[Freesurfer] FSL and freesurfer: combine runs in volume or on surface?

[Agnieszka Burzynska]

Dear all,
I am trying to figure out how to bring my fMRI data from FSL to the
freesurfer surface.

The way I understood it from the tutorial "3.0 Surface-based Group
Functional Analysis"(
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslGroupFeat)

There are two possibilities of combining multiple runs per subject:
- using mris_preproc for each run and having runs as frames in the
lh.copex.mhg file
- running first gfeat in FSL and registering gfeat copes to fsaverage ( Runs
combined in a GFEAT within a Subject), which would result in 1-frame
lh.copex.mhg file

I wonder if it is possible to say which procedure is better/more sensitive?
Should the fmri data be non-smoothed before this step for both above
options?

Thank you!
Cheers,
Aga

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[Freesurfer] Fw: manually specifying design matrix

[raka maitra]

Hello

Sorry for reposting again.
Would really appreciate a feedback on the following mail.

Thanks in advance for your time
Raka



- Forwarded Message 
From: raka maitra 
To: Douglas N Greve 
Sent: Fri, January 15, 2010 9:34:02 PM
Subject: Re: [Freesurfer] manually specifying design matrix


Thank you Doug.

I am trying to create a design matrix for repeated measures anova.

Lets say subjects A and B have been measured at sitting and standing positions.
As the same subjects have been measured at the same positions, hence both the 
factors i.e subjects and positions are fixed factors.
Hence a design matrix exploring the within subject effects of positions would 
be 
1 0 1 0
0 1 1 0
1 0 0 1
0 1 0 1
The first two columns are position and the last two are the subjects.

But mri_glmfit does not accept this design and I get the following error 
message:

'Matrix condition is 1e+08
ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08
Possible problem with experimental design:
Check for duplicate entries and/or lack of range of
continuous variables within a class.'

Looking forward to your suggestion
Thanks in advance
Raka











From: Douglas N Greve 
To: raka maitra 
Cc: freesurfer@nmr.mgh.harvard.edu
Sent: Thu, January 14, 2010 7:05:28 PM
Subject: Re: [Freesurfer] manually specifying design matrix

If you specify it manually, you don't specify groups, etc, or pass an 
fsgd file. You just create your design matrix  pass it to mri_glmfit 
directly with the --X flag.

doug

raka maitra wrote:
>
> Hi all
>
> I want to specify a design matrix manually.
>
> In the usual pipeline for analysis in freesurfer, one specifies the 
> groups, regressors in the fsgd and then when mri_glmfit is run, it 
> creates the design matrix.
> For eg if I have two classes with 3 subjects each, in my fsgd, 
> mri_glmfit would create the following  design matrix
> 1 0
> 1 0
> 1 0
> 0 1
> 0 1
> 0 1
>
> If I want to specify the above design matrix manually, how and where 
> do I specify the groups, regressors ?
>
>
> Thanks in advance
> Raka
>
> 
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

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[Freesurfer] number of vertices per hemisphere using mri_glmfit

[Stefan Brauns]

Hi there,

I am running surface based analysis of cortical thickness using FreeSurfer.
Sometimes I constrain the analysis to certain regions of the brain, e.g.
only frontal lobes. I would like to find out how many vertices per
hemisphere are analysed with the mri_glmfit I am running. Is there a
possibility to get these values from any of the log-files? What is the usual
number of vertices per hemisphere?

Many thanks,

Stefan
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Re: [Freesurfer] number of vertices per hemisphere using mri_glmfit

[Douglas N Greve]

In the mri_glmfit.log file, there is a "SearchSpace" this will be in mm2 
for surfaces and mm3 for vols. There will also be a mask.mgh file. You 
can run mri_segstats on this to give you the number of elements that are 
== 1.

doug

Stefan Brauns wrote:
> Hi there,
>
> I am running surface based analysis of cortical thickness using 
> FreeSurfer. Sometimes I constrain the analysis to certain regions of 
> the brain, e.g. only frontal lobes. I would like to find out how many 
> vertices per hemisphere are analysed with the mri_glmfit I am running. 
> Is there a possibility to get these values from any of the log-files? 
> What is the usual number of vertices per hemisphere?
>
> Many thanks,
>
> Stefan
>
> 
>
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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] FSL and freesurfer: combine runs in volume or on surface?

