 11:28:57 -0400
> > > From: gr...@nmr.mgh.harvard.edu
> > > To: freesurfer@nmr.mgh.harvard.edu
> > > Subject: Re: [Freesurfer] fsfast question
> > >
> > >
> > > Sorry, I don't follow what you are asking. FSFAST does not do any drift
> > > removal from the raw data, all of that is in the design matrix
> > > doug
> > >
> > > On 03/26/2014 10:45 AM, Xiaomin Yue wrote:
> > > > Hi,
> > > >
> > > > The analysis necessary to my study is to run some analysis on the raw
> > > > time course data. Before working on the raw time course data, it is
> > > > necessary to remove linear drifting, mean, and head motion. Can I
> > > > just specify those parameters without having conditions in the steps
> > > > of generating design matrix? If so, what command should be used?
> > > >
> > > > Thanks,
> > > > Xiaomin Yue
> > > >
> > > >
> > > > ___
> > > > Freesurfer mailing list
> > > > 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/
> > >
> > > ___
> > > 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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> > 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
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> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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>
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Re: [Freesurfer] B1 correction

[Bruce Fischl]

you should probably apply it before giving the data to recon-all

cheers
Bruce
On Wed, 26 
Mar 2014, Xiaomin Yue wrote:



Hi Bruce,
You are correct that it is B1.  How could I incorporate this data into the
reconstruction stream?

Thanks,
Xiaomin


From: yu...@hotmail.com
To: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] B1 correction
Date: Wed, 26 Mar 2014 13:54:37 -0400

thanks.
Xiaomin Yue

Date: Wed, 26 Mar 2014 11:54:58 -0400
From: fis...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] B1 correction

Hi Xiaomin

do you mean dividing by the Jacobian of the B0 unwarping field? Are you 
sure it's not B1? That is by far the more common intensity normalization 
for an mprage. The B0 effects are small due to the high bandwidth of the 
mprage.


I think Rudolph and/or Doug have tools for multiplying or dividing images, 
but I'm not sure what they are called.


cheers Bruce


On Wed, 26 Mar 2014, Xiaomin Yue wrote:

> Hi Bruce,
> Thanks for your response.  It is B0 normalization scan.  What it does is t
o
> get an homogeneity image, which could be used to normalize the MRRAGE imag
e
> by dividing it.  Is there an build in function in freesurfer to do this
> operation?
> 
> Thanks,

> Xiaomin 
> 
> Date: Mon, 24 Mar 2014 12:42:52 -0400

> From: fis...@nmr.mgh.harvard.edu
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] B1 correction
> 
> Hi Xiaomin
> 
> can you be more specific? What kind of B1 field map did you collect? Do 
> you mean B1 transmit or receive?
> 
> cheers

> Bruce
> On Mon, 24 Mar 2014, Xiaomin Yue wrote:
> 
> > Hi,
> > 
> > B1 field correction was collected during the scan.  My question is how i
t 
> can be used in the surface reconstruction?
> > 
> > Thanks,
> > 
> > Xiaomin Yue
> > 
> >
> 
> ___ Freesurfer mailing list

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on
> in this e-mail is intended only for the person to whom it is addressed. If
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Re: [Freesurfer] fsfast question

[Douglas N Greve]

that might work. You'd have to make sure that you specified native space 
in mkanalysis-sess
doug

On 03/26/2014 02:56 PM, Caspar M. Schwiedrzik wrote:
> you could try to run mkanalysis-sess with -notask and your nuisance 
> regressors specified as -nuisreg, then run selxavg3-sess with 
> -no-con-ok and -svres to save the residuals.
> maybe that solves your problem?
> caspar
>
>
> 2014-03-26 14:38 GMT-04:00 Douglas N Greve  >:
>
> No, sorry
> On 03/26/2014 01:54 PM, Xiaomin Yue wrote:
> > I like to regress out the linear drift, mean, and head motion
> > generated by the motion correction step of fsfast from the raw time
> > course only.  Is it possible using fsfast?
> >
> > Xiaomin
> >
> > > Date: Wed, 26 Mar 2014 11:28:57 -0400
> > > From: gr...@nmr.mgh.harvard.edu 
> > > To: freesurfer@nmr.mgh.harvard.edu
> 
> > > Subject: Re: [Freesurfer] fsfast question
> > >
> > >
> > > Sorry, I don't follow what you are asking. FSFAST does not do
> any drift
> > > removal from the raw data, all of that is in the design matrix
> > > doug
> > >
> > > On 03/26/2014 10:45 AM, Xiaomin Yue wrote:
> > > > Hi,
> > > >
> > > > The analysis necessary to my study is to run some analysis
> on the raw
> > > > time course data. Before working on the raw time course
> data, it is
> > > > necessary to remove linear drifting, mean, and head motion.
> Can I
> > > > just specify those parameters without having conditions in
> the steps
> > > > of generating design matrix? If so, what command should be used?
> > > >
> > > > Thanks,
> > > > Xiaomin Yue
> > > >
> > > >
> > > > ___
> > > > Freesurfer mailing list
> > > > 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/
> > >
> > > ___
> > > 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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> > 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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gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] B1 correction

[Xiaomin Yue]

Hi Bruce,
You are correct that it is B1.  How could I incorporate this data into the 
reconstruction stream?
Thanks,Xiaomin

From: yu...@hotmail.com
To: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] B1 correction
Date: Wed, 26 Mar 2014 13:54:37 -0400




thanks.
Xiaomin Yue

Date: Wed, 26 Mar 2014 11:54:58 -0400
From: fis...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] B1 correction

Hi Xiaomin
 
do you mean dividing by the Jacobian of the B0 unwarping field? Are you 
sure it's not B1? That is by far the more common intensity normalization 
for an mprage. The B0 effects are small due to the high bandwidth of the 
mprage.
 
