Re: [Freesurfer] number of vertices

[Yang, Daniel]

Thanks! That number helps. Just want to get an approx. number in general.

Best,
Daniel

-- 
Daniel Yang, Ph.D.
Yale Child Study Center

E-mail: daniel.yj.y...@yale.edu




On 2/29/16, 11:52 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Bruce Fischl" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
fis...@nmr.mgh.harvard.edu> wrote:

>it's usually a bit less than that - aroudn 140K or so
>Bruce
>
>On Mon, 29 Feb 2016,
>Yang, Daniel wrote:
>
>> Hi Bruce,
>>
>> Is it okay to say that it is approximately 160,000 vertices per
>> hemisphere? I found the answer from a paper
>> 
>>(https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ncbi.nlm.nih.gov
>>_pmc_articles_PMC3824100_pdf_fnhum-2D07-2D00722.pdf=AwIBAg=-dg2m7zWuu
>>DZ0MUcV7Sdqw=vhD8z919MORXy6GkKdTAw3V58rxzUZGOKpGXPDgqUHY=z_5IoiYhMwET
>>NcHWHhQzvAvNmllYCkZY02MMWkBOj_A=0bpC-Abjox4A5ZgIdt-inwG08b5S26qYBdABg43
>>hTTo= 
>> ).
>>
>> Best,
>> Daniel
>>
>>
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[Freesurfer] number of vertices

[Yang, Daniel]

Dear FreeSurfer experts,

Can you please indicate the number of vertices FreeSurfer use in each 
hemisphere to reconstruct the brain (e.g., cortical thickness)? Is there a 
fixed number or an approx. number?

Many thanks,
Daniel

--
Daniel Yang, Ph.D.
Yale Child Study Center
E-mail: daniel.yj.y...@yale.edu
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Re: [Freesurfer] number of vertices

[Yang, Daniel]

Hi Bruce,

Is it okay to say that it is approximately 160,000 vertices per
hemisphere? I found the answer from a paper
(http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3824100/pdf/fnhum-07-00722.pdf
).

Best,
Daniel

-- 
Daniel Yang, Ph.D.
Yale Child Study Center

E-mail: daniel.yj.y...@yale.edu




On 2/29/16, 11:42 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Bruce Fischl" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
fis...@nmr.mgh.harvard.edu> wrote:

>Hi Daniel
>
>the number of vertices will vary depending on the surface area and
>geometry 
>of the white matter for each hemisphere.
>
>cheers
>Bruce
>
>
>On Mon, 29 Feb 2016, Yang, Daniel wrote:
>
>> Dear FreeSurfer experts,
>> 
>> Can you please indicate the number of vertices FreeSurfer use in each
>>hemisphere to reconstruct the brain (e.g., cortical
>> thickness)? Is there a fixed number or an approx. number?
>> 
>> Many thanks,
>> Daniel
>> 
>> -- 
>> Daniel Yang, Ph.D.
>> Yale Child Study Center
>> E-mail: daniel.yj.y...@yale.edu
>> 


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Re: [Freesurfer] mri_convert and image orientation

[Yang, Daniel]

Just to note for people who are interested:

It does seem that when voxel-to-ras determinant > 0, then the file is
neurological.

-- 
Daniel Yang, Ph.D.
Yale Child Study Center

E-mail: daniel.yj.y...@yale.edu




On 1/26/16, 10:09 PM, "Yang, Daniel" <daniel.yj.y...@yale.edu> wrote:

>Thanks so much, I see that voxel-to-ras determinant is -1 in my file, so
>it’s most likely to be radiological.
>
>Just curious, so determinant > 0 means neurological then?
>
>Daniel
>
>
>-- 
>Daniel Yang, Ph.D.
>Yale Child Study Center
>
>E-mail: daniel.yj.y...@yale.edu
>
>
>
>
>On 1/26/16, 4:26 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
>Douglas N Greve" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
>gr...@nmr.mgh.harvard.edu> wrote:
>
>>If the determinant is less than 0, then it is radiological (probably it
>>will be radiological).
>>
>>On 01/26/2016 04:20 PM, Yang, Daniel wrote:
>>> Dear Doug,
>>>
>>> Thanks for your reply. Is it possible to upload the raw DICOM to a
>>>server
>>> so that you can see if mri_convert is making the orientation in the
>>>output
>>> NII file neurological? I just want to make sure what my image
>>>orientation
>>> is and how mri_convert interacts with it.
>>>
>>> Many thanks!
>>> Daniel
>>>
>>>
>>
>>-- 
>>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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>>l
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>>z
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Re: [Freesurfer] mri_convert and image orientation

[Yang, Daniel]

Dear Doug,

Thanks for your reply. Is it possible to upload the raw DICOM to a server
so that you can see if mri_convert is making the orientation in the output
NII file neurological? I just want to make sure what my image orientation
is and how mri_convert interacts with it.

Many thanks!
Daniel


-- 
Daniel Yang, Ph.D.
Yale Child Study Center

E-mail: daniel.yj.y...@yale.edu




On 1/25/16, 1:47 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Douglas N Greve" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
gr...@nmr.mgh.harvard.edu> wrote:

>not necessarily. For FSL, the determinant must be less than 0 (see
>mri_info output). Having said that, even if the det<0, it may still show
>up funny in fslview
>
>On 01/25/2016 12:11 PM, Yang, Daniel wrote:
>> Dear FreeSurfer experts,
>>
>> I find that mri_convert will convert DICOM of structural scan to
>> neurological orientation by default.
>>
>> For example, mri_convert --in_type dicom --out_type mii > the DICOM directory> 
>>
>> Thus, the NII may need to be swapped in x for use in FSL.
>>
>> In this the case?
>>
>> Many thanks,
>> Daniel
>>
>> -- 
>> Daniel Yang, Ph.D.
>> Yale Child Study Center
>> E-mail: daniel.yj.y...@yale.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
>
>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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Re: [Freesurfer] mri_convert and image orientation

[Yang, Daniel]

Thanks so much, I see that voxel-to-ras determinant is -1 in my file, so
it’s most likely to be radiological.

Just curious, so determinant > 0 means neurological then?

Daniel


-- 
Daniel Yang, Ph.D.
Yale Child Study Center

E-mail: daniel.yj.y...@yale.edu




On 1/26/16, 4:26 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Douglas N Greve" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
gr...@nmr.mgh.harvard.edu> wrote:

>If the determinant is less than 0, then it is radiological (probably it
>will be radiological).
>
>On 01/26/2016 04:20 PM, Yang, Daniel wrote:
>> Dear Doug,
>>
>> Thanks for your reply. Is it possible to upload the raw DICOM to a
>>server
>> so that you can see if mri_convert is making the orientation in the
>>output
>> NII file neurological? I just want to make sure what my image
>>orientation
>> is and how mri_convert interacts with it.
>>
>> Many thanks!
>> Daniel
>>
>>
>
>-- 
>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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[Freesurfer] mri_convert and image orientation

[Yang, Daniel]

Dear FreeSurfer experts,

I find that mri_convert will convert DICOM of structural scan to neurological 
orientation by default.

For example, mri_convert --in_type dicom --out_type mii  

Thus, the NII may need to be swapped in x for use in FSL.

In this the case?

Many thanks,
Daniel

--
Daniel Yang, Ph.D.
Yale Child Study Center
E-mail: daniel.yj.y...@yale.edu
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Re: [Freesurfer] TalX TalY TalZ

[Yang, Daniel]

Thanks, Doug! Got it. So FreeSurfer registers the individual scans to the 
MNI305 atlas but mri_surfcluster reports approx. Talairach coordinates with the 
default option: —fixmni

I was a little bit confused because this website 
(https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems) says that the 
following: "Note on Talairach: 
FreeSurfer<https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurfer> does not 
report true "Talairach" coordinates. The coordinates listed unter "Talairach" 
are actually based on Matthew Brett's 10/8/98 non-linear transform from MNI305 
space (see http://www.mrc-cbu.cam.ac.uk/Imaging/mnispace.html). 
FreeSurfer<https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurfer> also reports 
"Talairach MNI" coordinates. These are MNI305 space.”

If my understanding is correct, by default, the “Talairach” coordinates 
reported by mri_surfcluster (with —fixmni) are non-linear transformation from 
the MNI305 space; they are approx. Talairach coord as you suggested. And If I 
ever use —nofixmni, then it is what is internally used by FreeSurfer, the 
MNI305 space, or the "Talairach MNI” coordinates.

Is the understanding above correct?

Thanks!

--
Daniel Yang, Ph.D.
Yale Child Study Center
E-mail: daniel.yj.y...@yale.edu

From: 
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Douglas Greve 
<gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu>>
Reply-To: Freesurfer support list 
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Wednesday, November 11, 2015 at 11:01 AM
To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" 
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] TalX TalY TalZ

If you use --fixmni, then they are reported in approximate talairach space

On 11/11/15 10:08 AM, Yang, Daniel wrote:
Dear FreeSurfer Experts,

Are these coordinates reported in mri_surfcluster in MNI305 space? (with 
—fixmni)

Thanks,
Daniel

--
Daniel Yang, Ph.D.
Yale Child Study Center
E-mail: daniel.yj.y...@yale.edu<mailto:daniel.yj.y...@yale.edu>



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[Freesurfer] TalX TalY TalZ

[Yang, Daniel]

Dear FreeSurfer Experts,

Are these coordinates reported in mri_surfcluster in MNI305 space? (with 
—fixmni)

Thanks,
Daniel

--
Daniel Yang, Ph.D.
Yale Child Study Center
E-mail: daniel.yj.y...@yale.edu
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Re: [Freesurfer] mri_surfcluster statistics and label question

[Yang, Daniel]

Thanks! The F.mgh works well, and it also increases precision as
converting from the exponent itself is less precise.

-- 
Daniel Yang, Ph.D.

Yale Child Study Center
E-mail: daniel.yj.y...@yale.edu




On 11/9/15, 10:57 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Douglas Greve" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
gr...@nmr.mgh.harvard.edu> wrote:

>There should be a t.mgh file there (or maybe F.mgh). You can just pull
>the value out of the vertex out of that.
>
>On 11/9/15 6:46 PM, Yang, Daniel wrote:
>> Hi Doug,
>>
>> Got it! Sorry that I keep forgetting this. So it’s an exponent
>>statistic.
>>
>> The reviewers asked for a statistic and df. I think I can convert it to
>>a
>> Z-statistic so it’s more “conventional”.
>>
>> I also noticed that qdec provides a df when I set up the model. It is
>> valid to use that df to derive the t-statistic?
>>
>> Best,
>> Daniel
>>
>
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[Freesurfer] convert label to mgh

[Yang, Daniel]

Dear FreeSurfer Experts,

Is it possible to convert a label file to a surface-based mgh file? Could you 
please provide an example (e.g., on a white surface)?

Best,
Daniel
--
Daniel Yang, Ph.D.
Yale Child Study Center
E-mail: daniel.yj.y...@yale.edu
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[Freesurfer] mri_surfcluster statistics and label question

[Yang, Daniel]

Dear FreeSurfer experts,

In the output mri_surfcluster (e.g., 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisClusterSummary),
 what is the statistics behind the Max?

Is it either t-statistic (if only 1 line of contrast) or F-statistic (if two 
lines of contrast), but not Z-statistics?

Also, I notice that the annotation is picking only one of the anatomical 
regions in which the cluster is located. Is it possible to tell all the 
anatomical regions that a label has?

Thanks,
Daniel

--
Daniel Yang, Ph.D.
Yale Child Study Center
E-mail: daniel.yj.y...@yale.edu
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Re: [Freesurfer] convert label to mgh

[Yang, Daniel]

Hi Doug,

Thanks a lot! The --outmask option appears to be working well!!

Best,
Daniel

-- 
Daniel Yang, Ph.D.

Yale Child Study Center
E-mail: daniel.yj.y...@yale.edu




On 11/9/15, 1:47 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Douglas N Greve" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
gr...@nmr.mgh.harvard.edu> wrote:

>use mri_label2label with the --mask option
>
>On 11/09/2015 01:34 PM, Yang, Daniel wrote:
>> Dear FreeSurfer Experts,
>>
>> Is it possible to convert a label file to a surface-based mgh file?
>> Could you please provide an example (e.g., on a white surface)?
>>
>> Best,
>> Daniel
>> -- 
>> Daniel Yang, Ph.D.
>> Yale Child Study Center
>> E-mail: daniel.yj.y...@yale.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
>
>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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Re: [Freesurfer] mri_surfcluster statistics and label question

[Yang, Daniel]

Hi Doug,

Got it! Sorry that I keep forgetting this. So it’s an exponent statistic.

The reviewers asked for a statistic and df. I think I can convert it to a
Z-statistic so it’s more “conventional”.

I also noticed that qdec provides a df when I set up the model. It is
valid to use that df to derive the t-statistic?

Best,
Daniel

-- 
Daniel Yang, Ph.D.

Yale Child Study Center
E-mail: daniel.yj.y...@yale.edu




On 11/9/15, 6:02 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Douglas N Greve" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
gr...@nmr.mgh.harvard.edu> wrote:

>
>
>On 11/09/2015 10:51 AM, Yang, Daniel wrote:
>> Dear FreeSurfer experts,
>>
>> In the output mri_surfcluster (e.g.,
>> 
>>https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisCluster
>>Summary), 
>> what is the statistics behind the Max?
>>
>> Is it either t-statistic (if only 1 line of contrast) or F-statistic
>> (if two lines of contrast), but not Z-statistics?
>it is the maximum of the abs(-log10(p))


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Re: [Freesurfer] Curvilinear interaction with age

[Yang, Daniel]

Thanks so much for your help!

-- 
Daniel Yang, Ph.D.

Yale Child Study Center
E-mail: daniel.yj.y...@yale.edu




On 11/6/15, 9:23 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Martin Reuter" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
mreu...@nmr.mgh.harvard.edu> wrote:

>Hi Daniel,
>
>you can always specify your own design matrix X in mri_glmfit. So just
>create those columns, fit and test. Of course you need to make sure that
>the order of subjects in Y is identical with the one used in X.
>
>Cheers, Martin
>
>On 11/06/2015 06:14 PM, Yang, Daniel wrote:
>> Dear FreeSurfer experts,
>>
>> I have a group variable (X) with two levels and I want to test if there
>>is a curvilinear interaction with age (Z). Can this be tested in
>>FreeSurfer?
>>
>> Specifically, the model would be
>>
>> Y = b0 + b1X + b2Z + b3Z*Z + b4X*Z + b5X*Z*Z + error
>>
>> I want to test b5 while controlling for b0-b4.
>>
>> Many thanks!
>> Daniel
>> ___
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>>
>>
>
>-- 
>Martin Reuter, PhD
>Assistant Professor of Radiology, Harvard Medical School
>Assistant Professor of Neurology, Harvard Medical School
>A.A.Martinos Center for Biomedical Imaging
>Massachusetts General Hospital
>Research Affiliate, CSAIL, MIT
>Phone: +1-617-724-5652
>Web  : 
>https://urldefense.proofpoint.com/v2/url?u=http-3A__reuter.mit.edu=AwIBA
>g=-dg2m7zWuuDZ0MUcV7Sdqw=vhD8z919MORXy6GkKdTAw3V58rxzUZGOKpGXPDgqUHY
>=cb9CorGJuJmEK4aPCmFuaMdl2fQb1F9u09ewaw0BJp8=ab1OEzviyC2H214Ar7pPsOizune
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>
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[Freesurfer] Curvilinear interaction with age

[Yang, Daniel]

Dear FreeSurfer experts,

I have a group variable (X) with two levels and I want to test if there is a 
curvilinear interaction with age (Z). Can this be tested in FreeSurfer?

Specifically, the model would be 

Y = b0 + b1X + b2Z + b3Z*Z + b4X*Z + b5X*Z*Z + error

I want to test b5 while controlling for b0-b4.

Many thanks!
Daniel
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[Freesurfer] aparcstats2table

[Yang, Daniel]

Dear FreeSurfer Experts,

When I perform aparcstats2table —meas area, does it get it pial.area or white 
area?