[Douglas N Greve]

I have not tested the different methods to find out. I prefer the first 
method because it involves one fewer resampling steps. Also, if you have 
a newer version of freesurfer that uses BBR, then reg-feat2anat will use 
BBR, which will be more accurate. And do not spatially smooth your fMRI 
data for the surface-based processing.

doug

Agnieszka Burzynska wrote:
> Dear all,
> I am trying to figure out how to bring my fMRI data from FSL to the
> freesurfer surface.
>
> The way I understood it from the tutorial "3.0 Surface-based Group
> Functional Analysis"(
> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslGroupFeat)
>
> There are two possibilities of combining multiple runs per subject:
> - using mris_preproc for each run and having runs as frames in the
> lh.copex.mhg file
> - running first gfeat in FSL and registering gfeat copes to fsaverage ( Runs
> combined in a GFEAT within a Subject), which would result in 1-frame
> lh.copex.mhg file
>
> I wonder if it is possible to say which procedure is better/more sensitive?
> Should the fmri data be non-smoothed before this step for both above
> options?
>
> Thank you!
> Cheers,
> Aga
>
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> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] Fw: manually specifying design matrix

[Douglas N Greve]

It would probably be more like this:
1. 00.5000
1. 0   -0.5000
 01.0.5000
 01.   -0.5000
The 1st col codes subject 1. The 1st row is the 1st measure of subject 1 
and the 2nd row is the 2nd measure of subject 1.

doug


raka maitra wrote:
> Hello
>
> Sorry for reposting again.
> Would really appreciate a feedback on the following mail.
>
> Thanks in advance for your time
> Raka
>
>
> - Forwarded Message 
> *From:* raka maitra 
> *To:* Douglas N Greve 
> *Sent:* Fri, January 15, 2010 9:34:02 PM
> *Subject:* Re: [Freesurfer] manually specifying design matrix
>
> Thank you Doug.
>
> I am trying to create a design matrix for repeated measures anova.
>
> Lets say subjects A and B have been measured at sitting and standing 
> positions.
> As the same subjects have been measured at the same positions, hence 
> both the factors i.e subjects and positions are fixed factors.
> Hence a design matrix exploring the within subject effects of 
> positions would be 
> 1 0 1 0
> 0 1 1 0
> 1 0 0 1
> 0 1 0 1
> The first two columns are position and the last two are the subjects.
>
> But mri_glmfit does not accept this design and I get the following 
> error message:
>
> 'Matrix condition is 1e+08
> ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08
> Possible problem with experimental design:
> Check for duplicate entries and/or lack of range of
> continuous variables within a class.'
>
> Looking forward to your suggestion
> Thanks in advance
> Raka
>
>
>
>
>
>
>
>
> 
> *From:* Douglas N Greve 
> *To:* raka maitra 
> *Cc:* freesurfer@nmr.mgh.harvard.edu
> *Sent:* Thu, January 14, 2010 7:05:28 PM
> *Subject:* Re: [Freesurfer] manually specifying design matrix
>
> If you specify it manually, you don't specify groups, etc, or pass an
> fsgd file. You just create your design matrix  pass it to mri_glmfit
> directly with the --X flag.
>
> doug
>
> raka maitra wrote:
> >
> > Hi all
> >
> > I want to specify a design matrix manually.
> >
> > In the usual pipeline for analysis in freesurfer, one specifies the
> > groups, regressors in the fsgd and then when mri_glmfit is run, it
> > creates the design matrix.
> > For eg if I have two classes with 3 subjects each, in my fsgd,
> > mri_glmfit would create the following  design matrix
> > 1 0
> > 1 0
> > 1 0
> > 0 1
> > 0 1
> > 0 1
> >
> > If I want to specify the above design matrix manually, how and where
> > do I specify the groups, regressors ?
> >
> >
> > Thanks in advance
> > Raka
> >
> > 
> >
> > ___
> > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html 
> 
>
> ___
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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
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[Freesurfer] a question about rebuild_gca_atlas.csh

[Guang Zeng]

Hi, there,

In rebuild_gca_atlas.csh, I read something like:

# A talairach registration should be generated for this first subject as well,
# in order to align the final atlas to the Talairach space.