I think Rudolph and/or Doug have tools for multiplying or dividing images, 
but I'm not sure what they are called.
 
cheers Bruce
 
 
On Wed, 26 Mar 2014, Xiaomin Yue wrote:
 
> Hi Bruce,
> Thanks for your response.  It is B0 normalization scan.  What it does is to
> get an homogeneity image, which could be used to normalize the MRRAGE image
> by dividing it.  Is there an build in function in freesurfer to do this
> operation?
> 
> Thanks,
> Xiaomin 
> 
> Date: Mon, 24 Mar 2014 12:42:52 -0400
> From: fis...@nmr.mgh.harvard.edu
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] B1 correction
> 
> Hi Xiaomin
> 
> can you be more specific? What kind of B1 field map did you collect? Do 
> you mean B1 transmit or receive?
> 
> cheers
> Bruce
> On Mon, 24 Mar 2014, Xiaomin Yue wrote:
> 
> > Hi,
> > 
> > B1 field correction was collected during the scan.  My question is how it 
> can be used in the surface reconstruction?
> > 
> > Thanks,
> > 
> > Xiaomin Yue
> > 
> >
> 
> ___ Freesurfer mailing list
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> 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
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> and properly dispose of the e-mail.
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Re: [Freesurfer] mris_anatomical_stats aparc pial and aparcstats2table

[Louis Nicholas Vinke]

Hi Andreia,
If you remove the underscore from aparc_pial for the --parc flag in the 
aparcstats2table command, that should do the trick.
-Louis

On Wed, 26 Mar 2014, _andre...@sapo.pt wrote:

> Hello list,
>
> I'm trying to get aparc surface area from the pial surface in a table
> using aparcstats2table but I'm not being able to...
>
> I've already created the file aparc_pial.stats inside the stats dir
> running the following command line from the subjects's label dir:
>
> mris_anatomical_stats -mgz -f ../stats/rh.aparcpial -b -a
> ./rh.aparc.annot -c ./aparc.ctab subjectname rh pial
>
> And if I open the aparc_pial.stats file the surfaces are bigger then
> in aparc (white matter).
>
> But when I try to get the table using:
>
> aparcstats2table --hemi rh --subjects subjectname --parc aparc_pial
> --meas area -t rh_aparc_surface_pial.txt
>
> I get the message:
>
> Number of subjects : 1
> Building the table..
> ERROR: cannot find
> /home/user/visao/Freesurfer/subjectname/stats/rh.aparc_pial.stats
> Use --skip flag if you want to continue in such cases
>
> What's wrong?
>
> Thank you,
> Andreia
>
>
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Re: [Freesurfer] fsfast question

[Douglas N Greve]

No, sorry
On 03/26/2014 01:54 PM, Xiaomin Yue wrote:
> I like to regress out the linear drift, mean, and head motion 
> generated by the motion correction step of fsfast from the raw time 
> course only.  Is it possible using fsfast?
>
> Xiaomin
>
> > Date: Wed, 26 Mar 2014 11:28:57 -0400
> > From: gr...@nmr.mgh.harvard.edu
> > To: freesurfer@nmr.mgh.harvard.edu
> > Subject: Re: [Freesurfer] fsfast question
> >
> >
> > Sorry, I don't follow what you are asking. FSFAST does not do any drift
> > removal from the raw data, all of that is in the design matrix
> > doug
> >
> > On 03/26/2014 10:45 AM, Xiaomin Yue wrote:
> > > Hi,
> > >
> > > The analysis necessary to my study is to run some analysis on the raw
> > > time course data. Before working on the raw time course data, it is
> > > necessary to remove linear drifting, mean, and head motion. Can I
> > > just specify those parameters without having conditions in the steps
> > > of generating design matrix? If so, what command should be used?
> > >
> > > Thanks,
> > > Xiaomin Yue
> > >
> > >
> > > ___
> > > Freesurfer mailing list
> > > 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/
> >
> > ___
> > 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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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
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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
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] B1 correction

[Xiaomin Yue]

thanks.
Xiaomin Yue

Date: Wed, 26 Mar 2014 11:54:58 -0400
From: fis...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] B1 correction

Hi Xiaomin
 
do you mean dividing by the Jacobian of the B0 unwarping field? Are you 
sure it's not B1? That is by far the more common intensity normalization 
for an mprage. The B0 effects are small due to the high bandwidth of the 
mprage.
 
I think Rudolph and/or Doug have tools for multiplying or dividing images, 
but I'm not sure what they are called.
 
cheers Bruce
 
 
On Wed, 26 Mar 2014, Xiaomin Yue wrote:
 
> Hi Bruce,
> Thanks for your response.  It is B0 normalization scan.  What it does is to
> get an homogeneity image, which could be used to normalize the MRRAGE image
> by dividing it.  Is there an build in function in freesurfer to do this
> operation?
> 
> Thanks,
> Xiaomin 
> 
> Date: Mon, 24 Mar 2014 12:42:52 -0400
> From: fis...@nmr.mgh.harvard.edu
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] B1 correction
> 
> Hi Xiaomin
> 
> can you be more specific? What kind of B1 field map did you collect? Do 
> you mean B1 transmit or receive?
> 
> cheers
> Bruce
> On Mon, 24 Mar 2014, Xiaomin Yue wrote:
> 
> > Hi,
> > 
> > B1 field correction was collected during the scan.  My question is how it 
> can be used in the surface reconstruction?
> > 
> > Thanks,
> > 
> > Xiaomin Yue
> > 
> >
> 
> ___ 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
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> and properly dispose of the e-mail.
> 
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Re: [Freesurfer] Problem about the fMRI Analysis?