I believe it is the pial.area, but this is not documented. If yes, what can I 
obtain white area via aparcstats2table?

Thanks,
Daniel

--
Daniel Yang, Ph.D.
Yale Child Study Center
E-mail: daniel.yj.y...@yale.edu
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Re: [Freesurfer] how to obtain individual's pial_lgi value

[Yang, Daniel]

Hi all,

Found an answer here: 
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-March/036542.html

It works for me!

Best,
Daniel

From: 
>
 on behalf of Daniel Yang 
>
Reply-To: Freesurfer support list 
>
Date: Wednesday, November 4, 2015 at 3:30 PM
To: Freesurfer support list 
>
Subject: [Freesurfer] how to obtain individual's pial_lgi value

Dear FreeSurfer Experts,

When I specify --measure pial_lgi, aparcstats2table says it’s an invalid option.

Could you please advise how I can obtain an individual’s pial_lgi value, give a 
label?

Many thanks!
Daniel
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[Freesurfer] how to obtain individual's pial_lgi value

[Yang, Daniel]

Dear FreeSurfer Experts,

When I specify --measure pial_lgi, aparcstats2table says it’s an invalid option.

Could you please advise how I can obtain an individual’s pial_lgi value, give a 
label?

Many thanks!
Daniel
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[Freesurfer] stat/math tools for MGH file

[Yang, Daniel]

Dear FreeSurfer experts,

I have a number of *.cluster.mgh files and I would like to calculate their 
difference and peak coordinate etc like in fslmaths or fslstats in FSL.

For example, given two images, I want to know the brain regions in image1 but 
not in image2.

Could you please recommend the general command line tools I can use for these 
purposes?

Many thanks,
Daniel


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Re: [Freesurfer] stat/math tools for MGH file

[Yang, Daniel]

Hi Bruce,

Yes, that’s perfect! Thanks for the reply!! :)

Best,
Daniel

On 11/2/15, 8:48 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Bruce Fischl" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
fis...@nmr.mgh.harvard.edu> wrote:

>Hi Daniel
>
>you can always convert to nifti via:
>
>mri_convert cluster.mgh cluster.nii
>
>and you will be able to use the FSL tools
>
>cheers
>Bruce
>
>
>On Tue, 3 Nov 2015, Yang, Daniel
>wrote:
>
>> Dear FreeSurfer experts,
>> 
>> I have a number of *.cluster.mgh files and I would like to calculate
>>their
>> difference and peak coordinate etc like in fslmaths or fslstats in FSL.
>> 
>> For example, given two images, I want to know the brain regions in
>>image1
>> but not in image2.
>> 
>> Could you please recommend the general command line tools I can use for
>> these purposes?
>> 
>> Many thanks,
>> Daniel
>> 
>> 
>> 
>>
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Re: [Freesurfer] how to obtain sulcal depth in a given region for a specific subject

[Yang, Daniel]

Thanks so much for your help!!

- Daniel

On 8/6/15, 3:06 PM, freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Bruce Fischl freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
fis...@nmr.mgh.harvard.edu wrote:

ignore grayvol, the other two will be the mean and standard deviation of
the sulc

cheers
Bruce
On Thu, 6 Aug 2015, Yang, Daniel wrote:

 Hi Bruce,

 Thanks so much! From the output of mris_anatomical_stats, I can see that
 it affects the following three variables:

 GrayVol ThickAvg ThickStd

 When sulc is used instead of thickness, do you know what the meaning of
 these three variables is changed to?

 Many thanks,
 Daniel

 On 8/6/15, 1:35 PM, freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
 Bruce Fischl freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
 fis...@nmr.mgh.harvard.edu wrote:

 sure, you can use mris_anatomical_stats with the label (-l) and specify
 sulc instead of thickness on the command line
 Bruce
 On Thu, 6 Aug 2015, Yang,
 Daniel wrote:

 Dear FreeSurfer Experts,

 Is there a way to obtain sulcal depth in a given region (label) for a
 particular subject?

 Many thanks!
 Daniel


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[Freesurfer] how to obtain sulcal depth in a given region for a specific subject

[Yang, Daniel]

Dear FreeSurfer Experts,

Is there a way to obtain sulcal depth in a given region (label) for a 
particular subject?

Many thanks!
Daniel
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Re: [Freesurfer] how to obtain sulcal depth in a given region for a specific subject

[Yang, Daniel]

Hi Bruce,

Thanks so much! From the output of mris_anatomical_stats, I can see that
it affects the following three variables:

GrayVol ThickAvg ThickStd

When sulc is used instead of thickness, do you know what the meaning of
these three variables is changed to?

Many thanks,
Daniel

On 8/6/15, 1:35 PM, freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Bruce Fischl freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
fis...@nmr.mgh.harvard.edu wrote:

sure, you can use mris_anatomical_stats with the label (-l) and specify
sulc instead of thickness on the command line
Bruce
On Thu, 6 Aug 2015, Yang,
Daniel wrote:

 Dear FreeSurfer Experts,
 
 Is there a way to obtain sulcal depth in a given region (label) for a
 particular subject?
 
 Many thanks!
 Daniel
 

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Re: [Freesurfer] visualize subcortical areas in tksurfer?

[Yang, Daniel]

Thanks, Bruce!!

Daniel

 On Feb 23, 2015, at 8:23 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:
 
 Hi Daniel
 
 I wouldn't advise this - you will miss most of the activation unless it 
 happens to be right next to where the surface runs adjacent to the structure 
 of interest. For subcortical structures you are better off showing the 
 results in slices.
 
 cheers
 Bruce
 
 
 On Mon, 23 Feb 2015, Yang, Daniel wrote:
 
 Hi Bruce,
 Thanks for the reply. My main question is how to best visualize subcortical
 activation in a figure.
 Sometimes we do see some subcortical activation (like the attached, which is 
 a random search) (if the attachment does not work, please see the 
 examplehere: 
 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.frontiersin.org_files_Articles_18483_fnhum-2D06-2D00021-2DHTML_d=AwIDaQc=-dg2m7zWuuDZ0MUcV7Sdqwr=vhD8z919MORXy6GkKdTAw3V58rxzUZGOKpGXPDgqUHYm=FY2aLrzWyEp88KG_1MRXz7kOCWAb3NfLU7iRz6Ftg_4s=AsAyDkBwKH1FHSCReHATnZnHPXl7wm3478H1viSUbpce=
  image_m/fnhum-06-00021-g003.jpg).
 Is it okay to visualize such subcortical activation via tksurfer? If not,
 could you please recommend a method to visualize subcortical activation?
 Sincerely,
 Daniel
 On 2/20/15, 9:06 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:
 
  HI Daniel
 no, that won't work. Vol2surf samples a volume to an existig surface
 and
 none of the subcortical structures will be anywere near the cortical
 surface. You would need to run mri_tessellate on each subcortical
 label
 that you want to generate a  surface for, but I'm still not sure what
 you
 are trying to do.
 cheers
 Bruce
   On Fri, 20 Feb 2015, Yang, Daniel wrote:
 
  Hi Bruce,
 Thanks! and yes, I used mri_vol2surf to convert subcortical
 region as a
 volume file to surface (mgh file) and then visualize it with
 tksurfer.
 According to what you said, this is still valid, right?
 Best,
 Daniel
 On 2/19/15, 5:59 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu
 wrote:
 
  Hi Daniel
 no, tksurfer visualizes surfaces exclusively, and the
 subcortical
 structures are volumetric by and large. You could
 tesselate their surface
 and view it in tksurfer, or just use tkmediit or freeview.
 cheers
 Bruce
 On Thu, 19 Feb
 2015, Yang, Daniel wrote:
 
  Dear FreeSurfer experts,
 I find that tksurfer allows me to visualize
 subcortical areas such as
 hippocampus. The
 visualization looks valid to me.
 Can tksurfer be used in this way?
 Thanks!!
 Daniel
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Re: [Freesurfer] visualize subcortical areas in tksurfer?

[Yang, Daniel]

Hi Bruce,

Thanks for the reply. My main question is how to best visualize subcortical 
activation in a figure.

Sometimes we do see some subcortical activation (like the attached, which is a 
random search) (if the attachment does not work, please see the example here: 
http://www.frontiersin.org/files/Articles/18483/fnhum-06-00021-HTML/image_m/fnhum-06-00021-g003.jpg).

Is it okay to visualize such subcortical activation via tksurfer? If not, could 
you please recommend a method to visualize subcortical activation?

Sincerely,
Daniel

On 2/20/15, 9:06 AM, Bruce Fischl 
fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote:

HI Daniel

no, that won't work. Vol2surf samples a volume to an existig surface and
none of the subcortical structures will be anywere near the cortical
surface. You would need to run mri_tessellate on each subcortical label
that you want to generate a  surface for, but I'm still not sure what you
are trying to do.

cheers
Bruce
  On Fri, 20 Feb 2015, Yang, Daniel wrote:

Hi Bruce,

Thanks! and yes, I used mri_vol2surf to convert subcortical region as a
volume file to surface (mgh file) and then visualize it with tksurfer.
According to what you said, this is still valid, right?

Best,
Daniel

On 2/19/15, 5:59 PM, Bruce Fischl 
fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote:

Hi Daniel

no, tksurfer visualizes surfaces exclusively, and the subcortical
structures are volumetric by and large. You could tesselate their surface
and view it in tksurfer, or just use tkmediit or freeview.

cheers
Bruce
On Thu, 19 Feb
2015, Yang, Daniel wrote:

Dear FreeSurfer experts,

I find that tksurfer allows me to visualize subcortical areas such as
hippocampus. The
visualization looks valid to me.

Can tksurfer be used in this way?

Thanks!!
Daniel


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[Freesurfer] extract individual label from Destrieux Atlas

[Yang, Daniel]

Dear FreeSurfer experts,

The following command works but how do I get the labels from —a2009s ?

mri_annotation2label --a2005s --subject fsaverage --hemi rh --outdir .

What is the difference between a2005s and a2009s?

Thanks!
Daniel
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Re: [Freesurfer] extract individual label from Destrieux Atlas

[Yang, Daniel]

Thanks!!

From: Douglas Greve 
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu
Reply-To: Freesurfer support list 
freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
Date: Thursday, February 19, 2015 at 3:18 PM
To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu 
freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] extract individual label from Destrieux Atlas

Use --annotation a2009s.aparc


On 2/19/15 8:34 PM, Yang, Daniel wrote:
Dear FreeSurfer experts,

The following command works but how do I get the labels from —a2009s ?

mri_annotation2label --a2005s --subject fsaverage --hemi rh --outdir .

What is the difference between a2005s and a2009s?

Thanks!
Daniel



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[Freesurfer] visualize subcortical areas in tksurfer?

[Yang, Daniel]

Dear FreeSurfer experts,

I find that tksurfer allows me to visualize subcortical areas such as 
hippocampus. The visualization looks valid to me.

Can tksurfer be used in this way?

Thanks!!
Daniel
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Re: [Freesurfer] visualize subcortical areas in tksurfer?

[Yang, Daniel]

Hi Bruce,

Thanks! and yes, I used mri_vol2surf to convert subcortical region as a
volume file to surface (mgh file) and then visualize it with tksurfer.
According to what you said, this is still valid, right?

Best,
Daniel

On 2/19/15, 5:59 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:

Hi Daniel

no, tksurfer visualizes surfaces exclusively, and the subcortical
structures are volumetric by and large. You could tesselate their surface
and view it in tksurfer, or just use tkmediit or freeview.

cheers
Bruce
On Thu, 19 Feb 
2015, Yang, Daniel wrote:

 Dear FreeSurfer experts,
 
 I find that tksurfer allows me to visualize subcortical areas such as
hippocampus. The
 visualization looks valid to me.
 
 Can tksurfer be used in this way?
 
 Thanks!!
 Daniel
 

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[Freesurfer] mri_label2label results

[Yang, Daniel]

Dear all,

I found that mri_label2label generates different results, depending on whether 
the software’s platform is MacOS Lion or CentOS 6.

Is this possible?

Thanks!
Daniel
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Re: [Freesurfer] mri_label2label results

[Yang, Daniel]

Ah, it¹s FreeSurfer 5.3 ‹ Release Date 15 May 2013.

Do you mean that the FreeSurfer 5.3 was updated after 05/15/2013?

Thanks,
Daniel

On 6/19/14, 7:55 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:

what version are you using? I think this is a bug we fixed a few months
ago. Or another one

Bruce

On Thu, 19 Jun 2014, Yang, Daniel wrote:

 Dear all,
 
 I found that mri_label2label generates different results, depending on
 whether the software¹s platform is MacOS Lion or CentOS 6.
 
 Is this possible?
 
 Thanks!
 Daniel
 


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Re: [Freesurfer] mri_label2label results

[Yang, Daniel]

I just tried a few different versions of FreeSurfer. Here are the results:

1. FreeSurfer-5.3 (Linux, CentOS 6, Release: 05/15/2013)
2. FreeSurfer-5.3 (Darwin, Lion, Release: 05/15/2013)
3. FreeSurfer-dev (Linux, CentOS 6, 06/19/2014)
4. FreeSurfer-dev (Darwin, Lion, 06/19/2014)

I am comparing the results of mri_label2label and then mris_anatomical_stats 
here.

The results of 3 and 4 are the same
The results of 1 and 2 are different
The results of 1 and 3 are different
The results or 2 and 4 are different

In my testing, I used an arbitrary label file and here is detail information of 
area, volume, thickness, thicknessstd, meancurv, gauscurv, foldind, and curvind

1: 1261.0,4900.0,2.763,0.818,0.145,0.048,28.0,3.7
2: 1109.0,4343.0,2.761,0.798,0.15,0.046,23.0,2.8
3: 1261.0,4900.0,2.763,0.818,0.132,0.032,22.0,2.3
4: 1261.0,4900.0,2.763,0.818,0.132,0.032,22.0,2.3

What should we do here? Is the difference between 1 and 3 trivial?

Thanks!
Daniel

On 6/19/14, 8:13 PM, Yang, Daniel 
yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu wrote:

Ah, it¹s FreeSurfer 5.3 ‹ Release Date 15 May 2013.

Do you mean that the FreeSurfer 5.3 was updated after 05/15/2013?

Thanks,
Daniel

On 6/19/14, 7:55 PM, Bruce Fischl 
fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote:

what version are you using? I think this is a bug we fixed a few months
ago. Or another one

Bruce

On Thu, 19 Jun 2014, Yang, Daniel wrote:

Dear all,
I found that mri_label2label generates different results, depending on
whether the software¹s platform is MacOS Lion or CentOS 6.
Is this possible?
Thanks!
Daniel


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Re: [Freesurfer] mri_label2label results

[Yang, Daniel]

Thanks! Is there a list of bug fixed (after release) somewhere? Should we use 
the development version instead?

Please tell me that it is only mri_label2label that has a bug …


On 6/19/14, 9:08 PM, Bruce Fischl 
fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote:

I think it was a bug we fixed after the release. We can send you new
versions on those operating systems and you can try them out.

Zeke: can you get Daniel new versions of mri_label2label?

thanks
Bruce


On Fri, 20 Jun 2014, Yang,
Daniel wrote:

Ah, it¹s FreeSurfer 5.3 ‹ Release Date 15 May 2013.

Do you mean that the FreeSurfer 5.3 was updated after 05/15/2013?

Thanks,
Daniel

On 6/19/14, 7:55 PM, Bruce Fischl 
fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote:

what version are you using? I think this is a bug we fixed a few months
ago. Or another one

Bruce

On Thu, 19 Jun 2014, Yang, Daniel wrote:

Dear all,

I found that mri_label2label generates different results, depending on
whether the software¹s platform is MacOS Lion or CentOS 6.

Is this possible?

Thanks!
Daniel



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Re: [Freesurfer] mri_label2label results

[Yang, Daniel]

That is great to know!

