Re: [Freesurfer] how to use mri_surf2surf

[Martin Reuter]

Hi Guang,

If you have the same subject and two timepoints, you might want to  
look at the longitudinal stream.


Martin

On Sep 23, 2009, at 17:52, Guang Zeng  wrote:


Hi, there,

mri_surf2surf resamples one CorticalSurface onto another.

If I have two subjects from different time points (tp1 and tp2), I'd  
like to compare the FreeSurfer analyzed surface data.
For example, could I use mri_surf2surf to resample the white matter  
surface of tp1 onto tp2, so I can overlay the white matter surface  
of tp2 to tp1 using tkmedit?



Thanks!

guang

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Re: [Freesurfer] how to use mri_surf2surf

[Douglas N Greve]

you have to register one to another using bbregister, fslregister, or 
spmregister. You can then run mri_surf2surf specifying --sval-xyz 
surfname and specifying --tval-xyz to get and output surface (instead of 
a scaler file). You will also have to spec the registration you created 
above with --reg (or --reg-inv).

Note that the number of  vertices will be different, but you should 
still be able to load it into tksurfer.

doug

Guang Zeng wrote:
> Hi, there,
>
> mri_surf2surf resamples one CorticalSurface 
>  onto another.
>
> If I have two subjects from different time points (tp1 and tp2), I'd 
> like to compare the FreeSurfer analyzed surface data.
> For example, could I use mri_surf2surf to resample the white matter 
> surface of tp1 onto tp2, so I can overlay the white matter surface of 
> tp2 to tp1 using tkmedit?
>
>
> Thanks!
>
> guang
>
> 
> Hotmail® has ever-growing storage! Don’t worry about storage limits. 
> Check it out. 
> 
>  
>
> 
>
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Re: [Freesurfer] FSL to FreeSurfer registration

[Estephan Moana]

Thanks Nick, this helps a lot!

Estephan

Nick Schmansky wrote:

Estaphan,

It turns out the freesurfer mailing list does support RSS feeds:

http://www.mail-archive.com/freesur...@surfer.nmr.mgh.harvard.edu/maillist.xml

Nick

On Thu, 2009-09-24 at 13:25 -0400, Nick Schmansky wrote:
  

Estephan,

I can ask our IT people about an RSS feed.

Another option is to turn-on digest mode under the mailing list options.
Freesurfer emails would arrive in once-a-day bundles.

https://mail.nmr.mgh.harvard.edu/mailman/options/freesurfer

Nick


On Thu, 2009-09-24 at 12:35 -0400, Estephan Moana wrote:


Thanks for you input Michael. For some reason, I only saw your answer
after Dougla's response. Assuming that I do not want to do
volume-based analysis and just want "nice pics" of my blobs over a 3D
brain, would Michael's suggestion work? If so, what is the next step
after using fslroi, as the input for reg-feat2anat is a feat directory
(an not a single example_func file)?

An unrelated question: is there a way to get the FreeSurfer mailing
list via a RSS feed? This would be help decrease the amount of emails
in my inbox...

Thanks again.

Estephan
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Re: [Freesurfer] hippocampus volume difference

[Douglas N Greve]

When we compute the aseg.stats, we include partial volume correction, we 
don't just count up the voxels in hippo.

doug

Guang Zeng wrote:
> Hi, there,
>
> I use the following matlab code to find right and left hippocampus in 
> aseg.mgz
>
> %%
> filename = 'case_1/mri/aseg.mgz';
> [vol, M, mr_parms, volsz] = load_mgh(filename);
> hippo_left = find( (vol > 16.99) & (vol < 17.01) );
> hippo_right = find( (vol > 52.99) & (vol < 53.01) );
> %%%
>
> I found size(hippo_left, 1) = 3075; size(hippo_right, 1) = 3237;
> However, the value I found in aseg.mgz is
>
> 3162 3162.0  Left-Hippocampus  
> 3390 3390.0  Right-Hippocampus 
>
>
> Why these values are different (3075 < 3162,  3237 < 3390)?
>
> Thanks a lot!
>
> Guang
>
> 
> Hotmail® has ever-growing storage! Don’t worry about storage limits. 
> Check it out. 
> 
>  
>
> 
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[Freesurfer] hippocampus volume difference

[Guang Zeng]

Hi, there,

I use the following matlab code to find right and left hippocampus in aseg.mgz

%%
filename = 'case_1/mri/aseg.mgz';
[vol, M, mr_parms, volsz] = load_mgh(filename);
hippo_left = find( (vol > 16.99) & (vol < 17.01) );
hippo_right = find( (vol > 52.99) & (vol < 53.01) );
%%%

I found size(hippo_left, 1) = 3075; size(hippo_right, 1) = 3237;
However, the value I found in aseg.mgz is

3162 3162.0  Left-Hippocampus   
3390 3390.0  Right-Hippocampus  


Why these values are different (3075 < 3162,  3237 < 3390)?