[Douglas N Greve]

Are the AFNI results already in talairach space? If so, then there is no 
point in going to surface space.
doug


On 03/26/2014 01:22 PM, Linda Xu wrote:
> I get the correlation result between two condition  of the functional 
> data by using AFNI( I do not know how to do correlation by using 
> freesurfer)
> And then I use the bbregister to aline the correlation result (produce 
> by Afni) to the anatomical result produced by using freesurfer.
> Next I using mri_vol2surf to aline the each one's functional result to 
> the  fsaverage offer by freesurfer.
> My question is :1 Should I need to do mri_vol2vol next for each subject?
>2 I have two group of subjects. I want to know 
> if there is some correlation different between them? What should I do 
> next?
> Thanks very much!
> Linda
>
>
>
> ___
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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
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Re: [Freesurfer] fsfast question

[Xiaomin Yue]

I like to regress out the linear drift, mean, and head motion generated by the 
motion correction step of fsfast from the raw time course only.  Is it possible 
using fsfast?
Xiaomin

> Date: Wed, 26 Mar 2014 11:28:57 -0400
> From: gr...@nmr.mgh.harvard.edu
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] fsfast question
> 
> 
> Sorry, I don't follow what you are asking. FSFAST does not do any drift 
> removal from the raw data, all of that is in the design matrix
> doug
> 
> On 03/26/2014 10:45 AM, Xiaomin Yue wrote:
> > Hi,
> >
> > The analysis necessary to my study is to run some analysis on the raw 
> > time course data.  Before working on the raw time course data, it is 
> > necessary to remove linear drifting, mean, and head motion.  Can I 
> > just specify those parameters without having conditions in the steps 
> > of generating design matrix?  If so, what command should be used?
> >
> > Thanks,
> > Xiaomin Yue
> >
> >
> > ___
> > Freesurfer mailing list
> > 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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> 
> 
> 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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[Freesurfer] Problem about the fMRI Analysis?

[Linda Xu]

I get the correlation result between two condition  of the functional data
by using AFNI( I do not know how to do correlation by using freesurfer)
And then I use the bbregister to aline the correlation result (produce by
Afni) to the anatomical result produced by using freesurfer.
Next I using mri_vol2surf to aline the each one's  functional result to
the  fsaverage offer by freesurfer.
My question is :1 Should I need to do mri_vol2vol next for each subject?
   2 I have two group of subjects. I want to know if
there is some correlation different between them? What should I do next?
Thanks very much!
Linda
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Re: [Freesurfer] White matter edits

[Bruce Fischl]

nope, that's why we usually trust the surfaces more than the volume 
segmentations.

cheers
Bruce
On Wed, 26 Mar 2014, Eleanor Stahura wrote:

> Hello,
> I am visually checking wm.mgz after running recon-all. There seems to be a
> pattern where I'm seeing white matter "bleed" past the (correct) white
> matter surface and into gray matter or appear in the sagittal sinus/dura.
> However, when I look at wmparc.mgz, the problem is no longer there and the
> white/gray matter is correctly segmented. Even if the wmparc volume is
> correct, do I need to do white matter edits?
> 
> Thanks,
> Elle
> 
>
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[Freesurfer] White matter edits

[Eleanor Stahura]

Hello,

I am visually checking wm.mgz after running recon-all. There seems to be a
pattern where I'm seeing white matter "bleed" past the (correct) white
matter surface and into gray matter or appear in the sagittal sinus/dura.
However, when I look at wmparc.mgz, the problem is no longer there and the
white/gray matter is correctly segmented. Even if the wmparc volume is
correct, do I need to do white matter edits?

Thanks,
Elle
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Re: [Freesurfer] lgi for longitudinal scans

[Martin Reuter]

Hi Anna,

no, you would still do:

recon-all -long tpid baseid -localGI

just not use the '-all'.

Best, Martin



On 03/26/2014 11:12 AM, Anna Jonsson wrote:
thank you. But if the lnog process has already been done and these 
induviduals already have long directories so to speak, I would just 
put the lgi flag on as normal but just replace the subject name with 
the long subject name eg ?

recon-all -s _long -localGI

Thank you


On Sat, Mar 15, 2014 at 2:07 PM, Martin Reuter 
mailto:mreu...@nmr.mgh.harvard.edu>> wrote:


Hi Anna,

for the image processing, you just add the lgi flag to the regular
longitudinal recon-all command
recon-all -long .. -lgi

for the analysis after that you use the long directories.

Best, Martin

On Mar 15, 2014, at 10:04 AM, Anna Jonsson mailto:ajonsso...@gmail.com>> wrote:


Dear group,

If I want conduct gyrification analyses on the long runs that
have been through the longitudinal stream, do I just perform the
"normal" baseline command on the .long data?

thank you,

kind wishes

Anna
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reu...@mit.edu 
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  Dept. of Neurology, Massachusetts General Hospital
Research Affiliate
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[Freesurfer] removal oblique sforms

[Righart, Ruthger]

Dear Freesurfers,

To obtain an accurate volume-surface alignment of Freesurfer surfaces 
in Caret, it is advised that oblique sforms should be removed from the 
header of the t1w images. I tried to remove the sform (using 
sform_code='0' and qform='1') and changed the nii header using 
fslcreatehd.

