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] 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
> 
> ___
> 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
> ___
> 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

[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

-- 
Douglas N. Greve, Ph.D.
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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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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>>
>> -- 
>> Douglas N. Greve, Ph.D.
>> 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
>>
>>
>> ___
>> 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

In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


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Re: [Freesurfer] FSL to FreeSurfer registration

[Douglas N Greve]

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 
>>>  
>>>
>>>
>>> ___
>>> 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

In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


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Re: [Freesurfer] FSL to FreeSurfer registration

[Estephan Moana]

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?


Also, can you explain if this smoothing on the FEAT GUI is the 3D you 
refer to? And how 2D smoothing is accomplished?


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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Re: [Freesurfer] FSL to FreeSurfer registration

[Douglas N Greve]

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 
> 
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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-- 
Douglas N. Greve, Ph.D.
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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[Freesurfer] FSL to FreeSurfer registration

[Estephan Moana]

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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