I personally feel that there should be some sort of autoupdate function or 
patch file list in FreeSurfer so that when a bug like this is fixed, FreeSurfer 
can be updated automatically or we can apply the patch from the website. I 
think the one currently released should be FreeSurfer 5.3.1, with this bug 
fixed. This bug could have invalidated the research results to some extent if 
one is retrieving ROI-based stats manually, I feel. Many major software tend to 
have bugs after release, like SPSS, so this should be a routine... These are 
just my two cents.

Daniel

On Jun 19, 2014, at 10:20 PM, Bruce Fischl 
fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote:

Yes, it was only mri_label2label has that bug

On Jun 19, 2014, at 10:14 PM, Yang, Daniel 
yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu wrote:

Thanks! Is there a list of bug fixed (after release) somewhere? Should we use 
the development version instead?

Please tell me that it is only mri_label2label that has a bug …


On 6/19/14, 9:08 PM, Bruce Fischl 
fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote:

I think it was a bug we fixed after the release. We can send you new
versions on those operating systems and you can try them out.

Zeke: can you get Daniel new versions of mri_label2label?

thanks
Bruce


On Fri, 20 Jun 2014, Yang,
Daniel wrote:

Ah, it¹s FreeSurfer 5.3 ‹ Release Date 15 May 2013.

Do you mean that the FreeSurfer 5.3 was updated after 05/15/2013?

Thanks,
Daniel

On 6/19/14, 7:55 PM, Bruce Fischl 
fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote:

what version are you using? I think this is a bug we fixed a few months
ago. Or another one

Bruce

On Thu, 19 Jun 2014, Yang, Daniel wrote:

Dear all,

I found that mri_label2label generates different results, depending on
whether the software¹s platform is MacOS Lion or CentOS 6.

Is this possible?

Thanks!
Daniel



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Re: [Freesurfer] subcortical segment NIFTI files

[Yang, Daniel]

Hi Doug,

Could you show us the full command of performing such a registration? Very 
curious! Thanks.

Best,
Daniel

From: Douglas Greve 
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu
Reply-To: Freesurfer support list 
freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
Date: Tuesday, June 17, 2014 at 4:30 AM
To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu 
freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] subcortical segment NIFTI files



Also curious, what is $FREESURFER_HOME/average/mni152.register.dat created?
I performed a registration between the MNI305 (ie, fsaverage) and the MNI152 to 
get this file
doug

Thanks!
Daniel

From: Douglas Greve 
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu
Reply-To: Freesurfer support list 
freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
Date: Monday, June 16, 2014 at 12:32 PM
To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu 
freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] subcortical segment NIFTI files


sorry, don't use the mri.2mm/aseg.mgz use the one from mri/
The --inv take the inverse so it maps in the right direction


On 6/16/14 6:16 PM, Yang, Daniel wrote:
Hi Doug,

The way you are referring is to convert from MNI152 to MNI305? But I wanted to 
do the opposite. You can see that the right_amygdala.mgz I have as the input is 
already in the MNI305 space?
mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o 
right_amygdala.mgz --match 54
If I use $FREESURFER_HOME/average/mni152.register.dat instead of 
reg.2mm.mni152.dat, the product does not look right.

Thanks,
Daniel

From: Douglas Greve 
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu
Reply-To: Freesurfer support list 
freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
Date: Monday, June 16, 2014 at 11:43 AM
To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu 
freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] subcortical segment NIFTI files


That is not the right registration. Use 
$FREESURFER_HOME/average/mni152.register.dat instead of reg.2mm.mni152.dat
specify right_amyg as the --targ and MNI152 as --mov and add --inv and spec 
--interp nearest

doug



On 6/16/14 3:13 PM, Yang, Daniel wrote:
Hi Doug,

I am trying to obtain FreeSurfer aseg label NIFTI files in the MNI152 2mm 
space. The code posted below, for example, generate the right amygdala in the 
MNI152 2mm space.

I am a little bit confused why my code is viewed as not doing sensible things. 
In that mri_vol2vol command, the right_amygdala.mgz is in MNI305 2mm space, 
thus I use the reg.2mm.mni152.dat to transform to MNI152 2mm space.

Could you tell me which part is wrong?

Thanks,
Daniel


From: Douglas Greve 
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu
Reply-To: Freesurfer support list 
freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
Date: Monday, June 16, 2014 at 8:16 AM
To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu 
freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] subcortical segment NIFTI files


Sorry, I was trying to find out what it is you are trying to do, not what your 
command line is. The command may run, it is not doing anything intelligible, 
ie, it appears to be using the 2mm reg from fsaverage/mni305 with the 2mm 
mni152, which does not make sense

doug


On 6/16/14 1:38 PM, Yang, Daniel wrote:
It appears that Email in Plaint Text makes the command line look ugly. Here is 
a cleaner view. These two should provide the right amygdala as the anatomical 
ROI in MNI152 2mm space.

mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o 
right_amygdala.mgz --match 54
mri_vol2vol --mov right_amygdala.mgz --targ 
${FSLDIR}/data/standard/MNI152_T1_2mm_brain.nii.gz —reg 
${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat --o 
right_amygdala.nii.gz

If you run them, you will see what they do. They work for me.

Again, my next question is, where can I find reg.1mm.mni152.dat? Or how can I 
generate one?

Thanks!

On 6/16/14, 3:51 AM, Douglas Greve 
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote:


Sorry, what are you trying to do with that vol2vol command? The command
line is surely wrong ...


On 6/16/14 5:57 AM, Yang, Daniel wrote:
Thanks! I see that mri_binarize + mri_vol2vol is what I wanted.

I am able to obtain, for example, the right amygdala, using the following
commands:

mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz
--o right_amygdala.mgz --match 54
mri_vol2vol --mov right_amygdala.mgz --targ
${FSLDIR}/data/standard/MNI152_T1_2mm_brain.nii.gz --reg
${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat --o
right_amygdala.nii.gz
rm

Re: [Freesurfer] subcortical segment NIFTI files

[Yang, Daniel]

Hi Doug,

Thanks! I ran this: bbregister --mov 
$FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz --s fsaverage --t1 --reg 
1mmreg.dat --init-fsl

And obtained the following:

fsaverage
1.00
1.00
0.15
9.999634623527527e-01 -4.681387450546026e-03 7.184753660112619e-03 
1.294338703155518e+00
-7.163462694734335e-03 4.548550583422184e-03 9.999641776084900e-01 
-1.810301017761230e+01
-4.713898524641991e-03 -9.999790787696838e-01 4.514861386269331e-03 
-1.897199630737305e+01
0 0 0 1
round

Which is a little bit different from mni152.register.dat:

fsaverage
1.00
1.00
0.15
9.975314e-01 -7.324822e-03 1.760415e-02 9.570923e-01
-1.296475e-02 -9.262221e-03 9.970638e-01 -1.781596e+01
-1.459537e-02 -1.000945e+00 2.444772e-03 -1.854964e+01
0 0 0 1
tkregister

I am curious about this transformation because I want to transform BrainVoyager 
Talairach brain template to another common space. Two questions:

1. Why are the two different? Is one better than the one, or the difference is 
trivial? Is it okay to use the one I generated myself? What “tweaks” were done 
in mni152.register.dat?

2. I see that there are multiple options in bbregister. For example, is it 
better to use --nearest?

Thanks!
Daniel

From: Douglas Greve 
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu
Reply-To: Freesurfer support list 
freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
Date: Tuesday, June 17, 2014 at 7:15 AM
To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu 
freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] subcortical segment NIFTI files


I think I just ran something like

bbregister --mov MNI152_T1_2mm.nii.gz --s fsaverage --t1 --reg reg.dat 
--init-fsl

Maybe I tweeked it manually


On 6/17/14 1:10 PM, Yang, Daniel wrote:
Hi Doug,

Could you show us the full command of performing such a registration? Very 
curious! Thanks.

Best,
Daniel

From: Douglas Greve 
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu
Reply-To: Freesurfer support list 
freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
Date: Tuesday, June 17, 2014 at 4:30 AM
To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu 
freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] subcortical segment NIFTI files



Also curious, what is $FREESURFER_HOME/average/mni152.register.dat created?
I performed a registration between the MNI305 (ie, fsaverage) and the MNI152 to 
get this file
doug

Thanks!
Daniel

From: Douglas Greve 
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu
Reply-To: Freesurfer support list 
freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
Date: Monday, June 16, 2014 at 12:32 PM
To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu 
freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] subcortical segment NIFTI files


sorry, don't use the mri.2mm/aseg.mgz use the one from mri/
The --inv take the inverse so it maps in the right direction


On 6/16/14 6:16 PM, Yang, Daniel wrote:
Hi Doug,

The way you are referring is to convert from MNI152 to MNI305? But I wanted to 
do the opposite. You can see that the right_amygdala.mgz I have as the input is 
already in the MNI305 space?
mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o 
right_amygdala.mgz --match 54
If I use $FREESURFER_HOME/average/mni152.register.dat instead of 
reg.2mm.mni152.dat, the product does not look right.

Thanks,
Daniel

From: Douglas Greve 
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu
Reply-To: Freesurfer support list 
freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
Date: Monday, June 16, 2014 at 11:43 AM
To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu 
freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] subcortical segment NIFTI files


That is not the right registration. Use 
$FREESURFER_HOME/average/mni152.register.dat instead of reg.2mm.mni152.dat
specify right_amyg as the --targ and MNI152 as --mov and add --inv and spec 
--interp nearest

doug



On 6/16/14 3:13 PM, Yang, Daniel wrote:
Hi Doug,

I am trying to obtain FreeSurfer aseg label NIFTI files in the MNI152 2mm 
space. The code posted below, for example, generate the right amygdala in the 
MNI152 2mm space.

I am a little bit confused why my code is viewed as not doing sensible things. 
In that mri_vol2vol command, the right_amygdala.mgz is in MNI305 2mm space, 
thus I use the reg.2mm.mni152.dat to transform to MNI152 2mm space.

Could you tell me which part is wrong?

Thanks,
Daniel


From: Douglas Greve 
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu
Reply-To: Freesurfer support list 
freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
Date: Monday, June 16, 2014 at 8:16 AM
To: freesurfer

Re: [Freesurfer] subcortical segment NIFTI files

[Yang, Daniel]

Thanks! Does bbregister use orig.mgz in --s? If yes, I guess I should use 
MNI152_T1_1mm.nii.gz instead, since it has skull, like 
$FREESURFER_HOME/subjects/fsaverage/mri/orig.mgz.

Daniel


From: Douglas Greve 
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu
Reply-To: Freesurfer support list 
freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
Date: Tuesday, June 17, 2014 at 10:51 AM
To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu 
freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] subcortical segment NIFTI files

They look pretty similar. I doubt that there will be much practical difference.


On 6/17/14 3:08 PM, Yang, Daniel wrote:
Hi Doug,

Thanks! I ran this: bbregister --mov 
$FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz --s fsaverage --t1 --reg 
1mmreg.dat --init-fsl

And obtained the following:

fsaverage
1.00
1.00
0.15
9.999634623527527e-01 -4.681387450546026e-03 7.184753660112619e-03 
1.294338703155518e+00
-7.163462694734335e-03 4.548550583422184e-03 9.999641776084900e-01 
-1.810301017761230e+01
-4.713898524641991e-03 -9.999790787696838e-01 4.514861386269331e-03 
-1.897199630737305e+01
0 0 0 1
round

Which is a little bit different from mni152.register.dat:

fsaverage
1.00
1.00
0.15
9.975314e-01 -7.324822e-03 1.760415e-02 9.570923e-01
-1.296475e-02 -9.262221e-03 9.970638e-01 -1.781596e+01
-1.459537e-02 -1.000945e+00 2.444772e-03 -1.854964e+01
0 0 0 1
tkregister

I am curious about this transformation because I want to transform BrainVoyager 
Talairach brain template to another common space. Two questions:

1. Why are the two different? Is one better than the one, or the difference is 
trivial? Is it okay to use the one I generated myself? What “tweaks” were done 
in mni152.register.dat?

2. I see that there are multiple options in bbregister. For example, is it 
better to use --nearest?

Thanks!
Daniel

From: Douglas Greve 
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu
Reply-To: Freesurfer support list 
freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
Date: Tuesday, June 17, 2014 at 7:15 AM
To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu 
freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] subcortical segment NIFTI files


I think I just ran something like

bbregister --mov MNI152_T1_2mm.nii.gz --s fsaverage --t1 --reg reg.dat 
--init-fsl

Maybe I tweeked it manually


On 6/17/14 1:10 PM, Yang, Daniel wrote:
Hi Doug,

Could you show us the full command of performing such a registration? Very 
curious! Thanks.

Best,
Daniel

From: Douglas Greve 
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu
Reply-To: Freesurfer support list 
freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
Date: Tuesday, June 17, 2014 at 4:30 AM
To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu 
freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] subcortical segment NIFTI files



Also curious, what is $FREESURFER_HOME/average/mni152.register.dat created?
I performed a registration between the MNI305 (ie, fsaverage) and the MNI152 to 
get this file
doug

Thanks!
Daniel

From: Douglas Greve 
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu
Reply-To: Freesurfer support list 
freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
Date: Monday, June 16, 2014 at 12:32 PM
To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu 
freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] subcortical segment NIFTI files


sorry, don't use the mri.2mm/aseg.mgz use the one from mri/
The --inv take the inverse so it maps in the right direction


On 6/16/14 6:16 PM, Yang, Daniel wrote:
Hi Doug,

The way you are referring is to convert from MNI152 to MNI305? But I wanted to 
do the opposite. You can see that the right_amygdala.mgz I have as the input is 
already in the MNI305 space?
mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o 
right_amygdala.mgz --match 54
If I use $FREESURFER_HOME/average/mni152.register.dat instead of 
reg.2mm.mni152.dat, the product does not look right.

Thanks,
Daniel

From: Douglas Greve 
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu
Reply-To: Freesurfer support list 
freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
Date: Monday, June 16, 2014 at 11:43 AM
To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu 
freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] subcortical segment NIFTI files


That is not the right registration. Use 
$FREESURFER_HOME/average/mni152.register.dat instead of reg.2mm.mni152.dat
specify right_amyg as the --targ and MNI152 as --mov and add --inv and spec 
--interp nearest

doug



On 6/16/14 3:13

Re: [Freesurfer] subcortical segment NIFTI files

[Yang, Daniel]

It appears that Email in Plaint Text makes the command line look ugly. Here is 
a cleaner view. These two should provide the right amygdala as the anatomical 
ROI in MNI152 2mm space.

mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o 
right_amygdala.mgz --match 54
mri_vol2vol --mov right_amygdala.mgz --targ 
${FSLDIR}/data/standard/MNI152_T1_2mm_brain.nii.gz —reg 
${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat --o 
right_amygdala.nii.gz

If you run them, you will see what they do. They work for me.

Again, my next question is, where can I find reg.1mm.mni152.dat? Or how can I 
generate one?

Thanks!

On 6/16/14, 3:51 AM, Douglas Greve 
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote:


Sorry, what are you trying to do with that vol2vol command? The command
line is surely wrong ...


On 6/16/14 5:57 AM, Yang, Daniel wrote:
Thanks! I see that mri_binarize + mri_vol2vol is what I wanted.

I am able to obtain, for example, the right amygdala, using the following
commands:

mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz
--o right_amygdala.mgz --match 54
mri_vol2vol --mov right_amygdala.mgz --targ
${FSLDIR}/data/standard/MNI152_T1_2mm_brain.nii.gz --reg
${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat --o
right_amygdala.nii.gz
rm right_amygdala.mgz


One question: I don’t see a file like reg.1mm.mni152.dat. How do I obtain
a similar file in MNI152 1mm space, based on
${FREESURFER_HOME}/subjects/fsaverage/mri/aseg.mgz ― I think this is a
1mm file?

Best,
Daniel

On 6/15/14, 10:58 PM, Bruce Fischl 
fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote:

mri_vol2vol with the transforms/talairach.xfm as the transform should do
the trick. Make sure that the resample type is nearest neighbor

Cheers
Bruce

On Jun 15, 2014, at 10:28 PM, Yang, Daniel 
yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu
wrote:

Hi Bruce,

Sorry, I wasn¹t clear. It¹s great to know that the FreeSurfer is very
flexible. I meant to obtain the aseg individual label files in MNI152
space as NIfTI files, for example, the different parts of the CC.