However, something seems to go wrong, as my thickness data of the same 
subject are different than the thickness data from the original t1w 
images. In addition, alignment in Caret is still poor.
I am puzzled and I would be happy to have your suggestions about 
removing sforms. Thank you very much in advance! FS 5.3. was run on a 
Linux machine x86_64.

Ruthger

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Re: [Freesurfer] B1 correction

[Douglas N Greve]

You can use fscalc, something like

fscalc file1.mgz div file2.mgz -o file1-div-file2.nii



On 03/26/2014 11:54 AM, Bruce Fischl wrote:
> Hi Xiaomin
>
> do you mean dividing by the Jacobian of the B0 unwarping field? Are 
> you sure it's not B1? That is by far the more common intensity 
> normalization for an mprage. The B0 effects are small due to the high 
> bandwidth of the mprage.
>
> I think Rudolph and/or Doug have tools for multiplying or dividing 
> images, but I'm not sure what they are called.
>
> cheers Bruce
>
>
> On Wed, 26 Mar 2014, Xiaomin Yue wrote:
>
>> Hi Bruce,
>> Thanks for your response.  It is B0 normalization scan.  What it does 
>> is to
>> get an homogeneity image, which could be used to normalize the MRRAGE 
>> image
>> by dividing it.  Is there an build in function in freesurfer to do this
>> operation?
>>
>> Thanks,
>> Xiaomin
>>
>> Date: Mon, 24 Mar 2014 12:42:52 -0400
>> From: fis...@nmr.mgh.harvard.edu
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] B1 correction
>>
>> Hi Xiaomin
>>
>> can you be more specific? What kind of B1 field map did you collect? 
>> Do you mean B1 transmit or receive?
>>
>> cheers
>> Bruce
>> On Mon, 24 Mar 2014, Xiaomin Yue wrote:
>>
>> > Hi,
>> > > B1 field correction was collected during the scan.  My question 
>> is how it can be used in the surface reconstruction?
>> > > Thanks,
>> > > Xiaomin Yue
>> > >
>>
>> ___ Freesurfer mailing list
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>> in this e-mail is intended only for the person to whom it is 
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>> and properly dispose of the e-mail.
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>
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Re: [Freesurfer] B1 correction

[Bruce Fischl]

Hi Xiaomin

do you mean dividing by the Jacobian of the B0 unwarping field? Are you 
sure it's not B1? That is by far the more common intensity normalization 
for an mprage. The B0 effects are small due to the high bandwidth of the 
mprage.


I think Rudolph and/or Doug have tools for multiplying or dividing images, 
but I'm not sure what they are called.


cheers Bruce


On Wed, 26 Mar 2014, Xiaomin Yue wrote:


Hi Bruce,
Thanks for your response.  It is B0 normalization scan.  What it does is to
get an homogeneity image, which could be used to normalize the MRRAGE image
by dividing it.  Is there an build in function in freesurfer to do this
operation?

Thanks,
Xiaomin 

Date: Mon, 24 Mar 2014 12:42:52 -0400
From: fis...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] B1 correction

Hi Xiaomin

can you be more specific? What kind of B1 field map did you collect? Do 
you mean B1 transmit or receive?


cheers
Bruce
On Mon, 24 Mar 2014, Xiaomin Yue wrote:

> Hi,
> 
> B1 field correction was collected during the scan.  My question is how it 
can be used in the surface reconstruction?
> 
> Thanks,
> 
> Xiaomin Yue
> 
>


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Re: [Freesurfer] norm2b, norm2n

[Bruce Fischl]

Hi Jason

the only documentation is in mri_normalize --help (and the code). Try 
running it directly on your data (you can get the command line syntax from 
the recon-all.log). It only take a couple of min/call so you should be able 
to try a bunch of the options pretty quickly, then set them for recon-all 
using expert options


cheers
Bruce


On Wed, 26 Mar 2014, 
Jason Tourville wrote:



Greetings,
I am working with pediatric data and have some early evidence that running
recon-all with the flag -norm2-b 20 -norm2-n 5 improves the anterior
temporal lobe segmention as suggested in the v5.2 release notes (I am
running this with v5.3). I'd like to experiment more with this parameters to
see if I can further improve the segmentation but have been unable to find a
a description of how these parameters influence the 2nd norm. Can someone
point me to such a description?

Thanks,
Jason


Jason A. Tourville, Ph.D.
Research Assistant Professor
Department of Speech, Language,
and Hearing Sciences
Boston University
677 Beacon St.
Boston, MA 02215
Phone: (617)353-9484
Fax: (617)353-7755

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[Freesurfer] mris_anatomical_stats aparc pial and aparcstats2table

[_andreia_]

Hello list,

I'm trying to get aparc surface area from the pial surface in a table  
using aparcstats2table but I'm not being able to...

I've already created the file aparc_pial.stats inside the stats dir  
running the following command line from the subjects's label dir:

mris_anatomical_stats -mgz -f ../stats/rh.aparcpial -b -a  
./rh.aparc.annot -c ./aparc.ctab subjectname rh pial

And if I open the aparc_pial.stats file the surfaces are bigger then  
in aparc (white matter).