Thanks a lot!

Guang
  
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Re: [Freesurfer] cortex.label stats

[Douglas N Greve]

what is no longer there? The cortex.label should be there, then you'd 
use your cmd below to compute the stats file.

doug

Dankner, Nathan (NIH/NIMH) [F] wrote:
> Hi all,
>
> In past versions, I have been using this command to generate average cortical 
> thickness across the cortex:
>
> Mris_anatomical_stats -l (hemi).cortex.label -f 
> (id)/stats/(hemi).cortex.stats (id) (hemi)
>
> However, I have noticed that in version 4.5 the cortex.stats files are no 
> longer in the stats folder.  Are they somewhere else, or is there a different 
> method which I should now use to compute these statistics?
>
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Re: [Freesurfer] fsgd and contrast matrix

[Martin Kavec]

Thanks, Dough.

On Thursday 24 September 2009 21:31:34 Douglas N Greve wrote:
> Just set the CDR-related slope components in the contrast matrix to 0.
> If you truly believe that the CDR has no effect, then you can create a
> new fsgd without CDR as a variable.

No no, I believe that the CDR has an effect, I just want to see whether the 
atrophy areas correlated with CDR and MMSE differ.

Thanks,

Martin

> This will improve both DOF and 
> efficiency.
>
> doug
>
> Martin Kavec wrote:
> > Hi,
> >
> > I would like to study cortical thickness in a cohort of patient with
> > respect to MMSE and CDR. I prepared a fsgd file where I have both MMSE
> > and CDR listed:
> >
> > GroupDescriptorFile 1
> > Title Mytitle
> > Class Male
> > Class Female
> > Variable Age
> > Variable MMSE
> > Variable CDR
> > Class Ctrl
> > Class MCI
> > Input subject1 Male 70 27 0.5 MCI
> > Input subject2 Female 65 28 0 Ctrl
> >
> > My design matrix should thus have 4*(3+1)=16 columns/regressors.
> >
> > I am puzzeled a bit, how would I set the contrast matrix to study only
> > correlation of thickness with MMSE, while ignoring CDR. Or should I have
> > a separate fsgd file?
> >
> > Thanks,
> >
> > Martin
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Re: [Freesurfer] fsgd and contrast matrix

[Douglas N Greve]

Just set the CDR-related slope components in the contrast matrix to 0. 
If you truly believe that the CDR has no effect, then you can create a 
new fsgd without CDR as a variable. This will improve both DOF and 
efficiency.

doug

Martin Kavec wrote:
> Hi,
>
> I would like to study cortical thickness in a cohort of patient with respect 
> to MMSE and CDR. I prepared a fsgd file where I have both MMSE and CDR 
> listed:
>
> GroupDescriptorFile 1
> Title Mytitle
> Class Male
> Class Female
> Variable Age
> Variable MMSE
> Variable CDR
> Class Ctrl
> Class MCI
> Input subject1 Male 70 27 0.5 MCI
> Input subject2 Female 65 28 0 Ctrl
>
> My design matrix should thus have 4*(3+1)=16 columns/regressors.
>
> I am puzzeled a bit, how would I set the contrast matrix to study only 
> correlation of thickness with MMSE, while ignoring CDR. Or should I have a 
> separate fsgd file?
>
> Thanks,
>
> Martin
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>   

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Fax: 617-726-7422

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[Freesurfer] Labels for the auditory cortex

[Nasim Maleki]

Dear developers,


I was wondering if you would have labels for the Broadman areas  
corresponding to the auditory cortex for the fsaverage subject.