Could you please point me to the right direction, as to what tool I
should
use for this purpose (preferably a command line tool, rather than a
visualization tool)?

Best,
Daniel

On 6/15/14, 10:16 PM, Bruce Fischl 
fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu
wrote:

Hi Daniel
Any of our tools can write nifti if you give the output volume the
extension .nii or .nii.gz


Cheers
Bruce

On Jun 15, 2014, at 5:54 PM, Yang, Daniel 
yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu
wrote:

Dear all,

While it is possible to obtain NIfTI files for cortical parcellation
using mri_annotation2label, I am running if it is possible to obtain
NIfTI files associated with aseg parts?

Thanks!
Daniel

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Re: [Freesurfer] subcortical segment NIFTI files

[Yang, Daniel]

Hi Doug,

I am trying to obtain FreeSurfer aseg label NIFTI files in the MNI152 2mm 
space. The code posted below, for example, generate the right amygdala in the 
MNI152 2mm space.

I am a little bit confused why my code is viewed as not doing sensible things. 
In that mri_vol2vol command, the right_amygdala.mgz is in MNI305 2mm space, 
thus I use the reg.2mm.mni152.dat to transform to MNI152 2mm space.

Could you tell me which part is wrong?

Thanks,
Daniel


From: Douglas Greve 
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu
Reply-To: Freesurfer support list 
freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
Date: Monday, June 16, 2014 at 8:16 AM
To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu 
freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] subcortical segment NIFTI files


Sorry, I was trying to find out what it is you are trying to do, not what your 
command line is. The command may run, it is not doing anything intelligible, 
ie, it appears to be using the 2mm reg from fsaverage/mni305 with the 2mm 
mni152, which does not make sense

doug


On 6/16/14 1:38 PM, Yang, Daniel wrote:
It appears that Email in Plaint Text makes the command line look ugly. Here is 
a cleaner view. These two should provide the right amygdala as the anatomical 
ROI in MNI152 2mm space.

mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o 
right_amygdala.mgz --match 54
mri_vol2vol --mov right_amygdala.mgz --targ 
${FSLDIR}/data/standard/MNI152_T1_2mm_brain.nii.gz —reg 
${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat --o 
right_amygdala.nii.gz

If you run them, you will see what they do. They work for me.

Again, my next question is, where can I find reg.1mm.mni152.dat? Or how can I 
generate one?

Thanks!

On 6/16/14, 3:51 AM, Douglas Greve 
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote:


Sorry, what are you trying to do with that vol2vol command? The command
line is surely wrong ...


On 6/16/14 5:57 AM, Yang, Daniel wrote:
Thanks! I see that mri_binarize + mri_vol2vol is what I wanted.

I am able to obtain, for example, the right amygdala, using the following
commands:

mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz
--o right_amygdala.mgz --match 54
mri_vol2vol --mov right_amygdala.mgz --targ
${FSLDIR}/data/standard/MNI152_T1_2mm_brain.nii.gz --reg
${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat --o
right_amygdala.nii.gz
rm right_amygdala.mgz


One question: I don’t see a file like reg.1mm.mni152.dat. How do I obtain
a similar file in MNI152 1mm space, based on
${FREESURFER_HOME}/subjects/fsaverage/mri/aseg.mgz ― I think this is a
1mm file?

Best,
Daniel

On 6/15/14, 10:58 PM, Bruce Fischl 
fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote:

mri_vol2vol with the transforms/talairach.xfm as the transform should do
the trick. Make sure that the resample type is nearest neighbor

Cheers
Bruce

On Jun 15, 2014, at 10:28 PM, Yang, Daniel 
yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu
wrote:

Hi Bruce,

Sorry, I wasn¹t clear. It¹s great to know that the FreeSurfer is very
flexible. I meant to obtain the aseg individual label files in MNI152
space as NIfTI files, for example, the different parts of the CC.

Could you please point me to the right direction, as to what tool I
should
use for this purpose (preferably a command line tool, rather than a
visualization tool)?

Best,
Daniel

On 6/15/14, 10:16 PM, Bruce Fischl 
fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu
wrote:

Hi Daniel
Any of our tools can write nifti if you give the output volume the
extension .nii or .nii.gz


Cheers
Bruce

On Jun 15, 2014, at 5:54 PM, Yang, Daniel 
yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu
wrote:

Dear all,

While it is possible to obtain NIfTI files for cortical parcellation
using mri_annotation2label, I am running if it is possible to obtain
NIfTI files associated with aseg parts?

Thanks!
Daniel

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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
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but does not contain patient information, please contact the sender and
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Freesurfer

Re: [Freesurfer] subcortical segment NIFTI files

[Yang, Daniel]

Hi Doug,

The way you are referring is to convert from MNI152 to MNI305? But I wanted to 
do the opposite. You can see that the right_amygdala.mgz I have as the input is 
already in the MNI305 space?
mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o 
right_amygdala.mgz --match 54
If I use $FREESURFER_HOME/average/mni152.register.dat instead of 
reg.2mm.mni152.dat, the product does not look right.

Thanks,
Daniel

From: Douglas Greve 
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu
Reply-To: Freesurfer support list 
freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
Date: Monday, June 16, 2014 at 11:43 AM
To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu 
freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] subcortical segment NIFTI files


That is not the right registration. Use 
$FREESURFER_HOME/average/mni152.register.dat instead of reg.2mm.mni152.dat
specify right_amyg as the --targ and MNI152 as --mov and add --inv and spec 
--interp nearest

doug



On 6/16/14 3:13 PM, Yang, Daniel wrote:
Hi Doug,

I am trying to obtain FreeSurfer aseg label NIFTI files in the MNI152 2mm 
space. The code posted below, for example, generate the right amygdala in the 
MNI152 2mm space.

I am a little bit confused why my code is viewed as not doing sensible things. 
In that mri_vol2vol command, the right_amygdala.mgz is in MNI305 2mm space, 
thus I use the reg.2mm.mni152.dat to transform to MNI152 2mm space.

Could you tell me which part is wrong?

Thanks,
Daniel


From: Douglas Greve 
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu
Reply-To: Freesurfer support list 
freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
Date: Monday, June 16, 2014 at 8:16 AM
To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu 
freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] subcortical segment NIFTI files


Sorry, I was trying to find out what it is you are trying to do, not what your 
command line is. The command may run, it is not doing anything intelligible, 
ie, it appears to be using the 2mm reg from fsaverage/mni305 with the 2mm 
mni152, which does not make sense

doug


On 6/16/14 1:38 PM, Yang, Daniel wrote:
It appears that Email in Plaint Text makes the command line look ugly. Here is 
a cleaner view. These two should provide the right amygdala as the anatomical 
ROI in MNI152 2mm space.

mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o 
right_amygdala.mgz --match 54
mri_vol2vol --mov right_amygdala.mgz --targ 
${FSLDIR}/data/standard/MNI152_T1_2mm_brain.nii.gz —reg 
${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat --o 
right_amygdala.nii.gz

If you run them, you will see what they do. They work for me.

Again, my next question is, where can I find reg.1mm.mni152.dat? Or how can I 
generate one?

Thanks!

On 6/16/14, 3:51 AM, Douglas Greve 
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote:


Sorry, what are you trying to do with that vol2vol command? The command
line is surely wrong ...


On 6/16/14 5:57 AM, Yang, Daniel wrote:
Thanks! I see that mri_binarize + mri_vol2vol is what I wanted.

I am able to obtain, for example, the right amygdala, using the following
commands:

mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz
--o right_amygdala.mgz --match 54
mri_vol2vol --mov right_amygdala.mgz --targ
${FSLDIR}/data/standard/MNI152_T1_2mm_brain.nii.gz --reg
${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat --o
right_amygdala.nii.gz
rm right_amygdala.mgz


One question: I don’t see a file like reg.1mm.mni152.dat. How do I obtain
a similar file in MNI152 1mm space, based on
${FREESURFER_HOME}/subjects/fsaverage/mri/aseg.mgz ― I think this is a
1mm file?

Best,
Daniel

On 6/15/14, 10:58 PM, Bruce Fischl 
fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote:

mri_vol2vol with the transforms/talairach.xfm as the transform should do
the trick. Make sure that the resample type is nearest neighbor

Cheers
Bruce

On Jun 15, 2014, at 10:28 PM, Yang, Daniel 
yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu
wrote:

Hi Bruce,

Sorry, I wasn¹t clear. It¹s great to know that the FreeSurfer is very
flexible. I meant to obtain the aseg individual label files in MNI152
space as NIfTI files, for example, the different parts of the CC.

Could you please point me to the right direction, as to what tool I
should
use for this purpose (preferably a command line tool, rather than a
visualization tool)?

Best,
Daniel

On 6/15/14, 10:16 PM, Bruce Fischl 
fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu
wrote:

Hi Daniel
Any of our tools can write nifti if you give the output volume the
extension .nii or .nii.gz


Cheers
Bruce

On Jun 15, 2014, at 5:54 PM, Yang, Daniel 
yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu
wrote:

Dear

Re: [Freesurfer] subcortical segment NIFTI files

[Yang, Daniel]

Hi Doug,

I see. It works well. Just curious, when should we use reg.2mm.mni152.dat then?

Also curious, what is $FREESURFER_HOME/average/mni152.register.dat created?

Thanks!
Daniel

From: Douglas Greve 
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu
Reply-To: Freesurfer support list 
freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
Date: Monday, June 16, 2014 at 12:32 PM
To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu 
freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] subcortical segment NIFTI files


sorry, don't use the mri.2mm/aseg.mgz use the one from mri/
The --inv take the inverse so it maps in the right direction


On 6/16/14 6:16 PM, Yang, Daniel wrote:
Hi Doug,

The way you are referring is to convert from MNI152 to MNI305? But I wanted to 
do the opposite. You can see that the right_amygdala.mgz I have as the input is 
already in the MNI305 space?
mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o 
right_amygdala.mgz --match 54
If I use $FREESURFER_HOME/average/mni152.register.dat instead of 
reg.2mm.mni152.dat, the product does not look right.

Thanks,
Daniel

From: Douglas Greve 
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu
Reply-To: Freesurfer support list 
freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
Date: Monday, June 16, 2014 at 11:43 AM
To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu 
freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] subcortical segment NIFTI files


That is not the right registration. Use 
$FREESURFER_HOME/average/mni152.register.dat instead of reg.2mm.mni152.dat
specify right_amyg as the --targ and MNI152 as --mov and add --inv and spec 
--interp nearest

doug



On 6/16/14 3:13 PM, Yang, Daniel wrote:
Hi Doug,

I am trying to obtain FreeSurfer aseg label NIFTI files in the MNI152 2mm 
space. The code posted below, for example, generate the right amygdala in the 
MNI152 2mm space.

I am a little bit confused why my code is viewed as not doing sensible things. 
In that mri_vol2vol command, the right_amygdala.mgz is in MNI305 2mm space, 
thus I use the reg.2mm.mni152.dat to transform to MNI152 2mm space.

Could you tell me which part is wrong?

Thanks,
Daniel


From: Douglas Greve 
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu
Reply-To: Freesurfer support list 
freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
Date: Monday, June 16, 2014 at 8:16 AM
To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu 
freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] subcortical segment NIFTI files


Sorry, I was trying to find out what it is you are trying to do, not what your 
command line is. The command may run, it is not doing anything intelligible, 
ie, it appears to be using the 2mm reg from fsaverage/mni305 with the 2mm 
mni152, which does not make sense

doug


On 6/16/14 1:38 PM, Yang, Daniel wrote:
It appears that Email in Plaint Text makes the command line look ugly. Here is 
a cleaner view. These two should provide the right amygdala as the anatomical 
ROI in MNI152 2mm space.

mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz --o 
right_amygdala.mgz --match 54
mri_vol2vol --mov right_amygdala.mgz --targ 
${FSLDIR}/data/standard/MNI152_T1_2mm_brain.nii.gz —reg 
${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat --o 
right_amygdala.nii.gz

If you run them, you will see what they do. They work for me.

Again, my next question is, where can I find reg.1mm.mni152.dat? Or how can I 
generate one?

Thanks!

On 6/16/14, 3:51 AM, Douglas Greve 
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote:


Sorry, what are you trying to do with that vol2vol command? The command
line is surely wrong ...


On 6/16/14 5:57 AM, Yang, Daniel wrote:
Thanks! I see that mri_binarize + mri_vol2vol is what I wanted.

I am able to obtain, for example, the right amygdala, using the following
commands:

mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz
--o right_amygdala.mgz --match 54
mri_vol2vol --mov right_amygdala.mgz --targ
${FSLDIR}/data/standard/MNI152_T1_2mm_brain.nii.gz --reg
${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat --o
right_amygdala.nii.gz
rm right_amygdala.mgz


One question: I don’t see a file like reg.1mm.mni152.dat. How do I obtain
a similar file in MNI152 1mm space, based on
${FREESURFER_HOME}/subjects/fsaverage/mri/aseg.mgz ― I think this is a
1mm file?

Best,
Daniel

On 6/15/14, 10:58 PM, Bruce Fischl 
fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote:

mri_vol2vol with the transforms/talairach.xfm as the transform should do
the trick. Make sure that the resample type is nearest neighbor

Cheers
Bruce

On Jun 15, 2014, at 10:28 PM, Yang, Daniel 
yung-jui.y

[Freesurfer] subcortical segment NIFTI files

[Yang, Daniel]

Dear all,

While it is possible to obtain NIfTI files for cortical parcellation using 
mri_annotation2label, I am running if it is possible to obtain NIfTI files 
associated with aseg parts?

Thanks!
Daniel

___
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.

Re: [Freesurfer] subcortical segment NIFTI files

[Yang, Daniel]

Hi Bruce,

Sorry, I wasn¹t clear. It¹s great to know that the FreeSurfer is very
flexible. I meant to obtain the aseg individual label files in MNI152
space as NIfTI files, for example, the different parts of the CC.

Could you please point me to the right direction, as to what tool I should
use for this purpose (preferably a command line tool, rather than a
visualization tool)?

Best,
Daniel

On 6/15/14, 10:16 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:

Hi Daniel
Any of our tools can write nifti if you give the output volume the
extension .nii or .nii.gz


Cheers
Bruce

 On Jun 15, 2014, at 5:54 PM, Yang, Daniel yung-jui.y...@yale.edu
wrote:
 
 Dear all,
 
 While it is possible to obtain NIfTI files for cortical parcellation
using mri_annotation2label, I am running if it is possible to obtain
NIfTI files associated with aseg parts?
 
 Thanks!
 Daniel
 
 ___
 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


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.



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] subcortical segment NIFTI files

[Yang, Daniel]

Thanks! I see that mri_binarize + mri_vol2vol is what I wanted.

I am able to obtain, for example, the right amygdala, using the following
commands:

mri_binarize --i ${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/aseg.mgz
--o right_amygdala.mgz --match 54
mri_vol2vol --mov right_amygdala.mgz --targ
${FSLDIR}/data/standard/MNI152_T1_2mm_brain.nii.gz --reg
${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat --o
right_amygdala.nii.gz
rm right_amygdala.mgz


One question: I don’t see a file like reg.1mm.mni152.dat. How do I obtain
a similar file in MNI152 1mm space, based on
${FREESURFER_HOME}/subjects/fsaverage/mri/aseg.mgz ― I think this is a
1mm file?

Best,
Daniel

On 6/15/14, 10:58 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:

mri_vol2vol with the transforms/talairach.xfm as the transform should do
the trick. Make sure that the resample type is nearest neighbor

Cheers
Bruce

 On Jun 15, 2014, at 10:28 PM, Yang, Daniel yung-jui.y...@yale.edu
wrote:
 
 Hi Bruce,
 
 Sorry, I wasn¹t clear. It¹s great to know that the FreeSurfer is very
 flexible. I meant to obtain the aseg individual label files in MNI152
 space as NIfTI files, for example, the different parts of the CC.
 