But when I try to get the table using:

aparcstats2table --hemi rh --subjects subjectname --parc aparc_pial  
--meas area -t rh_aparc_surface_pial.txt

I get the message:

Number of subjects : 1
Building the table..
ERROR: cannot find  
/home/user/visao/Freesurfer/subjectname/stats/rh.aparc_pial.stats
Use --skip flag if you want to continue in such cases

What's wrong?

Thank you,
Andreia


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Re: [Freesurfer] fsfast question

[Douglas N Greve]

Sorry, I don't follow what you are asking. FSFAST does not do any drift 
removal from the raw data, all of that is in the design matrix
doug

On 03/26/2014 10:45 AM, Xiaomin Yue wrote:
> Hi,
>
> The analysis necessary to my study is to run some analysis on the raw 
> time course data.  Before working on the raw time course data, it is 
> necessary to remove linear drifting, mean, and head motion.  Can I 
> just specify those parameters without having conditions in the steps 
> of generating design matrix?  If so, what command should be used?
>
> Thanks,
> Xiaomin Yue
>
>
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Re: [Freesurfer] lgi for longitudinal scans

[Anna Jonsson]

thank you. But if the lnog process has already been done and these
induviduals already have long directories so to speak, I would just put the
lgi flag on as normal but just replace the subject name with the long
subject name eg ?

recon-all -s _long -localGI

Thank you



On Sat, Mar 15, 2014 at 2:07 PM, Martin Reuter
wrote:

> Hi Anna,
>
> for the image processing, you just add the lgi flag to the regular
> longitudinal recon-all command
> recon-all -long .. -lgi
>
> for the analysis after that you use the long directories.
>
> Best, Martin
>
> On Mar 15, 2014, at 10:04 AM, Anna Jonsson  wrote:
>
> Dear group,
>
> If I want conduct gyrification analyses on the long runs that have been
> through the longitudinal stream, do I just perform the "normal" baseline
> command on the .long data?
>
> thank you,
>
> kind wishes
>
> Anna
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>
>
> -
> Dr. Martin Reuter
> Assistant in Neuroscience - Massachusetts General Hospital
> Instructor in Neurology   - Harvard Medical School
> MGH / HMS / MIT
>
> A.A.Martinos Center for Biomedical Imaging
> 149 Thirteenth Street, Suite 2301
> Charlestown, MA 02129
>
> Phone: +1-617-724-5652
> Email:
>mreu...@nmr.mgh.harvard.edu
>reu...@mit.edu
> Web  : http://reuter.mit.edu
>
>
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Re: [Freesurfer] how to capture blurred GM/WM junction?

[Douglas Greve]

On 3/26/14 8:24 AM, Markus Gschwind wrote:

Dear Doug and Bruce,

I have three more questions concerning 'pctsurfcon'.

1) The inner sampling distance is set to 1mm by default, but the outer 
sampling is done at a 30% of the cortical thickness. I saw that I 
could easily change the parameters or modify the script, but I wonder 
why this has been chosen like this. What was the rationale?
A fixed distance of 1mm was used to help prevent the WM sample from 
projecting so far back that it samples GM "behind" it. I can't remember 
how I choose 30% (instead of 50%). I think David Salat used slightly 
different parameters in his paper.


2) I think it is possible to run glmfit on the ?h.w-g.pct.mgh file in 
order to get some group stats, right?

Yes


3) Is it also possibe to run the xhemi on the w-g.pct.mgh file?

Yes
doug



Thank you so much!
Markus


2014-03-24 23:51 GMT+01:00 Markus Gschwind >:


Whow that is great!! Thank you so much Doug, I was not aware of
this! That's what I needed it seems.
Thanks Bruce and Doug!
Markus


2014-03-24 23:21 GMT+01:00 Douglas N Greve
mailto:gr...@nmr.mgh.harvard.edu>>:


you might want to look at the pctsurfcon script to see if that
gets you
where you want to be

On 03/24/2014 06:18 PM, Bruce Fischl wrote:
> it really depends on the size of the abnormality. I would
guess 2 is
> too big, and you want something more like 1, and sampling
not averaging
> On Mon, 24 Mar 2014, Markus Gschwind wrote:
>
>> Hi Bruce!
>> Ok I see, great! Tank you!
>>
>> So to double check, this will be something like :
>>
>> mri_vol2surf \
>>
>>
>>   --mov /mri/nu.mgz \
>>   --ref /mri/nu.mgz \
>>
>>   --surf /surf/lh.white
>>   --projdist mmdist -2 \ # for inside white
>>
>>
>>   # --projdist mmdist 2 \ # for outside white
>>   --interp trilinear \
>>   --hemi lh \
>>   --out lh.nu_inside_white.mgh
>>
>>
>> I am not sure which one to use from those, as I want to
compare stable
>> values but distant from white.
>>
>>
>>--projfrac-avg min max del : average along normal
>>--projdist mmdist : distance projection along normal
>>--projdist-avg min max del : average along normal
>>
>> What would you recommend?
>> Thank you again!
>> Markus
>>
>>
>>
>>
>>
>>
>>
>> 2014-03-24 21:29 GMT+01:00 Bruce Fischl
mailto:fis...@nmr.mgh.harvard.edu>>:
>>   Hi Markus
>>
>>   I wouldn't use brainmask as it has been normalized too
>>   aggressivley. Maybe the nu.mgz. Look at the
difference between
>>   values just outside of it and just inside of it
>>
>>   cheers
>>   Bruce
>>
>>
>>   On Mon, 24 Mar 2014, Markus Gschwind wrote:
>>
>> Dear Bruce,
>> Thanks for the rapid answer!
>>
>> Do you mean that I take the voxel values of
>> brainmask.mgz at the place where
>> the ?h.white surface passes, right?
>>
>> I thought that the ?l.white surface marks the limit
>> between GM and WM as a
>> result of a binary decision.
>> I would be interested in the local certainty of
this
>> decision. I thought
>> this is represented by the slope between the values
>> around 70 and those
>> >100.
>>
>> Thanks again,
>> Markus
>>
>>
>>
>>
>>
>>
>> 2014-03-24 19:26 GMT+01:00 Bruce Fischl
>> mailto:fis...@nmr.mgh.harvard.edu>>:
>>   Hi Markus
>>
>>   I would think that looking at the gray/white
>> contrast across the
>>   ?h.white surface would be more informative
>>
>>   cheers
>>   Bruce
>>   On Mon, 24 Mar 2014, Markus Gschwind wrote:
>>
>> Dear all,
>> I would like to capture regions where
>> the gray
>> matter/ white matter junction is
blurred
>> in order to
>> detect possible focal
>> cortical dysplasias.
>>
>>   