Thank you,
Nasim

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[Freesurfer] fsgd and contrast matrix

[Martin Kavec]

Hi,

I would like to study cortical thickness in a cohort of patient with respect 
to MMSE and CDR. I prepared a fsgd file where I have both MMSE and CDR 
listed:

GroupDescriptorFile 1
Title Mytitle
Class Male
Class Female
Variable Age
Variable MMSE
Variable CDR
Class Ctrl
Class MCI
Input subject1 Male 70 27 0.5 MCI
Input subject2 Female 65 28 0 Ctrl

My design matrix should thus have 4*(3+1)=16 columns/regressors.

I am puzzeled a bit, how would I set the contrast matrix to study only 
correlation of thickness with MMSE, while ignoring CDR. Or should I have a 
separate fsgd file?

Thanks,

Martin
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Re: [Freesurfer] FSL to FreeSurfer registration

[Nick Schmansky]

Estaphan,

It turns out the freesurfer mailing list does support RSS feeds:

http://www.mail-archive.com/freesur...@surfer.nmr.mgh.harvard.edu/maillist.xml

Nick

On Thu, 2009-09-24 at 13:25 -0400, Nick Schmansky wrote:
> Estephan,
> 
> I can ask our IT people about an RSS feed.
> 
> Another option is to turn-on digest mode under the mailing list options.
> Freesurfer emails would arrive in once-a-day bundles.
> 
> https://mail.nmr.mgh.harvard.edu/mailman/options/freesurfer
> 
> Nick
> 
> 
> On Thu, 2009-09-24 at 12:35 -0400, Estephan Moana wrote:
> > Thanks for you input Michael. For some reason, I only saw your answer
> > after Dougla's response. Assuming that I do not want to do
> > volume-based analysis and just want "nice pics" of my blobs over a 3D
> > brain, would Michael's suggestion work? If so, what is the next step
> > after using fslroi, as the input for reg-feat2anat is a feat directory
> > (an not a single example_func file)?
> > 
> > An unrelated question: is there a way to get the FreeSurfer mailing
> > list via a RSS feed? This would be help decrease the amount of emails
> > in my inbox...
> > 
> > Thanks again.
> > 
> > Estephan
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
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Re: [Freesurfer] FSL to FreeSurfer registration

[Nick Schmansky]

Estephan,

I can ask our IT people about an RSS feed.

Another option is to turn-on digest mode under the mailing list options.
Freesurfer emails would arrive in once-a-day bundles.

https://mail.nmr.mgh.harvard.edu/mailman/options/freesurfer

Nick


On Thu, 2009-09-24 at 12:35 -0400, Estephan Moana wrote:
> Thanks for you input Michael. For some reason, I only saw your answer
> after Dougla's response. Assuming that I do not want to do
> volume-based analysis and just want "nice pics" of my blobs over a 3D
> brain, would Michael's suggestion work? If so, what is the next step
> after using fslroi, as the input for reg-feat2anat is a feat directory
> (an not a single example_func file)?
> 
> An unrelated question: is there a way to get the FreeSurfer mailing
> list via a RSS feed? This would be help decrease the amount of emails
> in my inbox...
> 
> Thanks again.
> 
> Estephan
> ___
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Re: [Freesurfer] FSL to FreeSurfer registration

[Douglas N Greve]

Estephan Moana wrote:
> Thanks for you input Michael. For some reason, I only saw your answer 
> after Dougla's response. Assuming that I do not want to do 
> volume-based analysis and just want "nice pics" of my blobs over a 3D 
> brain, would Michael's suggestion work? If so, what is the next step 
> after using fslroi, as the input for reg-feat2anat is a feat directory 
> (an not a single example_func file)?
At what level do you want pics? The group or individual level? If the 
group (after Flame1 or Flame2), then you can skip smoothing the raw data 
and just smooth prior to group analysis. If the individual level, then 
smoothing the raw data will affect the maps. You cannot use fslmaths to 
do cortical 2D smoothing.
>
> An unrelated question: is there a way to get the FreeSurfer mailing 
> list via a RSS feed? This would be help decrease the amount of emails 
> in my inbox...
>
> Thanks again.
>
> Estephan

-- 
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Phone Number: 617-724-2358 
Fax: 617-726-7422

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Re: [Freesurfer] FSL to FreeSurfer registration

[Estephan Moana]

Thanks for you input Michael. For some reason, I only saw your answer 
after Dougla's response. Assuming that I do not want to do volume-based 
analysis and just want "nice pics" of my blobs over a 3D brain, would 
Michael's suggestion work? If so, what is the next step after using 
fslroi, as the input for reg-feat2anat is a feat directory (an not a 
single example_func file)?