 Could you please point me to the right direction, as to what tool I
should
 use for this purpose (preferably a command line tool, rather than a
 visualization tool)?
 
 Best,
 Daniel
 
 On 6/15/14, 10:16 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu
wrote:
 
 Hi Daniel
 Any of our tools can write nifti if you give the output volume the
 extension .nii or .nii.gz
 
 
 Cheers
 Bruce
 
 On Jun 15, 2014, at 5:54 PM, Yang, Daniel yung-jui.y...@yale.edu
 wrote:
 
 Dear all,
 
 While it is possible to obtain NIfTI files for cortical parcellation
 using mri_annotation2label, I am running if it is possible to obtain
 NIfTI files associated with aseg parts?
 
 Thanks!
 Daniel
 
 ___
 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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[Freesurfer] reg.1mm.mni152.dat

[Yang, Daniel]

Dear all,

While there is the file 
${FREESURFER_HOME}/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat, there is no 
such file as:

${FREESURFER_HOME}/subjects/fsaverage/mri/reg.1mm.mni152.dat  or   
${FREESURFER_HOME}/subjects/fsaverage/mri/transforms/reg.1mm.mni152.dat ?

I am wondering how we can create the reg.1mm.mni152.dat file?

Thanks!
Daniel


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[Freesurfer] Frontal WM volume

[Yang, Daniel]

Dear FreeSurfer group,

If I want to extract frontal WM volume, is it something doable in FreeSurfer?

Much obliged,
Daniel

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Re: [Freesurfer] Frontal WM volume

[Yang, Daniel]

Hi Doug,

Do you mean wmparc.stats? If yes, that is my understanding of the only way (so 
far) to estimate WM volume by FreeSurfer too, and you already told me (before) 
that it is only 5mm from white surface down into the brain center, correct??

I don't have a better way to do this so far.

If there is another way to get those WM volume by area other than wmparc.stats, 
can you let me know too?

Best,
Daniel

On 5/14/14 5:58 PM, Douglas N Greve 
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote:


  You can choose the areas that you want to define frontal from
wmparc.mgz and add up the volumes. If you have another way to define
frontal, then you'd have to tell us what that is.

doug

On 05/14/2014 05:37 PM, Yang, Daniel wrote:
Dear FreeSurfer group,

If I want to extract frontal WM volume, is it something doable in FreeSurfer?

Much obliged,
Daniel

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

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[Freesurfer] MeanThickness

[Yang, Daniel]

Dear FreeSurfer Experts,

I would like to extract the mean thickness for each subject, and I can see that 
in the lh.aparc.stats, there are three lines. For example:

# Measure Cortex, NumVert, Number of Vertices, 107414, unitless
# Measure Cortex, WhiteSurfArea, White Surface Total Area, 73280.4, mm^2
# Measure Cortex, MeanThickness, Mean Thickness, 2.56763, mm

I am wondering what command I can run with aparcstats2table or mris_calc to 
retrieve these three pieces of information for each subject?

And is the MeanThickness across the whole brain supposed to be (lh + rh)/2?

Best,
Daniel

--
Daniel (Yung-Jui) Yang, Ph.D.
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
Tel: (203) 737-5454
E-mail: yung-jui.y...@yale.edu
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Re: [Freesurfer] MeanThickness

[Yang, Daniel]

Thanks! Instead of aparcstats2table, I just used grep and awk to retrieve those 
directly from the ?h.aparc.stats, and then I calculated the mean_thickness = 
((lh_mean_thickness * lh_white_surface_area ) + (rh_mean_thickness * 
rh_white_surface_area)) / (lh_white_surface_area + rh_white_surface_area)...

Best,
Daniel

--
Daniel (Yung-Jui) Yang, Ph.D.
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
Tel: (203) 737-5454
E-mail: yung-jui.y...@yale.edu

On 3/30/14 2:40 PM, Douglas Greve 
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote:


I think aparcstats2table automatically includes these measures. Can you check? 
And, yes, mean thickness can be computed as (lh+rh)/2
doug

On 3/30/14 12:58 PM, Yang, Daniel wrote:
Dear FreeSurfer Experts,

I would like to extract the mean thickness for each subject, and I can see that 
in the lh.aparc.stats, there are three lines. For example:

# Measure Cortex, NumVert, Number of Vertices, 107414, unitless
# Measure Cortex, WhiteSurfArea, White Surface Total Area, 73280.4, mm^2
# Measure Cortex, MeanThickness, Mean Thickness, 2.56763, mm

I am wondering what command I can run with aparcstats2table or mris_calc to 
retrieve these three pieces of information for each subject?

And is the MeanThickness across the whole brain supposed to be (lh + rh)/2?

Best,
Daniel

--
Daniel (Yung-Jui) Yang, Ph.D.
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
Tel: (203) 737-5454
E-mail: yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu



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Re: [Freesurfer] WM vol as measure

[Yang, Daniel]

Dear all,

I notice that there is a file called wmparc_stats.txt
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI#Tableofwhitematterparcellationvolumes

Is it possible to get corresponding WM info for a given label?

Best,
Daniel

--
Daniel (Yung-Jui) Yang, Ph.D.
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
Tel: (203) 737-5454
E-mail: yung-jui.y...@yale.edu

On 3/2/14 7:18 PM, Yang, Daniel 
yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu wrote:

Dear FreeSurfer Experts,

FS provides thickness as the DV in qdec and mri-glmfit. Do you know how I can 
have WM vol as the DV in these tools with the same GLM model? For example, I 
want to test the WM regions that is most strongly positively correlated with a 
given factor.

Thanks!
Daniel
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Re: [Freesurfer] WM vol as measure

[Yang, Daniel]

Thanks, Doug! But that is about using wmparc.stats as IV or 
continuous/covariate variables. I would like to use WM vol as the DV (measure).

--
Daniel (Yung-Jui) Yang, Ph.D.
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
Tel: (203) 737-5454
E-mail: yung-jui.y...@yale.edu

On 3/3/14 12:58 PM, Douglas N Greve 
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote:

you can just add them into your qdec file (from wmparc.stats)
doug

On 03/02/2014 07:18 PM, Yang, Daniel wrote:
Dear FreeSurfer Experts,

FS provides thickness as the DV in qdec and mri-glmfit. Do you know how I can 
have WM vol as the DV in these tools with the same GLM model? For example, I 
want to test the WM regions that is most strongly positively correlated with a 
given factor.

Thanks!
Daniel
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edumailto: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] WM vol as measure

[Yang, Daniel]

Hi Doug,

I am able to find wmparc.stats in stats. It shows WM vol based on pre-defined 
ROIs.

However, do you know how can we generate corresponding WM vol for a given label 
(not the D-K ROIs)?

I'd like to use WM vol as DV but are limited to pre-defined ROIs.

Best,
Daniel

--
Daniel (Yung-Jui) Yang, Ph.D.
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
Tel: (203) 737-5454
E-mail: yung-jui.y...@yale.edu

On 3/3/14 1:14 PM, Douglas N Greve 
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote:

It should be there if the recon did not fail. The file is called
wmparc.stats (not wmparc_stats.txt)
On 03/03/2014 01:07 PM, Yang, Daniel wrote:
Thanks, Doug! But that is about using wmparc.stats as IV or
continuous/covariate variables. I would like to use WM vol as the DV
(measure).

--
Daniel (Yung-Jui) Yang, Ph.D.
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
Tel: (203) 737-5454
E-mail: _yung-jui.yang@yale.edu_mailto:_yung-jui.yang@yale.edu_

On 3/3/14 12:58 PM, Douglas N Greve 
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu wrote:

 you can just add them into your qdec file (from wmparc.stats)
 doug

 On 03/02/2014 07:18 PM, Yang, Daniel wrote:

 Dear FreeSurfer Experts,

 FS provides thickness as the DV in qdec and mri-glmfit. Do you
 know how I can have WM vol as the DV in these tools with the
 same GLM model? For example, I want to test the WM regions
 that is most strongly positively correlated with a given factor.

 Thanks!
 Daniel
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 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu 
mailto: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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MGH-NMR Center
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] WM vol as measure

[Yang, Daniel]

Sorry, I wasn't clear. It's a cortical label that I manually created, based on 
the pial surface.

Is it possible to generate the corresponding WM vol based on a new label (not 
pre-defined)?


--
Daniel (Yung-Jui) Yang, Ph.D.
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
Tel: (203) 737-5454
E-mail: yung-jui.y...@yale.edu

On 3/3/14 2:17 PM, Douglas N Greve 
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote:


I don't understand. What label do you have? Do you mean a WM label or a
cortical label that you want to find the WM under?

On 03/03/2014 02:12 PM, Yang, Daniel wrote:
Hi Doug,

I am able to find wmparc.stats in stats. It shows WM vol based on
pre-defined ROIs.

However, do you know how can we generate corresponding WM vol for a
given label (not the D-K ROIs)?

I'd like to use WM vol as DV but are limited to pre-defined ROIs.

Best,
Daniel

--
Daniel (Yung-Jui) Yang, Ph.D.
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
Tel: (203) 737-5454
E-mail: _yung-jui.yang@yale.edu_mailto:_yung-jui.yang@yale.edu_

On 3/3/14 1:14 PM, Douglas N Greve 
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu wrote:

 It should be there if the recon did not fail. The file is called
 wmparc.stats (not wmparc_stats.txt)
 On 03/03/2014 01:07 PM, Yang, Daniel wrote:

 Thanks, Doug! But that is about using wmparc.stats as IV or
 continuous/covariate variables. I would like to use WM vol as
 the DV
 (measure).

 --
 Daniel (Yung-Jui) Yang, Ph.D.
 Postdoctoral Researcher
 Yale Child Study Center
 New Haven, CT
 Tel: (203) 737-5454
 E-mail: _yung-jui.yang@yale.edu_mailto:_yung-jui.yang@yale.edu_ 
mailto:_yung-jui.yang@yale.edu_

 On 3/3/14 12:58 PM, Douglas N Greve
 gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu 
mailto:gr...@nmr.mgh.harvard.edu
 mailto:gr...@nmr.mgh.harvard.edu
 mailto:gr...@nmr.mgh.harvard.edu%3E wrote:

  you can just add them into your qdec file (from wmparc.stats)
  doug

  On 03/02/2014 07:18 PM, Yang, Daniel wrote:

  Dear FreeSurfer Experts,

  FS provides thickness as the DV in qdec and
 mri-glmfit. Do you
  know how I can have WM vol as the DV in these tools
 with the
  same GLM model? For example, I want to test the WM
 regions
  that is most strongly positively correlated with a
 given factor.

  Thanks!
  Daniel
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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.edumailto:gr...@nmr.mgh.harvard.edu 
mailto:gr...@nmr.mgh.harvard.edu
 mailto: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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 person to
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 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu 
mailto: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

Re: [Freesurfer] WM vol as measure

[Yang, Daniel]

Sounds like a lot of work, but thanks for your reply.

By the way, the wm vol generated this way is 5mm from white surface into the 
center of the brain, correct? Thus, it is not necessarily the complete WM vol 
underneath the label?

Daniel

--
Daniel (Yung-Jui) Yang, Ph.D.
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
Tel: (203) 737-5454
E-mail: yung-jui.y...@yale.edu

On 3/3/14 2:48 PM, Douglas N Greve 
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote:

yes, but not easily. You will have to create an annotation with your new
label in it (and any other label for the other parts of cortex)
(probably using mris_label2annot), then run mri_aparc2aseg to generate a
new wmparc-style volume, then run mri_segstats. You can look in the
recon-all.log file for example command lines for mri_aparc2aseg (used to
generate the wmparc.mgz)
doug
On 03/03/2014 02:31 PM, Yang, Daniel wrote:
Sorry, I wasn't clear. It's a cortical label that I manually created,
based on the pial surface.

Is it possible to generate the corresponding WM vol based on a new
label (not pre-defined)?


--
Daniel (Yung-Jui) Yang, Ph.D.
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
Tel: (203) 737-5454
E-mail: _yung-jui.yang@yale.edu_mailto:_yung-jui.yang@yale.edu_

On 3/3/14 2:17 PM, Douglas N Greve 
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu wrote:


 I don't understand. What label do you have? Do you mean a WM label
 or a
 cortical label that you want to find the WM under?

 On 03/03/2014 02:12 PM, Yang, Daniel wrote:

 Hi Doug,

 I am able to find wmparc.stats in stats. It shows WM vol based on
 pre-defined ROIs.

 However, do you know how can we generate corresponding WM vol
 for a
 given label (not the D-K ROIs)?

 I'd like to use WM vol as DV but are limited to pre-defined ROIs.

 Best,
 Daniel

 --
 Daniel (Yung-Jui) Yang, Ph.D.
 Postdoctoral Researcher
 Yale Child Study Center
 New Haven, CT
 Tel: (203) 737-5454
 E-mail: _yung-jui.yang@yale.edu_mailto:_yung-jui.yang@yale.edu_ 
mailto:_yung-jui.yang@yale.edu_

 On 3/3/14 1:14 PM, Douglas N Greve
 gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu 
mailto:gr...@nmr.mgh.harvard.edu
 mailto:gr...@nmr.mgh.harvard.edu
 mailto:gr...@nmr.mgh.harvard.edu%3E wrote:

  It should be there if the recon did not fail. The file is
 called
  wmparc.stats (not wmparc_stats.txt)
  On 03/03/2014 01:07 PM, Yang, Daniel wrote:

  Thanks, Doug! But that is about using wmparc.stats as
 IV or
  continuous/covariate variables. I would like to use
 WM vol as
  the DV
  (measure).

  --
  Daniel (Yung-Jui) Yang, Ph.D.
  Postdoctoral Researcher
  Yale Child Study Center
  New Haven, CT
  Tel: (203) 737-5454
  E-mail: 
_yung-jui.yang@yale.edu_mailto:_yung-jui.yang@yale.edu_
 mailto:_yung-jui.yang@yale.edu_
 mailto:_yung-jui.yang@yale.edu_

  On 3/3/14 12:58 PM, Douglas N Greve
  gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu
 mailto:gr...@nmr.mgh.harvard.edu
 mailto:gr...@nmr.mgh.harvard.edu
  mailto:gr...@nmr.mgh.harvard.edu
  mailto:gr...@nmr.mgh.harvard.edu%3E
 mailto:gr...@nmr.mgh.harvard.edu%3E%3E wrote:

   you can just add them into your qdec file (from
 wmparc.stats)
   doug

   On 03/02/2014 07:18 PM, Yang, Daniel wrote:

   Dear FreeSurfer Experts,

   FS provides thickness as the DV in qdec and
  mri-glmfit. Do you
   know how I can have WM vol as the DV in
 these tools
  with the
   same GLM model? For example, I want to test
 the WM
  regions
   that is most strongly positively correlated
 with a
  given factor.

   Thanks!
   Daniel
 ___
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 Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
 mailto:Freesurfer@nmr.mgh.harvard.edu
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   --
   Douglas N. Greve, Ph.D.
   MGH-NMR Center
 gr

[Freesurfer] WM vol as measure

[Yang, Daniel]

Dear FreeSurfer Experts,

FS provides thickness as the DV in qdec and mri-glmfit. Do you know how I can 
have WM vol as the DV in these tools with the same GLM model? For example, I 
want to test the WM regions that is most strongly positively correlated with a 
given factor.

Thanks!
Daniel
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Re: [Freesurfer] WM vol as measure

[Yang, Daniel]

Hi FreeSurfers,

A related question (I can't find the answers on the FS website): what's 
jacobian_white (as a measure)?

Thanks!
Daniel

--
Daniel (Yung-Jui) Yang, Ph.D.
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
Tel: (203) 737-5454
E-mail: yung-jui.y...@yale.edu

On 3/2/14 7:18 PM, Yang, Daniel 
yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu wrote:

Dear FreeSurfer Experts,

FS provides thickness as the DV in qdec and mri-glmfit. Do you know how I can 
have WM vol as the DV in these tools with the same GLM model? For example, I 
want to test the WM regions that is most strongly positively correlated with a 
given factor.