Re: [Freesurfer] B1 correction

[Xiaomin Yue]

Hi Bruce,
Thanks for your response.  It is B0 normalization scan.  What it does is to get 
an homogeneity image, which could be used to normalize the MRRAGE image by 
dividing it.  Is there an build in function in freesurfer to do this operation?
Thanks,Xiaomin 

Date: Mon, 24 Mar 2014 12:42:52 -0400
From: fis...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] B1 correction

Hi Xiaomin
 
can you be more specific? What kind of B1 field map did you collect? Do 
you mean B1 transmit or receive?
 
cheers
Bruce
On Mon, 24 Mar 2014, Xiaomin Yue wrote:
 
> Hi,
> 
> B1 field correction was collected during the scan.  My question is how it can 
> be used in the surface reconstruction?
> 
> Thanks,
> 
> Xiaomin Yue
> 
>

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[Freesurfer] fsfast question

[Xiaomin Yue]

Hi,   
The analysis necessary to my study is to run some analysis on the raw time 
course data.  Before working on the raw time course data, it is necessary to 
remove linear drifting, mean, and head motion.  Can I just specify those 
parameters without having conditions in the steps of generating design matrix?  
If so, what command should be used?
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[Freesurfer] norm2b, norm2n

[Jason Tourville]

Greetings,
I am working with pediatric data and have some early evidence that running
recon-all with the flag -norm2-b 20 -norm2-n 5 improves the anterior
temporal lobe segmention as suggested in the v5.2 release notes (I am
running this with v5.3). I'd like to experiment more with this parameters
to see if I can further improve the segmentation but have been unable to
find a a description of how these parameters influence the 2nd norm. Can
someone point me to such a description?

Thanks,
Jason


Jason A. Tourville, Ph.D.
Research Assistant Professor
Department of Speech, Language,
and Hearing Sciences
Boston University
677 Beacon St.
Boston, MA 02215
Phone: (617)353-9484
Fax: (617)353-7755
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[Freesurfer] Thickness analysis on fetal brain

[stdp82]

Hi list,
we would like to perform cortical thickness analysis on fetal brain.
We have a single shot T2 image (good quality) and T1 image (poor quality). All 
images are in 2D with overlapping and they are acquired by using 1.5 tesla. 
We have some questions:
1. Do you know a post-processing way to trasform 2D in 3D images and to reduce 
motion artifacts?
2. Is adapt single shot T2 image to measure the thickness?
3. Given that we are still acquiring data, do you advise a specific protocol to 
improve T1 or other sequences?

Thank you very much,

Stefano
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Re: [Freesurfer] Tksurfer + Histogram

[Bruce Fischl]

Hi Saurabh

I'm not sure I understand. This is the purpose of recon-all - to generate 
morphomological models, including the thickness estimates in lh.thickness. 
Is that would you mean? BTW: I wouldn't look at thickness in the 
hippocampus, the results will be unreliable due to all the internal 
structure in the hippocampus that is not well-resolved at current 
resolutions.


cheers
Bruce

On Wed, 26 Mar 2014, Saurabh Thakur 
wrote:



Hello Bruce,

I am referring to link

http://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness

to calculate the cortical thickness of particular area such as Left
hippocampus for our own data set.

But i am looking for forward to generate lh.thickness file in freesurfer for
own data set which can be used as overlay. (Used for surface to surface
overlay)

Can u suggest how to generate lh.thickness file for my own data using
freesurfer...?

Thanks in advanced.

cheers
Saurabh Thakur,






On Tue, Mar 11, 2014 at 10:28 PM, Bruce Fischl 
wrote:
  try configure->functional overlay or something like that after
  loading the thickness into a functional overlay
  On Tue, 11 Mar 2014, Saurabh Thakur wrote:

I am referring one paper.
It mentioned about the freesurfer and cortical
thickness they hv got in
tksurfer.

I m just want to know how to get that done in
tksurfer.

