[Freesurfer] The atlas specification

[Youngsang Cho]

Hi, everybody.

 

I am wondering the specification of the atlas which is used for surface
registration.

Please answer what kinds of subjects are used and how many subjects are used
to generate the atlas included in Freesurfer.

Or please tell me the link about the atlas specification.

 

Sincerely,

 

Youngsang Cho

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Re: [Freesurfer] Vertex-by-vertex analyses within ROIS?

[Bruce Fischl]

1. Yes.
2. Ignore everything outside of the ROI and do a bonferroni correction by 
the # of vertices in the ROI.

cheers
Bruce

On Thu, 24 Mar 2011, Dalwani, Manish wrote:

> Hello Freesurfers,
>
> We are interested in comparing cortical thickness in 2 groups. Due to small 
> sample size (and thus less power), we are swaying away from whole-brain 
> vertex analyses.  Instead we would like to compare specific ROIs between two 
> groups.  We understand that we can get an estimate of average cortical 
> thickness from each ROI. We fear that by comparing those estimates over a 
> large ROI may cause it to be less sensitive in picking up a very small region 
> of severe cortical thinning.
>
> Therefore, our questions are as follows:
>
> 1.  Can we perform vertex-by-vertex analyses between groups but not on 
> whole-brain and only on the specific apriori ROIs?
> 2.  If we can do vertex-by-vertex ROI analyses, is there a reasonable 
> statistical method to correct for multiple comparisons?
>
> Kindly advise!
>
> Regards,
> Manish Dalwani
> Sr. PRA
> Dept. of Psychiatry
> University of Colorado Denver
> Tel: 303-724-3185
> Email: manish.dalw...@ucdenver.edu
>
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[Freesurfer] N3 correction issues

[Nandita Vijayakumar]

Hi all,



We are processing longitudinal structural MRI data on Freesurfer 5. 0.  As our
images have some intensity problems, we were running an N3 correction
outside of FreeSurfer using a mask in order to maximize this step (as per
recommended by Boyes et al., 2008). We first ran autorecon1 and then used
the brainsmask.mgz as a mask for the N3 correction, using the following
steps.



mri_convert orig.mgz orig.mnc

mri_binarize --i brainmask.mgz --min 1 --o binmask.mgz*

mri_convert binmask.mgz binmask.mnc*

mincnorm orig.mnc orig_norm.mnc

nu_correct -mask binmask.mnc -distance 50 -iterations 1000 -stop 0.0001
-shrink 2 -fwhm .05 orig_norm.mnc nu.mnc

mri_convert nu.mnc nu.mgz*



This nu.mgz was then fed into freesurfer and autorecon1 was run over
again without
nuintensity correction. However, during this step, many of our scans are
crashing, with the T1.mgz being very dark. When the same scans were run
through Freesurfer with the nuintensitycor-3T flag (without using a mask),
there were no crashes. Do you have any advice on why the N3 correction using
the mask is crashing when re-running autorecon 1? Should we be using
different nu_correct parameters to help the process?



Thanks for your help!



Nandi
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[Freesurfer] Vertex-by-vertex analyses within ROIS?

[Dalwani, Manish]

Hello Freesurfers,

We are interested in comparing cortical thickness in 2 groups. Due to small 
sample size (and thus less power), we are swaying away from whole-brain vertex 
analyses.  Instead we would like to compare specific ROIs between two groups.  
We understand that we can get an estimate of average cortical thickness from 
each ROI. We fear that by comparing those estimates over a large ROI may cause 
it to be less sensitive in picking up a very small region of severe cortical 
thinning.

Therefore, our questions are as follows:

 1.  Can we perform vertex-by-vertex analyses between groups but not on 
whole-brain and only on the specific apriori ROIs?
 2.  If we can do vertex-by-vertex ROI analyses, is there a reasonable 
statistical method to correct for multiple comparisons?

Kindly advise!

Regards,
Manish Dalwani
Sr. PRA
Dept. of Psychiatry
University of Colorado Denver
Tel: 303-724-3185
Email: manish.dalw...@ucdenver.edu
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Re: [Freesurfer] Fwd: fMRI and anatomical T1 overlaid

[Douglas N Greve]

You need to include a registration file with your tksurfer command, 
something like:
tksurfer subjectid rh inflated -reg featdir/reg/freesurfer/register.dat 
-overlay featdir/rendered_thresh_zstat1.nii.gz