Thanks!
Daniel
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[Freesurfer] two labels in tksurfer/freeview?

[Yang, Daniel]

Dear FreeSurfer experts,

Is it possible to display two labels in tksurfer or freeview, where one label 
is outlined with a certain color and the other label is filled with a different 
color?

I want to show two labels, one is within the other one.

If yes, could you please tell me the specific steps..?

thanks a lot!
Daniel

--
Daniel (Yung-Jui) Yang, Ph.D.
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
Tel: (203) 737-5454
E-mail: yung-jui.y...@yale.edu
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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] two labels in tksurfer/freeview?

[Yang, Daniel]

Doug,

Thanks for your reply! In the annotation, can one of the label be just outlined 
and the other filled?

I would really appreciate if you could provide a step-by-step example for this 
one… esp. how to create the colorLUT in this case...

Best,
Daniel

--
Daniel (Yung-Jui) Yang, Ph.D.
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
Tel: (203) 737-5454
E-mail: yung-jui.y...@yale.edu

On 2/26/14 5:14 PM, Douglas N Greve 
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote:


I'm not sure about freeview, but you cannot do it in tksurfer. You can
take your two labels and create an annotation with mris_label2annot (you
get to specify the color)

doug

On 02/26/2014 05:12 PM, Yang, Daniel wrote:
Dear FreeSurfer experts,

Is it possible to display two labels in tksurfer or freeview, where
one label is outlined with a certain color and the other label is
filled with a different color?

I want to show two labels, one is within the other one.

If yes, could you please tell me the specific steps..?

thanks a lot!
Daniel

--
Daniel (Yung-Jui) Yang, Ph.D.
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
Tel: (203) 737-5454
E-mail: _yung-jui.yang@yale.edu_mailto:_yung-jui.yang@yale.edu_


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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edumailto: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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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] two labels in tksurfer/freeview?

[Yang, Daniel]

Thanks for both of you for the helps! I also find a 3rd solution: convert one 
of the labels to mgh and thus use it as overlay and use the other one as label 
in freeview.

Doug: Creating an outlined label sounds pretty cool. I wonder whether either 
erosion or dilution would do the trick … some sort of tricky conjunction.

Bruce: thanks!!

--
Daniel (Yung-Jui) Yang, Ph.D.
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
Tel: (203) 737-5454
E-mail: yung-jui.y...@yale.edu

On 2/26/14 5:52 PM, Bruce Fischl 
fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote:

the other thing you could do is draw a path in tksurfer and have it be
the outline, then load the inner label and display it as filled
On Wed, 26
Feb 2014, Douglas N Greve wrote:

No, you'd have to modify the label itself to exclude the center (and
create an outline). I don't have any code to do this. For the other
stuff, look at the help for mris_label2annot --help
doug
On 02/26/2014 05:35 PM, Yang, Daniel wrote:
Doug,

Thanks for your reply! In the annotation, can one of the label be just
outlined and the other filled?

I would really appreciate if you could provide a step-by-step example
for this one… esp. how to create the colorLUT in this case...

Best,
Daniel

--
Daniel (Yung-Jui) Yang, Ph.D.
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
Tel: (203) 737-5454
E-mail: _yung-jui.yang@yale.edu_mailto:_yung-jui.yang@yale.edu_

On 2/26/14 5:14 PM, Douglas N Greve 
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu wrote:


 I'm not sure about freeview, but you cannot do it in tksurfer. You
 can
 take your two labels and create an annotation with
 mris_label2annot (you
 get to specify the color)

 doug

 On 02/26/2014 05:12 PM, Yang, Daniel wrote:

 Dear FreeSurfer experts,

 Is it possible to display two labels in tksurfer or freeview,
 where
 one label is outlined with a certain color and the other label is
 filled with a different color?

 I want to show two labels, one is within the other one.

 If yes, could you please tell me the specific steps..?

 thanks a lot!
 Daniel

 --
 Daniel (Yung-Jui) Yang, Ph.D.
 Postdoctoral Researcher
 Yale Child Study Center
 New Haven, CT
 Tel: (203) 737-5454
 E-mail: _yung-jui.yang@yale.edu_mailto:_yung-jui.yang@yale.edu_ 
mailto:_yung-jui.yang@yale.edu_


 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
 mailto: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.edumailto:gr...@nmr.mgh.harvard.edu 
mailto: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
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 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
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 sender and properly
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Re: [Freesurfer] two labels in tksurfer/freeview?

[Yang, Daniel]

Thanks, Bruce! That is neat!!
--
Daniel (Yung-Jui) Yang, Ph.D.
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
Tel: (203) 737-5454
E-mail: yung-jui.y...@yale.edu

On 2/26/14 7:03 PM, Bruce Fischl 
fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote:

that's a good way to do it. You don't even need to save it as an mgz. You
can just do tools-labels-copy label stats to overlay, then delete the
label and you have an overlay from it (assuming the label-stat field is
not zero)
On Thu, 27 Feb 2014, Yang, Daniel wrote:

Thanks for both of you for the helps! I also find a 3rd solution: convert
one of the labels to mgh and thus use it as overlay and use the other one as
label in freeview.
Doug: Creating an outlined label sounds pretty cool. I wonder whether either
erosion or dilution would do the trick … some sort of tricky conjunction.
Bruce: thanks!!
--
Daniel (Yung-Jui) Yang, Ph.D.
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
Tel: (203) 737-5454
E-mail: yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu
On 2/26/14 5:52 PM, Bruce Fischl 
fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote:

   the other thing you could do is draw a path in tksurfer and have
   it be
the outline, then load the inner label and display it as filled
On Wed, 26
Feb 2014, Douglas N Greve wrote:

   No, you'd have to modify the label itself to exclude the
   center (and
create an outline). I don't have any code to do this. For the
other
stuff, look at the help for mris_label2annot --help
doug
On 02/26/2014 05:35 PM, Yang, Daniel wrote:
   Doug,
Thanks for your reply! In the annotation, can one of the
label be just
outlined and the other filled?
I would really appreciate if you could provide a
step-by-step example
for this one… esp. how to create the colorLUT in this
case...
Best,
Daniel
--
Daniel (Yung-Jui) Yang, Ph.D.
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
Tel: (203) 737-5454
E-mail: _yung-jui.yang@yale.edu_mailto:_yung-jui.yang@yale.edu_
On 2/26/14 5:14 PM, Douglas N Greve
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu wrote:
 I'm not sure about freeview, but you cannot do it in
tksurfer. You
 can
 take your two labels and create an annotation with
 mris_label2annot (you
 get to specify the color)
 doug
 On 02/26/2014 05:12 PM, Yang, Daniel wrote:
 Dear FreeSurfer experts,
 Is it possible to display two labels in tksurfer
or freeview,
 where
 one label is outlined with a certain color and
the other label is
 filled with a different color?
 I want to show two labels, one is within the
other one.
 If yes, could you please tell me the specific
steps..?
 thanks a lot!
 Daniel
 --
 Daniel (Yung-Jui) Yang, Ph.D.
 Postdoctoral Researcher
 Yale Child Study Center
 New Haven, CT
 Tel: (203) 737-5454
 E-mail: _yung-jui.yang@yale.edu_mailto:_yung-jui.yang@yale.edu_
mailto:_yung-jui.yang@yale.edu_
 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
 mailto: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.edumailto:gr...@nmr.mgh.harvard.edu
mailto: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
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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
 http://www.partners.org/complianceline . If the
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http

Re: [Freesurfer] two labels in tksurfer/freeview?

[Yang, Daniel]

By the way, what command can I use to erode a label/mgh..?
--
Daniel (Yung-Jui) Yang, Ph.D.
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
Tel: (203) 737-5454
E-mail: yung-jui.y...@yale.edu

On 2/26/14 7:03 PM, Bruce Fischl 
fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote:

that's a good way to do it. You don't even need to save it as an mgz. You
can just do tools-labels-copy label stats to overlay, then delete the
label and you have an overlay from it (assuming the label-stat field is
not zero)
On Thu, 27 Feb 2014, Yang, Daniel wrote:

Thanks for both of you for the helps! I also find a 3rd solution: convert
one of the labels to mgh and thus use it as overlay and use the other one as
label in freeview.
Doug: Creating an outlined label sounds pretty cool. I wonder whether either
erosion or dilution would do the trick … some sort of tricky conjunction.
Bruce: thanks!!
--
Daniel (Yung-Jui) Yang, Ph.D.
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
Tel: (203) 737-5454
E-mail: yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu
On 2/26/14 5:52 PM, Bruce Fischl 
fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote:

   the other thing you could do is draw a path in tksurfer and have
   it be
the outline, then load the inner label and display it as filled
On Wed, 26
Feb 2014, Douglas N Greve wrote:

   No, you'd have to modify the label itself to exclude the
   center (and
create an outline). I don't have any code to do this. For the
other
stuff, look at the help for mris_label2annot --help
doug
On 02/26/2014 05:35 PM, Yang, Daniel wrote:
   Doug,
Thanks for your reply! In the annotation, can one of the
label be just
outlined and the other filled?
I would really appreciate if you could provide a
step-by-step example
for this one… esp. how to create the colorLUT in this
case...
Best,
Daniel
--
Daniel (Yung-Jui) Yang, Ph.D.
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
Tel: (203) 737-5454
E-mail: _yung-jui.yang@yale.edu_mailto:_yung-jui.yang@yale.edu_
On 2/26/14 5:14 PM, Douglas N Greve
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu wrote:
 I'm not sure about freeview, but you cannot do it in
tksurfer. You
 can
 take your two labels and create an annotation with
 mris_label2annot (you
 get to specify the color)
 doug
 On 02/26/2014 05:12 PM, Yang, Daniel wrote:
 Dear FreeSurfer experts,
 Is it possible to display two labels in tksurfer
or freeview,
 where
 one label is outlined with a certain color and
the other label is
 filled with a different color?
 I want to show two labels, one is within the
other one.
 If yes, could you please tell me the specific
steps..?
 thanks a lot!
 Daniel
 --
 Daniel (Yung-Jui) Yang, Ph.D.
 Postdoctoral Researcher
 Yale Child Study Center
 New Haven, CT
 Tel: (203) 737-5454
 E-mail: _yung-jui.yang@yale.edu_mailto:_yung-jui.yang@yale.edu_
mailto:_yung-jui.yang@yale.edu_
 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
 mailto: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.edumailto:gr...@nmr.mgh.harvard.edu
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Re: [Freesurfer] two labels in tksurfer/freeview?

[Yang, Daniel]

Thanks, Bruce! I also found in tksurfer -- Tools -- Labels -- Erode/Dilate 
Selected Label !

--
Daniel (Yung-Jui) Yang, Ph.D.
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
Tel: (203) 737-5454
E-mail: yung-jui.y...@yale.edu

On 2/26/14 8:02 PM, Bruce Fischl 
fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote:

mri_morphology for the .mgz

for the label you can do it in tksurfer in the tools-label menu or use
mri_label2label (at least I put it in the dev version, not sure if it is
released yet)
On Thu, 27 Feb 2014, Yang, Daniel wrote:

By the way, what command can I use to erode a label/mgh..?
--
Daniel (Yung-Jui) Yang, Ph.D.
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
Tel: (203) 737-5454
E-mail: yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu
On 2/26/14 7:03 PM, Bruce Fischl 
fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote:

   that's a good way to do it. You don't even need to save it as an
   mgz. You
can just do tools-labels-copy label stats to overlay, then delete
the
label and you have an overlay from it (assuming the label-stat field
is
not zero)
On Thu, 27 Feb 2014, Yang, Daniel wrote:

   Thanks for both of you for the helps! I also find a 3rd
   solution: convert
one of the labels to mgh and thus use it as overlay and use the
other one as
label in freeview.
Doug: Creating an outlined label sounds pretty cool. I wonder
whether either
erosion or dilution would do the trick … some sort of tricky
conjunction.
Bruce: thanks!!
--
Daniel (Yung-Jui) Yang, Ph.D.
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
Tel: (203) 737-5454
E-mail: yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu
On 2/26/14 5:52 PM, Bruce Fischl 
fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu
wrote:
   the other thing you could do is draw a path in tksurfer
and have
   it be
the outline, then load the inner label and display it as
filled
On Wed, 26
Feb 2014, Douglas N Greve wrote:
   No, you'd have to modify the label itself to exclude the
   center (and
create an outline). I don't have any code to do this. For the
other
stuff, look at the help for mris_label2annot --help
doug
On 02/26/2014 05:35 PM, Yang, Daniel wrote:
   Doug,
Thanks for your reply! In the annotation, can one of the
label be just
outlined and the other filled?
I would really appreciate if you could provide a
step-by-step example
for this one… esp. how to create the colorLUT in this
case...
Best,
Daniel
--
Daniel (Yung-Jui) Yang, Ph.D.
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
Tel: (203) 737-5454
E-mail: _yung-jui.yang@yale.edu_mailto:_yung-jui.yang@yale.edu_
On 2/26/14 5:14 PM, Douglas N Greve
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu wrote:
 I'm not sure about freeview, but you cannot do it in
tksurfer. You
 can
 take your two labels and create an annotation with
 mris_label2annot (you
 get to specify the color)
 doug
 On 02/26/2014 05:12 PM, Yang, Daniel wrote:
 Dear FreeSurfer experts,
 Is it possible to display two labels in tksurfer
or freeview,
 where
 one label is outlined with a certain color and
the other label is
 filled with a different color?
 I want to show two labels, one is within the
other one.
 If yes, could you please tell me the specific
steps..?
 thanks a lot!
 Daniel
 --
 Daniel (Yung-Jui) Yang, Ph.D.
 Postdoctoral Researcher
 Yale Child Study Center
 New Haven, CT
 Tel: (203) 737-5454
 E-mail: _yung-jui.yang@yale.edu_mailto:_yung-jui.yang@yale.edu_
mailto:_yung-jui.yang@yale.edu_
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[Freesurfer] continusous x continuous interaction?

[Yang, Daniel]

Dear FreeSurfer Experts,

In the example here: http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G2V, it 
describes the testing of the main effects of two continuous variables.

In order to test the interaction effect, I think we can form an interaction 
term like age x weight as the third covariate, that is,

Regressor1: All ones. Codes intercept/mean for Main
Regressor2: age for each subject. Codes age slope for Main
Regressor3: weight for each subject. Codes weight slope for Main
Regressor4: age x weight for each subject. Codes age x weight interaction effect

and then specify a contrast [0 0 0 1]?

Is that the way to go?

Best,
Daniel

--
Daniel (Yung-Jui) Yang, Ph.D.
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
Tel: (203) 737-5454
E-mail: yung-jui.y...@yale.edu
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Re: [Freesurfer] interpretation of a 3-way interaction

[Yang, Daniel]

Thanks, Doug! I guess in order to interpret the interaction correctly, I would 
need to extract the thickness value and plot the interaction.

Best,
Daniel

--
Daniel (Yung-Jui) Yang, Ph.D.
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
Tel: (203) 737-5454
E-mail: yung-jui.y...@yale.edu

On 2/20/14 2:57 PM, Douglas N Greve 
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote:


The basic contrast is
(PM-PF)-(CM-CF)
If that is positive, then it will be red, otherwise blue

This opens up a lot of possibilities as to what is driving the
interaction, so it is hard to come up with a sentence like the one you
are trying to state

doug


On 02/20/2014 02:25 PM, Yang, Daniel wrote:
Dear FreeSurfers,

I have two discrete and binary factors (Dx: patients vs. controls;
Sex: female vs. male), one continuous variable (Age), one nuisance
factor (IQ). If there is a 3-way interaction of Dx x Sex x Age,
regressing out IQ, is the following interpretation correct?

Red/yellow: In females (vs. males), the Age effect of cortical
thickening is stronger in patients (vs. controls).
Blue/cyan: In females (vs. males), the Age effect of cortical thinning
is stronger in patients (vs. controls).

Note. by stronger, I mean greater magnitude without sign.

Thanks,
Daniel





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MGH-NMR Center
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Fax: 617-726-7422

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[Freesurfer] ocn?