Is this  talairach registration file the same as the talairach.xfm under each 
subject's /mri/transforms/ direcotry?

Thanks!
Guang
  
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Re: [Freesurfer] a question about rebuild_gca_atlas.csh

[Nick Schmansky]

yes.  be sure to double-check it with tkregister2.

On Tue, 2010-01-19 at 12:24 -0600, Guang Zeng wrote:
> Hi, there,
> 
> In rebuild_gca_atlas.csh, I read something like:
> 
> # A talairach registration should be generated for this first subject
> as well,
> # in order to align the final atlas to the Talairach space.
> 
> Is this talairach registration file the same as the talairach.xfm
> under each subject's /mri/transforms/ direcotry?
> 
> Thanks!
> Guang
> 
> 
> __
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> now.
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Re: [Freesurfer] number of vertices per hemisphere using mri_glmfit

[Bruce Fischl]

usually around 140k/hemi.  If you make a label and save it as a label file 
it will have 1 line/vertex

On Tue, 19 Jan 2010, Stefan Brauns wrote:

> Hi there,
>
> I am running surface based analysis of cortical thickness using FreeSurfer.
> Sometimes I constrain the analysis to certain regions of the brain, e.g.
> only frontal lobes. I would like to find out how many vertices per
> hemisphere are analysed with the mri_glmfit I am running. Is there a
> possibility to get these values from any of the log-files? What is the usual
> number of vertices per hemisphere?
>
> Many thanks,
>
> Stefan
>
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Re: [Freesurfer] a question about rebuild_gca_atlas.csh

[Bruce Fischl]

yes, or the talairach.lta

On Tue, 19 Jan 2010, Guang Zeng wrote:

>
> Hi, there,
>
> In rebuild_gca_atlas.csh, I read something like:
>
> # A talairach registration should be generated for this first subject as well,
> # in order to align the final atlas to the Talairach space.
>
> Is this  talairach registration file the same as the talairach.xfm under each 
> subject's /mri/transforms/ direcotry?
>
> Thanks!
> Guang
>
> _
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Re: [Freesurfer] number of vertices per hemisphere using mri_glmfit

[Rudolph Pienaar]

If you do:

$>mris_calc  stats

the first line reported back will be the number of vertices. So, if you 
want to know how many vertices on the left hemisphere:

$>mris_calc lh.thickness stats

and look at the

Size[ XXX ]

where XX will be number of vertices.


Stefan Brauns wrote:
> Hi there,
> 
> I am running surface based analysis of cortical thickness using 
> FreeSurfer. Sometimes I constrain the analysis to certain regions of the 
> brain, e.g. only frontal lobes. I would like to find out how many 
> vertices per hemisphere are analysed with the mri_glmfit I am running. 
> Is there a possibility to get these values from any of the log-files? 
> What is the usual number of vertices per hemisphere?
> 
> Many thanks,
> 
> Stefan
> 
> 
> 
> 
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Re: [Freesurfer] Paired Analysis, Smoothing Step

[Douglas N Greve]

Are those backslashes ("\") in your command-line? If so, try removing them.