An unrelated question: is there a way to get the FreeSurfer mailing list 
via a RSS feed? This would be help decrease the amount of emails in my 
inbox...


Thanks again.

Estephan
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Re: [Freesurfer] FSL to FreeSurfer registration

[Douglas N Greve]

Hi Michael,

while fslmaths has an option to do "2D" smoothing, this is still only 
smoothing in a slice of the volume and has the same problems as 3D 
smoothing (ie, smoothing across tissue types and sulci). The "2D" that 
FS implements with mris_volsmooth is along the cortical surface, which 
is unrelated to the volume axes. So, unfortunately, you do still have to 
do two analyses if you want a volume-based analysis with smoothing.

doug

Michael Scheel wrote:
> Hi Estephan,
>
> you don't necessarily have to rerun the full 1st level Analysis in total.
> What you have to find out is which of your volumes is the one that 
> example_func is created from.
> Normally this should be the middle timepoint fmri image of your 
> functional run (e.g. if you have 99 volumes then number 45
> will be taken as example_func) that's the default if you haven't 
> specified it otherwise.
> You can use fslroi as a command to extract this volume for the above 
> example e.g.:
> fslroi input_fmri.nii.gz middle_volume.nii.gz 44 1
> (fslroi starts counting from 0 thats why it is 44 instead of 45)
>
> 2D and 3D smoothing can also be done with
> fslmaths see the -s and the -kernel option
>
> Best, Michael
> On 23-Sep-09, at 6:52 PM, Douglas N Greve wrote:
>
>>
>>
>> Estephan Moana wrote:
>>> So what I need to do is to run the 1st level FEAT as usual for the FSL
>>> pipeline, and repeat this analysis for FS with the only difference
>>> been to set the "Spatial smoothing FWHM" to zero on the pre-stats tab
>>> of the FEAT GUI?
>> yes
>>>
>>> Also, can you explain if this smoothing on the FEAT GUI is the 3D you
>>> refer to? And how 2D smoothing is accomplished?
>> Yes, this the 3D smoothing. 2D smoothing on the raw data is more
>> difficult inside of feat. You'd have to use MC and then run
>> mris_volsmooth (FS program) outside of FEAT, then pass FEAT the
>> preprocessed data and tell it not to do MC or smoothing.
>>>
>>> Thank you.
>>>
>>> Estephan
>>>
>>> Douglas N Greve wrote:
 The example_func does not actually get smoothed, so smoothing itself
 will not affect the registration. 3D smoothing will smooth values
 from WM and CSF into gray and from across sulci into functionally
 distinct regions. For this reason we recommend not using 3D smoothing
 (or doing 2D smoothing on the surface). Unfortunately, this requires
 two different analyses.

 doug

 Estephan Moana wrote:
> Hello all, I took the FS course last June at the OHBM in San
> Francisco, and am now playing with it to get to know it better. One
> of the slides on the talk about FSL-FS integration mentioned that
> the input data (from FEAT) for the reg-feat2anat command should have
> not been smoothed prior to registering to FS.
>
> Considering that FEAT 1st level analysis has a default of 5mm
> spatial smoothing (and that's what I used on my data), it seems
> counterintuitive to need to run a 1st level analysis again so the
> output files are not spatially smoothed.
>
> So my questions are: 1) having the example_func file spatially
> smoothed will necessarily hinder a proper registration to the FS
> anatomical?; 2) if so, should I re-run all my FEAT 1st level
> analysis without smoothing or is there any other way?
>
> I know this is quite a beginners question, but I could not find the
> answers on the FS FAQ or the mailing list archives. I appreciate any
> light on this.
>
> Regards,
>
> Estephan Moana, DDS
> Graduate Student
> Oral Biology PhD Program - Neurobiology track
> School of Dentistry, UNC- Chapel Hill
> 2140 Old Dental Building, CB# 7455
> Chapel Hill, NC 27599
> Phone: (919) 966-5680  Fax: (919) 966-5339  Cell: (612) 702-3295
> mo...@email.unc.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
>>
>> In order to help us help you, please follow the steps in:
>> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>
>>
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>

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