Did you check the registration with tkregister2? If not, do so first.
You can also load it on the volume witth:

tkmedit subjectid orig -reg featdir/reg/freesurfer/register.dat -overlay 
featdir/rendered_thresh_zstat1.nii.gz

doug



leonardo kay wrote:
> Thanks Doug.
>
> After doing reg-feat2anat , I checked the registration and overlaid 
> zstat file:
>
> tksurfer subjectid rh inflated -overlay 
> featdir/rendered_thresh_zstat1.nii.gz
>
> I have attached an image of tksurfer interface . I'm not quite sure 
> about what blue and red clusters mean. They are suposed to be 
> activations, but I'm not watching the same in FSL-view. Could you give 
> me a hand please? Am I using the right stat file?
>
> Thanks in advance
> best regards.
>
>
>
> -- Forwarded message --
> From: *Douglas N Greve*  >
> Date: 2011/3/23
> Subject: Re: [Freesurfer] [Fressurfer] fMRI and anatomical T1
> To: leonardo kay mailto:leonardo@gmail.com>>
> Cc: freesurfer@nmr.mgh.harvard.edu 
>
>
> There is a tutorial on this on our wiki. Basically, you need to run 
> reg-feat2anat to get a registration file, then run tksurfer passing it 
> the registration file and the stat volume as the overlay.
>
>
> doug
>
> leonardo kay wrote:
>
> Hi all
>
> Can anyone help me overlaying fMRI activations from fsl on a
> anatomical T1 volume in freesurfer.
> Is there any previous format conversion to do before?
>
> Thanks in advance
> best regards,
>
> -- 
> Leo Kay.
>
> 
>
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> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu 
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>
>
>
> The information in this e-mail is intended only for the person to whom 
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> e-mail
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>
>
>
>
> -- 
> Leo Kay.
>
>
> 
>
> 
>
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[Freesurfer] Fwd: fMRI and anatomical T1 overlaid

[leonardo kay]

Thanks Doug.

After doing reg-feat2anat , I checked the registration and overlaid zstat
file:

tksurfer subjectid rh inflated -overlay
featdir/rendered_thresh_zstat1.nii.gz

I have attached an image of tksurfer interface . I'm not quite sure about
what blue and red clusters mean. They are suposed to be activations, but I'm
not watching the same in FSL-view. Could you give me a hand please? Am I
using the right stat file?

Thanks in advance
best regards.



-- Forwarded message --
From: Douglas N Greve 
Date: 2011/3/23
Subject: Re: [Freesurfer] [Fressurfer] fMRI and anatomical T1
To: leonardo kay 
Cc: freesurfer@nmr.mgh.harvard.edu


There is a tutorial on this on our wiki. Basically, you need to run
reg-feat2anat to get a registration file, then run tksurfer passing it the
registration file and the stat volume as the overlay.


doug

leonardo kay wrote:

> Hi all
>
> Can anyone help me overlaying fMRI activations from fsl on a anatomical T1
> volume in freesurfer.
> Is there any previous format conversion to do before?
>
> Thanks in advance
> best regards,
>
> --
> Leo Kay.
>
> 
>
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 Fax: 617-726-7422

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-- 
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Re: [Freesurfer] single subject versus a group map in qdec

[Derin Cobia]

I'm curious about the use of this method as well (thanks for the paper PPJ).  
Bruce/Doug, how exactly does QDEC treat this design?  Can a single-subject 
comparison properly be done?  Thanks.  

-Derin


On Mar 23, 2011, at 4:11 PM, Pedro Paulo de Magalhães Oliveira Junior wrote:

> We have dono something like this in Cortical thickness reduction of normal 
> appearing cortex in patients with polymicrogyria
> 
> cheers,
> 
> PPJ
> -
> Pedro Paulo de Magalhães Oliveira Junior
> Diretor de Operações
> Netfilter & SpeedComm Telecom
> -- www.netfilter.com.br
> -- For mobile: http://www.netfilter.com.br/mobile
> 
> 
> 
> 
> On Wed, Mar 23, 2011 at 14:21, Emily Rogalski  wrote:
> Using q dec we have run a single patient versus a group of healthy control 
> subjects (n=20ish) and found significant differences even after FDR 
> correction.
> 
> Could you describe the process qdec uses to compute these differences? 
> Is it legitimate to report these single subject maps?
> Practically this is very useful for case reports but Im concerned about 
> violating statistical rules. 
> 
> Thanks!
> -- 
> Emily J Rogalski, PhD
> Assistant Research Professor
> Northwestern University
> Cognitive Neurology and Alzheimer's Disease Center (CNADC)
> 320 E Superior Street
> Searle Building 11th Floor
> Chicago, IL 60611
> 312-503-1155 phone
> 312-908-8789 fax
> erogal...@gmail.com
> 
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Re: [Freesurfer] parametric modulator with FS-FAST

[Douglas N Greve]

Hi Yuko, this has been asked about several times, so I just prepared as 
wiki page for it:

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

Take a look and let me know if you have any questions.

doug



Yuko Yotsumoto wrote:
> Hi,
>
> I am wondering whether it is possible to use "parametric modulator 
> (SPM term)" in FS-FAST.
>
> For example, say I have 4 experimental conditions. These conditions 
> are not independent. Conditions 1-4 are determined post-hoc by 
> subjects responses - for example, attractiveness judgements.
> Condition 1 for least attractive, condition 4 for most attractive.. 
> and so on. Instead of making contrasts for each condition, I'd like to 
> find areas that show linear relationships (= % signal changes) with 
> the regressors (=attractiveness judgements). I heard there is a way to 
> do this with SPM, but I'd like to do this with FS-FAST.
>
> I found this post in the archive, but I need some more info.
> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg14181.html
>
> Thanks!
> Yuko Yotsumoto
> ---
> Yuko Yotsumoto, Ph. D.
> Associate Professor 
> The Global Centers of Excellence Program, Keio University
>
> TEL:011-81-3-5427-1156 x 23851
> e-mail: yuk...@a7.keio.jp
> HP  : http://web.keio.jp/~yukoyy/
> 
>
> 
>
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[Freesurfer] isxconcat-sess question

[SK]

Hi,



Is there a way to use” isxconcat-sess” to average monkey fMRI data? i.e.  I
have two groups of monkeys (say, test and control groups) and I want to do
group analysis on their data..