[Yang, Daniel]

Dear FreeSurfers,

I obtained a file from cluster analysis, called cache.th20.pos.sig.ocn.mgh

Can you tell me what OCN stand for? And what is this file for? I tried to view 
it but was unable to see anything.

Best,
Daniel

--
Daniel (Yung-Jui) Yang, Ph.D.
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
Tel: (203) 737-5454
E-mail: yung-jui.y...@yale.edu
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[Freesurfer] interpretation of a 3-way interaction

[Yang, Daniel]

Dear FreeSurfers,

I have two discrete and binary factors (Dx: patients vs. controls; Sex: female 
vs. male), one continuous variable (Age), one nuisance factor (IQ). If there is 
a 3-way interaction of Dx x Sex x Age, regressing out IQ, is the following 
interpretation correct?

Red/yellow: In females (vs. males), the Age effect of cortical thickening is 
stronger in patients (vs. controls).
Blue/cyan: In females (vs. males), the Age effect of cortical thinning is 
stronger in patients (vs. controls).

Note. by stronger, I mean greater magnitude without sign.

Thanks,
Daniel



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[Freesurfer] interaction between two covariates in qdec?

[Yang, Daniel]

Dear FreeSurfer Experts,

In this webpage (http://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples), it 
says Two Groups (1 Factor, Two Levels), Two Covariates. DODS only. QDEC-able.

However, I cannot select more than one covariate in qdec. Any suggestion? I'm 
using qdec in Mac, FreeSurfer 5.3.

Thanks!
Daniel

--
Daniel (Yung-Jui) Yang, Ph.D.
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
Tel: (203) 737-5454
E-mail: yung-jui.y...@yale.edu
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Re: [Freesurfer] interaction between two covariates in qdec?

[Yang, Daniel]

Sorry, I've found an answer to this here: 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg32928.html

Daniel
--
Daniel (Yung-Jui) Yang, Ph.D.
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
Tel: (203) 737-5454
E-mail: yung-jui.y...@yale.edu

On 2/19/14 6:47 PM, Yang, Daniel 
yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu wrote:

Dear FreeSurfer Experts,

In this webpage (http://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples), it 
says Two Groups (1 Factor, Two Levels), Two Covariates. DODS only. QDEC-able.

However, I cannot select more than one covariate in qdec. Any suggestion? I'm 
using qdec in Mac, FreeSurfer 5.3.

Thanks!
Daniel

--
Daniel (Yung-Jui) Yang, Ph.D.
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
Tel: (203) 737-5454
E-mail: yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu
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Re: [Freesurfer] Contrasts and regressors involving two binary factors, 1 covariate, and 1 nuisance factor

[Yang, Daniel]

Got it! I guess we may work around by specifying weighted contrast like [ 0.1   
0.2   0.3   0.4 ] ?
--
Daniel (Yung-Jui) Yang, Ph.D.
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
Tel: (203) 737-5454
E-mail: yung-jui.y...@yale.edu

On 2/18/14 11:25 PM, Douglas Greve 
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote:


Let's say you have four groups with 10 20 30 40 (100 total). The first group 
would get a weight of .25 where it only had 10% of the total. I don't think 
there is any way around this.


On 2/18/14 4:07 PM, Yang, Daniel wrote:
Doug, sorry, I am not sure I can fully understand.

Do you mean the results are weighted MORE toward groups with smaller sample 
sizes (than groups with larger sample sizes)?

--
Daniel (Yung-Jui) Yang, Ph.D.
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
Tel: (203) 737-5454
E-mail: yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu

On 2/18/14 2:13 PM, Douglas N Greve 
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote:

  It will tend to weight smaller groups by a proportion greater than the
number of subjects in the group.



On 02/18/2014 01:58 PM, Yang, Daniel wrote:
Thanks Doug! One follow-up question: since it's [0.25  0.25  0.25
  0.25], would the effect be biased toward large sample sizes in one of
the groups (versus the other groups)?

Or, does FreeSurfer qdec take care of the unequal cell, in a possible
way analogous to using Type III SS in the traditional ANOVA?

Best,
Daniel
--
Daniel (Yung-Jui) Yang, Ph.D.
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
Tel: (203) 737-5454
E-mail: _yung-jui.yang@yale.edu_mailto:_yung-jui.yang@yale.edu_

On 2/18/14 1:30 PM, Douglas N Greve 
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu%3E wrote:

 That looks right to me
 doug


 On 02/18/2014 10:08 AM, Yang, Daniel wrote:

 Dear FreeSurfer experts,

 I have two binary factors (F1: F1L1 F1L2; F2: F2L1 F2L2), 1
 covariate
 (COV), and 1 nuisance factor (NUI). I want to make sense of some
 specification of the regressors and contrasts.
 Because they are not described
 in http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G1V, I post my
 understanding below. Can you let me know if it is correct?

 This model using the DODS method will have 12 regressors:

 Regressor1: 1's for F1L1 F2L1, 0 otherwise (i.e., offset for
 Group 1)
 Regressor2: 1's for F1L1 F2L2, 0 otherwise (i.e, offset for
 Group 2)
 Regressor3: 1's for F1L2 F2L1, 0 otherwise (i.e., offset for
 Group 3)
 Regressor4: 1's for F1L2 F2L2, 0 otherwise (i.e., offset for
 Group 4)
 Regressor5: COV for Group1 subjects, 0 otherwise (i.e., COV
 slope for
 Group 1)
 Regressor6: COV for Group2 subjects, 0 otherwise (i.e., COV
 slope for
 Group 2)
 Regressor7: COV for Group3 subjects, 0 otherwise (i.e., COV
 slope for
 Group 3)
 Regressor8: COV for Group4 subjects, 0 otherwise (i.e., COV
 slope for
 Group 4)
 Regressor9: NUI for Group1 subjects, 0 otherwise (i.e., NUI
 slope for
 Group 1)
 Regressor10: NUI for Group2 subjects, 0 otherwise (i.e., NUI
 slope for
 Group 2)
 Regressor11: NUI for Group3 subjects, 0 otherwise (i.e., NUI
 slope for
 Group 3)
 Regressor12: NUI for Group4 subjects, 0 otherwise (i.e., NUI
 slope for
 Group 4)

 Description1: Does the correlation between thickness and COV,
 accounting for F1 and F2, differ from 0? Nuisance factors: NUI
 Contrast1: [0  0  0  0  0.25  0.25  0.25  0.25  0  0  0  0]

 Best,
 Daniel

 --
 Daniel (Yung-Jui) Yang, Ph.D.
 Postdoctoral Researcher
 Yale Child Study Center
 New Haven, CT
 Tel: (203) 737-5454
 E-mail: _yung-jui.yang@yale.edu_mailto:_yung-jui.yang@yale.edu_ 
mailto:_yung-jui.yang@yale.edu_


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 Douglas N. Greve, Ph.D.
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 gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu 
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 Phone Number: 617-724-2358
 Fax: 617-726-7422

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 Outgoing:
 ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve

[Freesurfer] Contrasts and regressors involving two binary factors, 1 covariate, and 1 nuisance factor

[Yang, Daniel]

Dear FreeSurfer experts,

I have two binary factors (F1: F1L1 F1L2; F2: F2L1 F2L2), 1 covariate (COV), 
and 1 nuisance factor (NUI). I want to make sense of some specification of the 
regressors and contrasts.
Because they are not described in 
http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G1V, I post my understanding 
below. Can you let me know if it is correct?

This model using the DODS method will have 12 regressors:

Regressor1: 1's for F1L1 F2L1, 0 otherwise (i.e., offset for Group 1)
Regressor2: 1's for F1L1 F2L2, 0 otherwise (i.e, offset for Group 2)
Regressor3: 1's for F1L2 F2L1, 0 otherwise (i.e., offset for Group 3)
Regressor4: 1's for F1L2 F2L2, 0 otherwise (i.e., offset for Group 4)
Regressor5: COV for Group1 subjects, 0 otherwise (i.e., COV slope for Group 1)
Regressor6: COV for Group2 subjects, 0 otherwise (i.e., COV slope for Group 2)
Regressor7: COV for Group3 subjects, 0 otherwise (i.e., COV slope for Group 3)
Regressor8: COV for Group4 subjects, 0 otherwise (i.e., COV slope for Group 4)
Regressor9: NUI for Group1 subjects, 0 otherwise (i.e., NUI slope for Group 1)
Regressor10: NUI for Group2 subjects, 0 otherwise (i.e., NUI slope for Group 2)
Regressor11: NUI for Group3 subjects, 0 otherwise (i.e., NUI slope for Group 3)
Regressor12: NUI for Group4 subjects, 0 otherwise (i.e., NUI slope for Group 4)

Description1: Does the correlation between thickness and COV, accounting for F1 
and F2, differ from 0? Nuisance factors: NUI
Contrast1: [0  0  0  0  0.25  0.25  0.25  0.25  0  0  0  0]

Best,
Daniel

--
Daniel (Yung-Jui) Yang, Ph.D.
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
Tel: (203) 737-5454
E-mail: yung-jui.y...@yale.edu
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Re: [Freesurfer] Contrasts and regressors involving two binary factors, 1 covariate, and 1 nuisance factor

[Yang, Daniel]

Thanks Doug! One follow-up question: since it's [0.25  0.25  0.25  0.25], would 
the effect be biased toward large sample sizes in one of the groups (versus the 
other groups)?

Or, does FreeSurfer qdec take care of the unequal cell, in a possible way 
analogous to using Type III SS in the traditional ANOVA?

Best,
Daniel
--
Daniel (Yung-Jui) Yang, Ph.D.
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
Tel: (203) 737-5454
E-mail: yung-jui.y...@yale.edu

On 2/18/14 1:30 PM, Douglas N Greve 
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote:

That looks right to me
doug


On 02/18/2014 10:08 AM, Yang, Daniel wrote:
Dear FreeSurfer experts,

I have two binary factors (F1: F1L1 F1L2; F2: F2L1 F2L2), 1 covariate
(COV), and 1 nuisance factor (NUI). I want to make sense of some
specification of the regressors and contrasts.
Because they are not described
in http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G1V, I post my
understanding below. Can you let me know if it is correct?

This model using the DODS method will have 12 regressors:

Regressor1: 1's for F1L1 F2L1, 0 otherwise (i.e., offset for Group 1)
Regressor2: 1's for F1L1 F2L2, 0 otherwise (i.e, offset for Group 2)
Regressor3: 1's for F1L2 F2L1, 0 otherwise (i.e., offset for Group 3)
Regressor4: 1's for F1L2 F2L2, 0 otherwise (i.e., offset for Group 4)
Regressor5: COV for Group1 subjects, 0 otherwise (i.e., COV slope for
Group 1)
Regressor6: COV for Group2 subjects, 0 otherwise (i.e., COV slope for
Group 2)
Regressor7: COV for Group3 subjects, 0 otherwise (i.e., COV slope for
Group 3)
Regressor8: COV for Group4 subjects, 0 otherwise (i.e., COV slope for
Group 4)
Regressor9: NUI for Group1 subjects, 0 otherwise (i.e., NUI slope for
Group 1)
Regressor10: NUI for Group2 subjects, 0 otherwise (i.e., NUI slope for
Group 2)
Regressor11: NUI for Group3 subjects, 0 otherwise (i.e., NUI slope for
Group 3)
Regressor12: NUI for Group4 subjects, 0 otherwise (i.e., NUI slope for
Group 4)

Description1: Does the correlation between thickness and COV,
accounting for F1 and F2, differ from 0? Nuisance factors: NUI
Contrast1: [0  0  0  0  0.25  0.25  0.25  0.25  0  0  0  0]

Best,
Daniel

--
Daniel (Yung-Jui) Yang, Ph.D.
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
Tel: (203) 737-5454
E-mail: _yung-jui.yang@yale.edu_mailto:_yung-jui.yang@yale.edu_


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Re: [Freesurfer] Contrasts and regressors involving two binary factors, 1 covariate, and 1 nuisance factor

[Yang, Daniel]

Doug, sorry, I am not sure I can fully understand.

Do you mean the results are weighted MORE toward groups with smaller sample 
sizes (than groups with larger sample sizes)?

--
Daniel (Yung-Jui) Yang, Ph.D.
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
Tel: (203) 737-5454
E-mail: yung-jui.y...@yale.edu

On 2/18/14 2:13 PM, Douglas N Greve 
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote:

  It will tend to weight smaller groups by a proportion greater than the
number of subjects in the group.



On 02/18/2014 01:58 PM, Yang, Daniel wrote:
Thanks Doug! One follow-up question: since it's [0.25  0.25  0.25
  0.25], would the effect be biased toward large sample sizes in one of
the groups (versus the other groups)?

Or, does FreeSurfer qdec take care of the unequal cell, in a possible
way analogous to using Type III SS in the traditional ANOVA?

Best,
Daniel
--
Daniel (Yung-Jui) Yang, Ph.D.
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
Tel: (203) 737-5454
E-mail: _yung-jui.yang@yale.edu_mailto:_yung-jui.yang@yale.edu_

On 2/18/14 1:30 PM, Douglas N Greve 
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu wrote:

 That looks right to me
 doug


 On 02/18/2014 10:08 AM, Yang, Daniel wrote:

 Dear FreeSurfer experts,

 I have two binary factors (F1: F1L1 F1L2; F2: F2L1 F2L2), 1
 covariate
 (COV), and 1 nuisance factor (NUI). I want to make sense of some
 specification of the regressors and contrasts.
 Because they are not described
 in http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G1V, I post my
 understanding below. Can you let me know if it is correct?

 This model using the DODS method will have 12 regressors:

 Regressor1: 1's for F1L1 F2L1, 0 otherwise (i.e., offset for
 Group 1)
 Regressor2: 1's for F1L1 F2L2, 0 otherwise (i.e, offset for
 Group 2)
 Regressor3: 1's for F1L2 F2L1, 0 otherwise (i.e., offset for
 Group 3)
 Regressor4: 1's for F1L2 F2L2, 0 otherwise (i.e., offset for
 Group 4)
 Regressor5: COV for Group1 subjects, 0 otherwise (i.e., COV
 slope for
 Group 1)
 Regressor6: COV for Group2 subjects, 0 otherwise (i.e., COV
 slope for
 Group 2)
 Regressor7: COV for Group3 subjects, 0 otherwise (i.e., COV
 slope for
 Group 3)
 Regressor8: COV for Group4 subjects, 0 otherwise (i.e., COV
 slope for
 Group 4)
 Regressor9: NUI for Group1 subjects, 0 otherwise (i.e., NUI
 slope for
 Group 1)
 Regressor10: NUI for Group2 subjects, 0 otherwise (i.e., NUI
 slope for
 Group 2)
 Regressor11: NUI for Group3 subjects, 0 otherwise (i.e., NUI
 slope for
 Group 3)
 Regressor12: NUI for Group4 subjects, 0 otherwise (i.e., NUI
 slope for
 Group 4)

 Description1: Does the correlation between thickness and COV,
 accounting for F1 and F2, differ from 0? Nuisance factors: NUI
 Contrast1: [0  0  0  0  0.25  0.25  0.25  0.25  0  0  0  0]

 Best,
 Daniel

 --
 Daniel (Yung-Jui) Yang, Ph.D.
 Postdoctoral Researcher
 Yale Child Study Center
 New Haven, CT
 Tel: (203) 737-5454
 E-mail: _yung-jui.yang@yale.edu_mailto:_yung-jui.yang@yale.edu_ 
mailto:_yung-jui.yang@yale.edu_


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 Douglas N. Greve, Ph.D.
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 gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu 
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 Phone Number: 617-724-2358
 Fax: 617-726-7422

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 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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[Freesurfer] one factor with three levels in qdec?

[Yang, Daniel]

Dear FreeSurfer creators and experts,

I am trying to run qdec with one discrete with three levels (i.e., 
https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf3G0V) but there is some error 
message:

ERROR: no contrasts specified.
Error in Analyze: command failed: mri_glmfit --y  …

I am wondering if three levels a discrete factor are currently supported in 
qdec in FS 5.3?