I hv attached that paper for the reference.

cheers
Saurabh Thakur,






On Tue, Mar 11, 2014 at 7:14 AM, Bruce Fischl

wrote:
      what is it that you want to histogram? If the
thickness,
      tksurfer will do
      this for you if you load it as an overlay. Or
you can read it
      into matlab
      and show it there

      On Tue, 11 Mar 2014, Saurabh Thakur
      wrote:

      > Hello Freesurfer Expert,
      >
      > Can anyone help me with histogram plotting
of different
      surfaces in
      > tksurfer.
      >
      > I looking to calculate the thickness of
cortex.
      >
      > Thanks in advance,
      >
      >
      > Saurabh Thakur,
      >
      >
      >
      >
      >
      >
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Re: [Freesurfer] fsaverage -> fsaverage3

[Bruce Fischl]

Hi Itamar,

fsaverage3/4 are just different icosahedral supersamplings. They were 
actually used to create fsaverage (which you can think of as fsaverage7).


That is, fsaverage1 has 12 vertices, fsaverage2 42, etc..., and the first 
12 of fsaverage[234567] are the ones from fsaverage1, the first 42 in 
fsaverage[34567] are the ones from fsaverage2, etc...


cheers
Bruce

On Wed, 26 Mar 2014, Itamar Kahn 
wrote:



Greetings,

We would like to downsample surfaces (e.g. using mris_decimate) but we want to 
duplicate the way it was done with fsaverage (namely, find out how 
fsaverage3/4/5 were created from the original fsaverage). Also, we wish to be 
able to project using mri_surf2surf but we don’t have sphere registration 
available (these are fetal imaging surfaces).

Thanks,
Itamar

_
Itamar Kahn, Ph. D., Assistant Professor
Department of Physiology and Biophysics
The Ruth and Bruce Rappaport Faculty of Medicine
Technion – Israel Institute of Technology
POB 9649 Bat Galim
Haifa 31096
Israel

(o) 972-4-829-5461
http://kahnlab.technion.ac.il/
_


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Re: [Freesurfer] how to capture blurred GM/WM junction?

[Markus Gschwind]

Dear Doug and Bruce,

I have three more questions concerning 'pctsurfcon'.

1) The inner sampling distance is set to 1mm by default, but the outer
sampling is done at a 30% of the cortical thickness. I saw that I could
easily change the parameters or modify the script, but I wonder why this
has been chosen like this. What was the rationale?

2) I think it is possible to run glmfit on the ?h.w-g.pct.mgh file in order
to get some group stats, right?

3) Is it also possibe to run the xhemi on the w-g.pct.mgh file?

Thank you so much!
Markus


2014-03-24 23:51 GMT+01:00 Markus Gschwind :

> Whow that is great!! Thank you so much Doug, I was not aware of this!
> That's what I needed it seems.
> Thanks Bruce and Doug!
> Markus
>
>
> 2014-03-24 23:21 GMT+01:00 Douglas N Greve :
>
>
>> you might want to look at the pctsurfcon script to see if that gets you
>> where you want to be
>>
>> On 03/24/2014 06:18 PM, Bruce Fischl wrote:
>> > it really depends on the size of the abnormality. I would guess 2 is
>> > too big, and you want something more like 1, and sampling not averaging
>> > On Mon, 24 Mar 2014, Markus Gschwind wrote:
>> >
>> >> Hi Bruce!
>> >> Ok I see, great! Tank you!
>> >>
>> >> So to double check, this will be something like :
>> >>
>> >> mri_vol2surf \
>> >>
>> >>
>> >>   --mov /mri/nu.mgz \
>> >>   --ref /mri/nu.mgz \
>> >>
>> >>   --surf /surf/lh.white
>> >>   --projdist mmdist -2 \ # for inside white
>> >>
>> >>
>> >>   # --projdist mmdist 2 \ # for outside white
>> >>   --interp trilinear \
>> >>   --hemi lh \
>> >>   --out lh.nu_inside_white.mgh
>> >>
>> >>
>> >> I am not sure which one to use from those, as I want to compare stable
>> >> values but distant from white.
>> >>
>> >>
>> >>--projfrac-avg min max del : average along normal
>> >>--projdist mmdist : distance projection along normal
>> >>--projdist-avg min max del : average along normal
>> >>
>> >> What would you recommend?
>> >> Thank you again!
>> >> Markus
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >> 2014-03-24 21:29 GMT+01:00 Bruce Fischl :
>> >>   Hi Markus
>> >>
>> >>   I wouldn't use brainmask as it has been normalized too
>> >>   aggressivley. Maybe the nu.mgz. Look at the difference between
>> >>   values just outside of it and just inside of it
>> >>
>> >>   cheers
>> >>   Bruce
>> >>
>> >>
>> >>   On Mon, 24 Mar 2014, Markus Gschwind wrote:
>> >>
>> >> Dear Bruce,
>> >> Thanks for the rapid answer!
>> >>
>> >> Do you mean that I take the voxel values of
>> >> brainmask.mgz at the place where
>> >> the ?h.white surface passes, right?
>> >>
>> >> I thought that the ?l.white surface marks the limit
>> >> between GM and WM as a
>> >> result of a binary decision.
>> >> I would be interested in the local certainty of this
>> >> decision. I thought
>> >> this is represented by the slope between the values
>> >> around 70 and those
>> >> >100.
>> >>
>> >> Thanks again,
>> >> Markus
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >> 2014-03-24 19:26 GMT+01:00 Bruce Fischl
>> >> :
>> >>   Hi Markus
>> >>
>> >>   I would think that looking at the gray/white
>> >> contrast across the
>> >>   ?h.white surface would be more informative
>> >>
>> >>   cheers
>> >>   Bruce
>> >>   On Mon, 24 Mar 2014, Markus Gschwind wrote:
>> >>
>> >> Dear all,
>> >> I would like to capture regions where
>> >> the gray
>> >> matter/ white matter junction is blurred
>> >> in order to
>> >> detect possible focal
>> >> cortical dysplasias.
>> >>
>> >> As I understood the WM/GM segmentation
>> >> is done by
>> >> the script mri_segment.
>> >>
>> >> Would it be possible detect those
>> >> regions where the
>> >> gradient between GM and WM regions is
>> >> low?
>> >>
>> >> I imagined that running mri_segment
>> >> several times,
>> >> with each time a different lower GM
>> >> threshold and
>> >> higher WM threshold, and
>> >> then calculating the diference between
>> >> the results,
>> >> might give such information.
>> >>
>> >> I am very much interested in what you
>> >> think about
>> >> this approach and how to do it
>> >> practically.
>> >>
>> >> For info here are the optional flags of
>> >> 