Regards,

krishna
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[Freesurfer] ROI-based fixed effect analysis

[ye xiao]

Hi everyone,

Is there any way to do ROI-based fixed effect group analysis in
Freesurfer? I want to get the average ces and cesvar (fixed effect) in
a specific ROI. Can I just average the gamma and gammavar that in the
osgm folder after I ran the voxel-based ffx group analysis in that ROI
to get those values, if I have a group data defined ROI? And how to
average the gammavar in a ROI? Just mean(gammavar), or
sqrt(mean(gammavar^2))?

Thanks very much for the answers.

regards,

Qi Zhu
Laboratorium voor Neuro- en Psychofysiologie
K.U.Leuven Medical School
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Re: [Freesurfer] data preparation for SVM classification

[Alexander Ivanov]

Thank you very much for such a quick response!

I am going to classify two group of patients: responders versus
non-responders... As the matter of fact, I also have fMRI and DTI data of
these subjects - but I would prefer to start from structural images...
Therefore I'd like to clarify structural (and possibly functional) patterns
of non-responders and try to make predictions...

Thank you for your time!

... and for the advertisement=) I'm reading that right now...
---
*Regards,*
*Alex*
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Re: [Freesurfer] data preparation for SVM classification

[Pedro Paulo de Magalhães Oliveira Junior]

Sorry for the advertisement :)

I wrote a paper using this technique:

Use of SVM methods with surface-based cortical and volumetric subcortical
measurements to detect Alzheimer's
disease.

Oliveira PP Jr, Nitrini R, Busatto G, Buchpiguel C, Sato JR, Amaro E Jr.

J Alzheimers Dis. 2010;19(4):1263-72.
 PMID:  20061613  [PubMed - indexed for MEDLINE]



On Thu, Mar 24, 2011 at 09:10, Bruce Fischl wrote:

> what are you trying to classify and what is your hypothesis?
>
> cheers,
> Bruce
> On Thu, 24 Mar
> 2011, Alexander Ivanov wrote:
>
> > *Dear Freesurfers,*
> >
> > Could you please suggest me the best way to prepare structural data for
> SVM
> > classification? I googled, searched the archives - there're no examples
> of
> > such preparation using freesurfer algorithms (to my knowledge)...
> > Thank you beforehand.
> > ---
> > *Regards,*
> > *A. Hasfatin*
> >
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Re: [Freesurfer] data preparation for SVM classification

[Bruce Fischl]

what are you trying to classify and what is your hypothesis?

cheers,
Bruce
On Thu, 24 Mar 
2011, Alexander Ivanov wrote:

> *Dear Freesurfers,*
>
> Could you please suggest me the best way to prepare structural data for SVM
> classification? I googled, searched the archives - there're no examples of
> such preparation using freesurfer algorithms (to my knowledge)...
> Thank you beforehand.
> ---
> *Regards,*
> *A. Hasfatin*
>
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[Freesurfer] data preparation for SVM classification

[Alexander Ivanov]

*Dear Freesurfers,*

Could you please suggest me the best way to prepare structural data for SVM
classification? I googled, searched the archives - there're no examples of
such preparation using freesurfer algorithms (to my knowledge)...
Thank you beforehand.
---
*Regards,*
*A. Hasfatin*
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[Freesurfer] parametric modulator with FS-FAST

[Yuko Yotsumoto]

Hi,

I am wondering whether it is possible to use "parametric modulator (SPM term)" 
in FS-FAST.

For example, say I have 4 experimental conditions. These conditions are not 
independent. Conditions 1-4 are determined post-hoc by subjects responses - for 
example, attractiveness judgements.
Condition 1 for least attractive, condition 4 for most attractive.. and so on. 
Instead of making contrasts for each condition, I'd like to find areas that 
show linear relationships (= % signal changes) with the regressors 
(=attractiveness judgements). I heard there is a way to do this with SPM, but 
I'd like to do this with FS-FAST.

I found this post in the archive, but I need some more info.
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg14181.html

Thanks!
Yuko Yotsumoto
---
Yuko Yotsumoto, Ph. D.
Associate Professor 
The Global Centers of Excellence Program, Keio University

TEL:011-81-3-5427-1156 x 23851
e-mail: yuk...@a7.keio.jp
HP  : http://web.keio.jp/~yukoyy/


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