Stidd, Reva (NIH/NIMH) [F] wrote:
> Hi there,
>
> I've got a sample of subjects with T1 and T2 scans that I'm trying to 
> compare. I did the entire longitudinal stream protocol, and am now doing the 
> paired analysis protocol. I'm stuck on the Spatial Smoothing step: I've only 
> gotten either a ">" or a message reading, "ERROR: Option -sval unknown." Is 
> there any reason why?
> Thanks,
> -Reva
>
> 
> CHP-MP6:subjects revastidd$ ls
> (all *.long.* files, base files and timepoint scans are listed plus the 
> following files/folders:)
> 12SIB
> FSGD
> README
> Random Output
> V1_average
> bert
> fsaverage
> lh.paired-diff.thickness.mgh
> mris_preproc.surface.lh.log
> mris_preproc.surface.rh.log
> random
> rh.paired-diff.thickness.mgh
> sample-001.mgz
> sample-002.mgz
>  wmparc.vol.table
> CHP-MP6:subjects revastidd$ mri_surf2surf --s fsaverage --hemi lh --fwhm 5 \ 
> --sval lh.paired-diff.thickness.mgh \ --tval lh.paired-diff.thickness.sm05mgh
> ERROR: Option  --sval unknown
> CHP-MP6:subjects revastidd$ mri_surf2surf --s faverage --hemi lh --fwhm 5 \ 
> --sval lh.paired-diff.thickness.mgh \ --tval 
> lh.paired-diff.thickness.sm05.mgh \
>
>
> FREESURFER_HOME: /Applications/freesurfer
>
> Build stamp: freesurfer-Darwin-leopard-i686-stable-pub-v4.5.0
>
> Kernel info: Darwin 9.8.0 i386
>
> Current Working Directory: /Applications/freesurfer/subjects
>
> Which freesurfer: /Applications/freesurfer/bin/freesurfer
>
> I've also attached a screenshot of the current files in my subject directory.
>
> Please let me know if you need anything else.
>
> Thank you for your help!
> -Reva
>   
> 
>
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Fax: 617-726-7422

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[Freesurfer] FreeSurfer two atalses

[Guang Zeng]

Hi, there,

Are there any place in FreeSurfer Wiki or journal paper explain why FreeSurfer 
need to atlases; Subcortical and Surface?


Thanks!
Guang
  
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[Freesurfer] brainmask

[Satrajit Ghosh]

if one wants to get at the brain only (similar to bet), is brainmask.mgz the
best file to use? on some of our data, we are noticing a lot of eyeball.

i presume one can use aseg as an alternative. is this more recommended than
brainmask.mgz? also, is the total brain volume computation based on aseg or
some other file?

cheers,

satra
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Re: [Freesurfer] brainmask

[Douglas N Greve]

aparc+aseg.mgz is probably better. See 
surfer.nmr.mgh.harvard.edu/fswiki/BrainVolume for the answer to your 
question.

Satrajit Ghosh wrote:
> if one wants to get at the brain only (similar to bet), is 
> brainmask.mgz the best file to use? on some of our data, we are 
> noticing a lot of eyeball.
>
> i presume one can use aseg as an alternative. is this more recommended 
> than brainmask.mgz? also, is the total brain volume computation based 
> on aseg or some other file?
>
> cheers,
>
> satra
> 
>
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[Freesurfer] Vol index to Talairach

[Oya, Hiroyuki]

Dear experts,

I like to find Tarairach and MNI coordinate from volume index  (data has 
been already processed with recon-all) off line using Matlab.

Which transform should I use to find it ?

Thank you.

Hiroyuki

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Re: [Freesurfer] FreeSurfer two atalses

[Bruce Fischl]

Hi Guang,

yes, you can read the Human Brain Mpaping (high-resolution inter-subject 
averaging), Neuron (whole brain segmentation) and Cerebral Cortex 
(parcellation) papers with me as first author.

cheers
Bruce


On Tue, 19 Jan 2010, 
Guang Zeng wrote:

>
> Hi, there,
>
> Are there any place in FreeSurfer Wiki or journal paper explain why 
> FreeSurfer need to atlases; Subcortical and Surface?
>
>
> Thanks!
> Guang
>
> _
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[Freesurfer] WM.mgz corrections in the ventricles & Individual Normalization

[Sherri Novis]

Hello -

I have two questions:

1) I noticed on wm.mgz volumes that were segmented properly, that even when the 
ventricles were 
automatically filled in, on some slices they are somewhat patchy (partially 
filled in with white, with some black/blank voxels).

Do these patchy wm fill-ins require manual fill-ins to make them entirely 
opaque?

I went through the tutorial, and it was not clear whether a patchy fill-in 
required a correction or not.

2) What is the best automated measurement that can be used to normalize an 
individual's cortical segmentation volumes for between subject comparison?  We 
have been using gray+white volumes (why we need the ventrical volume processing 
to be consistent) - but not sure if ICV would be better individual normalizer.

Thank you for your time -
Sherri
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