Re: [Freesurfer] Tksurfer + Histogram

[Saurabh Thakur]

On Wed, Mar 26, 2014 at 2:39 PM, Saurabh Thakur  wrote:

> Hello Bruce,
> I am referring to link
> http://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness
> to calculate the cortical thickness of particular area such as Left
> hippocampus for our own data set.
> But i am looking for forward to generate lh.thickness file in freesurferfor 
> own data set which can be used as overlay. (Used for surface to surface
> overlay)
> Can u suggest how to generate lh.thickness file for my own data using
> freesurfer...?
>
> cheers
>

Hello Freesurfer Expert,
I am referring to link
http://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness
to calculate the cortical thickness of particular area ex. Left hippocampus
for our own data set.But i am looking for forward to generate lh.thickness
file in freesurfer for own data set which can be used as overlay. (Used for
surface to surface overlay). Can u suggest how to generate lh.thickness
file for my own data using freesurfer...?
Thanks,
Saurabh Thakur,
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Re: [Freesurfer] Tksurfer + Histogram

[Saurabh Thakur]

Hello Bruce,

I am referring to link

http://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness

to calculate the cortical thickness of particular area such as Left
hippocampus for our own data set.

But i am looking for forward to generate lh.thickness file in freesurfer
for own data set which can be used as overlay. (Used for surface to surface
overlay)

Can u suggest how to generate lh.thickness file for my own data using
freesurfer...?

Thanks in advanced.

cheers
Saurabh Thakur,






On Tue, Mar 11, 2014 at 10:28 PM, Bruce Fischl
wrote:

> try configure->functional overlay or something like that after loading the
> thickness into a functional overlay
>
> On Tue, 11 Mar 2014, Saurabh Thakur wrote:
>
>  I am referring one paper.
>> It mentioned about the freesurfer and cortical thickness they hv got in
>> tksurfer.
>>
>> I m just want to know how to get that done in tksurfer.
>>
>> I hv attached that paper for the reference.
>>
>> cheers
>> Saurabh Thakur,
>>
>>
>>
>>
>>
>>
>> On Tue, Mar 11, 2014 at 7:14 AM, Bruce Fischl > >
>> wrote:
>>   what is it that you want to histogram? If the thickness,
>>   tksurfer will do
>>   this for you if you load it as an overlay. Or you can read it
>>   into matlab
>>   and show it there
>>
>>   On Tue, 11 Mar 2014, Saurabh Thakur
>>   wrote:
>>
>>   > Hello Freesurfer Expert,
>>   >
>>   > Can anyone help me with histogram plotting of different
>>   surfaces in
>>   > tksurfer.
>>   >
>>   > I looking to calculate the thickness of cortex.
>>   >
>>   > Thanks in advance,
>>   >
>>   >
>>   > Saurabh Thakur,
>>   >
>>   >
>>   >
>>   >
>>   >
>>   >
>> ___
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>>
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>> contains patient information, please contact the Partners Compliance
>> HelpLine at
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>> and properly
>> dispose of the e-mail.
>>
>>
>>
>>
>>
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[Freesurfer] missing codecs for mne_make_movie

[Joseph Dien]

Hi,
   I tried to use mne_make_movie but got the following error:

Movie production selected (from data)...
Scanning /Applications/MNE-2.7.3-3268-MacOSX-i386/lib for plugins
Found lqt_mjpeg.so...Getting codec info from module
Trying to load /Applications/MNE-2.7.3-3268-MacOSX-i386/lib/lqt_mjpeg.so...
dlopen failed for /Applications/MNE-2.7.3-3268-MacOSX-i386/lib/lqt_mjpeg.so: 
dlopen(/Applications/MNE-2.7.3-3268-MacOSX-i386/lib/lqt_mjpeg.so, 2): Library 
not loaded: /opt/local/lib/libjpeg.62.dylib
  Referenced from: /Applications/MNE-2.7.3-3268-MacOSX-i386/lib/lqt_mjpeg.so
  Reason: image not found
ERROR: lqt_find_video_codec failed to find codecs!

The command was:

mne_make_movie --inv RPforMNE-eeg-inv.fif --meas RPforMNE.fif --tmin 0 --tmax 
250 --tstep 10 --stc RPforMNE --view lat --mov RPforMNE

I’m using MNE 2.7.3 under OS X 10.9.2.

Any help would be appreciated.

Joe



Joseph Dien,
Senior Research Scientist
Maryland Neuroimaging Center
University of Maryland 

E-mail: jdie...@mac.com
Phone: 202-297-8117
http://joedien.com















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