Thanks!
Daniel
--
Daniel (Yung-Jui) Yang, Ph.D.
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
Tel: (203) 737-5454
E-mail: yung-jui.y...@yale.edu
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Re: [Freesurfer] one factor with three levels in qdec?

[Yang, Daniel]

Hi Doug,

Thanks, I see. That really helps a lot. I will try to use the command line 
version.

Best,
Daniel

--
Daniel (Yung-Jui) Yang, Ph.D.
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
Tel: (203) 737-5454
E-mail: yung-jui.y...@yale.edu

On 2/16/14 7:13 PM, Douglas Greve 
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote:


sorry, you cannot have three levels in qdec (two max). You will need to use the 
command line stream (ie, create a FSGD file and consrast files, run 
mris_preproc, mri_surf2surf to smooth, mri_glmfit, and mri_glmfit-sim). See the 
wiki for more details.

doug


On 2/16/14 4:53 PM, Yang, Daniel wrote:
Dear FreeSurfer creators and experts,

I am trying to run qdec with one discrete with three levels (i.e., 
https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf3G0V) but there is some error 
message:

ERROR: no contrasts specified.
Error in Analyze: command failed: mri_glmfit --y  …

I am wondering if three levels a discrete factor are currently supported in 
qdec in FS 5.3?

Thanks!
Daniel
--
Daniel (Yung-Jui) Yang, Ph.D.
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
Tel: (203) 737-5454
E-mail: yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu



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[Freesurfer] Interaction test

[Yang, Daniel]

Dear FreeSurfer developers and experts,

If I have a binary factor (Group1: patients, Group2: controls) and a continuous 
variable (age), I know I can follow Contrast2 in the following wiki to test the 
interaction effect.

http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G1V

Contrast2: [0  0  1  -1]  tests if Age slope in patients (Group1)  controls 
(Group2), and if Age slope_Group1 - Age slope_Group2  0, I can see red/yellow.
For example, cortical thickening is accelerated in patients (vs. controls).

I am wondering how I can test for whether cortical thinning is accelerated in 
patients (vs. controls)?

Here, the slope for Age would be negative. And if cortical thinning is 
accelerated in Group1 (vs. Group2), I should observe Age slope_Group1  Age 
slope_Group2, that is, Age slope_Group1 - Age slope_Group2  0, thus, I should 
expect to see blue/cyan?

Best,
Daniel

--
Daniel (Yung-Jui) Yang, Ph.D.
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
Tel: (203) 737-5454
E-mail: yung-jui.y...@yale.edu
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[Freesurfer] MPRAGE SNR

[Yang, Daniel]

Dear FreeSurfer Experts,

Is there a way to estimate the SNR in MPRAGE scans besides using wm-anat-snr ?

For examples, I read that SNR is improved in multiecho MPRAGE and I am 
wondering how that is computed?

Thanks!
Daniel
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Re: [Freesurfer] rh or lh?

[Yang, Daniel]

Thanks! Got you.

If only there can be a header/meta info/tag added into mgh -- that would be 
great.

I believe it can help prevent errors and improve processing efficiency :)

Best,
Daniel

--
Yung-Jui Daniel Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454

On 10/1/13 7:55 PM, Douglas N Greve 
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote:


Not really. If this is an individual subject, you can look at the number
of vertices and see whether it matches lh or rh. For fsaverage, the
number of vertices is the same for lh and rh.






On 10/01/2013 07:45 PM, Yang, Daniel wrote:
Dear FreeSurfer Experts,

Is there a program that can automatically judge whether a mgh is in
the rh or lh?

Thanks!
Daniel

--
Yung-Jui Daniel Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454


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MGH-NMR Center
gr...@nmr.mgh.harvard.edumailto: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
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Re: [Freesurfer] overlay mni152 activation -- difference between tksurfer and freeview

[Yang, Daniel]

Hi Doug,

Just checking again, because I haven't heard from you. So the purpose is to use 
mri_vol2surf is convert MNI152 to a FreeSurfer (MNI305) mgh file. I am not sure 
about the correct register.dat to use. The mni152.register.dat is for MNI305 - 
MNI152 though.

I'm assuming that there exists some sort of inverse mni152.register.dat 
somewhere?

Thanks!
Daniel
--
Yung-Jui Daniel Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454

On 9/27/13 6:44 AM, Yang, Daniel 
yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu wrote:

Thanks Doug!

Because it maps from a MNI152 space to the FreeSurfer average space, do you 
know what register.dat I can use?

Is it some sort of inverse mni152.register.dat?

Thanks!
Daniel

--
Yung-Jui Daniel Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454

On 9/26/13 12:26 PM, Douglas N Greve 
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote:

They might be sampling to different surfaces. To make sure they show the
same exact thing, try mapping the data to the surface with mri_vol2surf
doug
On 09/25/2013 08:31 AM, Yang, Daniel wrote:
Dear FreeSurfer Experts,

I am trying to visualize fMRI activation (generated from fsl) on the
fsaverage inflated surface, using mni152.register.dat.

It's odd that I find the results to be slightly different between
tksurfer and freeview. However, I made sure that I am using the same
threshold...

Judging from fslview, I think the result with freeview is more
accurate -- is it due to tksurfer loading orig.mgz by default, and
free view loading something else?

Thanks!
Daniel

--
Yung-Jui Daniel Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454


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MGH-NMR Center
gr...@nmr.mgh.harvard.edumailto: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] overlay mni152 activation -- difference between tksurfer and freeview

[Yang, Daniel]

Hi Doug,

I understand. But the end product turned out to be a much smaller brain … so I 
thought there is something wrong. What should I do here?

Thanks!
Daniel

--
Yung-Jui Daniel Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454

On 10/1/13 6:00 PM, Douglas N Greve 
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote:


The way the software is set up, you should use mni152.register.dat with
mri_vol2surf to map mni152 volumes to the fsaverage (ie MNI305) surfaces

doug


On 10/01/2013 05:49 PM, Yang, Daniel wrote:
Hi Doug,

Just checking again, because I haven't heard from you. So the purpose
is to use mri_vol2surf is convert MNI152 to a FreeSurfer (MNI305) mgh
file. I am not sure about the correct register.dat to use. The
mni152.register.dat is for MNI305 - MNI152 though.

I'm assuming that there exists some sort of inverse
mni152.register.dat somewhere?

Thanks!
Daniel
--
Yung-Jui Daniel Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454

On 9/27/13 6:44 AM, Yang, Daniel 
yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu
mailto:yung-jui.y...@yale.edu wrote:

 Thanks Doug!

 Because it maps from a MNI152 space to the FreeSurfer average
 space, do you know what register.dat I can use?

 Is it some sort of inverse mni152.register.dat?
 Thanks!
 Daniel

 --
 Yung-Jui Daniel Yang, PhD
 Postdoctoral Researcher
 Yale Child Study Center
 New Haven, CT
 (203) 737-5454

 On 9/26/13 12:26 PM, Douglas N Greve 
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu
 mailto:gr...@nmr.mgh.harvard.edu wrote:

 They might be sampling to different surfaces. To make sure
 they show the
 same exact thing, try mapping the data to the surface with
 mri_vol2surf
 doug
 On 09/25/2013 08:31 AM, Yang, Daniel wrote:

 Dear FreeSurfer Experts,

 I am trying to visualize fMRI activation (generated from
 fsl) on the
 fsaverage inflated surface, using mni152.register.dat.

 It's odd that I find the results to be slightly different
 between
 tksurfer and freeview. However, I made sure that I am
 using the same
 threshold...

 Judging from fslview, I think the result with freeview is
 more
 accurate -- is it due to tksurfer loading orig.mgz by
 default, and
 free view loading something else?

 Thanks!
 Daniel

 --
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 Yale Child Study Center
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[Freesurfer] rh or lh?

[Yang, Daniel]

Dear FreeSurfer Experts,

Is there a program that can automatically judge whether a mgh is in the rh or 
lh?

Thanks!
Daniel

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Postdoctoral Researcher
Yale Child Study Center
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Re: [Freesurfer] overlay mni152 activation -- difference between tksurfer and freeview

[Yang, Daniel]

Thanks Doug!

Because it maps from a MNI152 space to the FreeSurfer average space, do you 
know what register.dat I can use?

Is it some sort of inverse mni152.register.dat?

Thanks!
Daniel

--
Yung-Jui Daniel Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454

On 9/26/13 12:26 PM, Douglas N Greve 
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote:

They might be sampling to different surfaces. To make sure they show the
same exact thing, try mapping the data to the surface with mri_vol2surf
doug
On 09/25/2013 08:31 AM, Yang, Daniel wrote:
Dear FreeSurfer Experts,

I am trying to visualize fMRI activation (generated from fsl) on the
fsaverage inflated surface, using mni152.register.dat.

It's odd that I find the results to be slightly different between
tksurfer and freeview. However, I made sure that I am using the same
threshold...

Judging from fslview, I think the result with freeview is more
accurate -- is it due to tksurfer loading orig.mgz by default, and
free view loading something else?

Thanks!
Daniel

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Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454


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[Freesurfer] overlay mni152 activation -- difference between tksurfer and freeview

[Yang, Daniel]

Dear FreeSurfer Experts,

I am trying to visualize fMRI activation (generated from fsl) on the fsaverage 
inflated surface, using mni152.register.dat.

It's odd that I find the results to be slightly different between tksurfer and 
freeview. However, I made sure that I am using the same threshold...

Judging from fslview, I think the result with freeview is more accurate -- is 
it due to tksurfer loading orig.mgz by default, and free view loading something 
else?

Thanks!
Daniel

--
Yung-Jui Daniel Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454
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Re: [Freesurfer] label stats?

[Yang, Daniel]

Dear all,

I wanted to add that I would to obtain the stats associated with fsaverage.

When I used mris_anatomical_stats on fsaverage, it gave me a warning message: 
could not read fsaverage/mri/wm.mgz

Thanks!
Daniel

--
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Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454

On 9/23/13 3:40 PM, Yang, Daniel 
yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu wrote:

Dear FreeSurfer Experts,

Is there a way to use command line to obtain the stats (e.g., area) for a given 
label?

Thanks!
Daniel

--
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Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454
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[Freesurfer] label stats?

[Yang, Daniel]

Dear FreeSurfer Experts,

Is there a way to use command line to obtain the stats (e.g., area) for a given 
label?

Thanks!
Daniel

--
Yung-Jui Daniel Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454
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Re: [Freesurfer] label stats?

[Yang, Daniel]

Hi Bruce,

I am sorry. I wasn't clear.. I wanted to obtain the label stats associated with 
fsaverage.

I also just read this earlier message: 
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg10441.html

Are things different now -- is there an easy way to obtain fsaverage's stats 
with the standard labels? They will serve as a relative basis for comparison 
only.

Thanks!
Daniel

--
Yung-Jui Daniel Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454

On 9/23/13 4:37 PM, Bruce Fischl 
fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote:

Hi Daniel

you can give it to mris_anatomical_stats with the -l label command

cheers
Bruce
On Mon,
23 Sep 2013, Yang, Daniel wrote:

Dear FreeSurfer Experts,
Is there a way to use command line to obtain the stats (e.g., area) for a given 
label?
Thanks!
Daniel

--
Yung-Jui Daniel Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454



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[Freesurfer] break down a label?

[Yang, Daniel]

Dear FreeSurfer Experts,

If I have a label that spans across multiple anatomical regions, is it possible 
to automatically break it down according to aparc.annot?

Thanks!
Daniel

--
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Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
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Re: [Freesurfer] break down a label?

[Yang, Daniel]

Hi Bruce,

Cool! This works nicely! Thanks so much!

Best,
Daniel

--
Yung-Jui Daniel Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454

On 9/22/13 10:07 AM, Bruce Fischl 
fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote:

Hi Daniel

you could do this in tksurfer, but I don't think there is a commandline
facility for it (although you could write a matlab script to do so). In
tksurfer, I would:

1. Load the label.
2. Copy label statistics to overlay
3. Delete the label
4. Load the parcellation you want to use
5. Use the custom fill with up to functional threshold and up to
different labels check (not sure of the exact wording).
6. Left click in a region that you want, and click fill.
7. Save the label.
8. Right click to unselect and go to 6 until you are done with all the
subregions

cheers
Bruce

On Sun, 22 Sep 2013, Yang, Daniel wrote:

Dear FreeSurfer Experts,
If I have a label that spans across multiple anatomical regions, is it
possible to automatically break it down according to aparc.annot?
Thanks!
Daniel
--
Yung-Jui Daniel Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454



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[Freesurfer] dilate a label?

[Yang, Daniel]

Hi FreeSurfer Experts,

Is it possible to dilate a label using command line?

Thanks!
Daniel
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Postdoctoral Researcher
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New Haven, CT
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Re: [Freesurfer] dilate a label?

[Yang, Daniel]

Hi Bruce,

That's cool! Thanks so much!

Best,
Daniel

--
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Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454

On 9/22/13 9:24 PM, Bruce Fischl 
fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote:

Hi Daniel,

yes, mri_label2label will do this, at least the current dev version and
maybe 5.3:

mri_label2label | grep dilate
--dilate  Ndilate the label N times before writing


cheers
Bruce

On Mon, 23 Sep 2013, Yang, Daniel wrote:

Hi FreeSurfer Experts,
Is it possible to dilate a label using command line?
Thanks!
Daniel
--
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Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454



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Re: [Freesurfer] dilate a label?

[Yang, Daniel]

It seems that only in dev version, mri_label2label supports dilation.

But I find that in 5.3, mris_label_calc is able to perform dilation too!

Best,
Daniel

--
Yung-Jui Daniel Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454

On 9/22/13 9:38 PM, Yang, Daniel 
yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu wrote:

Hi Bruce,

That's cool! Thanks so much!

Best,
Daniel

--
Yung-Jui Daniel Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454

On 9/22/13 9:24 PM, Bruce Fischl 
fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote:

Hi Daniel,

yes, mri_label2label will do this, at least the current dev version and
maybe 5.3:

mri_label2label | grep dilate
--dilate  Ndilate the label N times before writing


cheers
Bruce

On Mon, 23 Sep 2013, Yang, Daniel wrote:

Hi FreeSurfer Experts,
Is it possible to dilate a label using command line?
Thanks!
Daniel
--
Yung-Jui Daniel Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454



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Re: [Freesurfer] TALx coordinates

[Yang, Daniel]

Hi Doug,

I'm looking at the $FREESURFER_HOME/average/mni152.register.dat and I can see 
some relation with the formula you provided.

It appears that y and z are swapped, and the offsets are all different. Do you 
know why they are so? By the way, is there a way I can ask mri_surfcluster to 
read mni152.register.dat?

fsaverage
1.00
1.00
0.15
9.975314e-01 -7.324822e-03 1.760415e-02 9.570923e-01
-1.296475e-02 -9.262221e-03 9.970638e-01 -1.781596e+01
-1.459537e-02 -1.000945e+00 2.444772e-03 -1.854964e+01
0 0 0 1
tkregister

Thanks a lot!
Daniel

--
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Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454

On 9/15/13 3:53 PM, Douglas Greve 
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote:

That converts from MNI305 to MNI152 without going through the talairach itself. 
When FS computes Tal coords, it does so nonlinearly.
doug


On 9/11/13 12:08 PM, Yang, Daniel wrote:
Hi Doug,

It's pretty awesome. So accordingly,

MNI152x = (0.9975) MNI305x + (-0.0073) MNI305y + (0.0176) MNI305z + (-0.0429) * 
1
MNI152y = (0.0146) MNI305x + (1.0009) MNI305y + (-0.0024) MNI305z + (1.5496) * 1
MNI152z = (-0.0130) MNI305 + (-0.0093) MNI305y + (0.9971) MNI305z + (1.1840) * 1

The last row of the M (i.e., [-0.0429 1.5496 1.1840]') looks like some sort of 
offset to me, correct?

In other words, we are obtaining MNI305 first, Freesurfer convert that to TAL 
by default (question: is it done linearly or non-linearly?), and then we can 
manually convert it to MNI152 also.

Thanks so much!
Daniel

--
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Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454

On 9/10/13 6:52 PM, Douglas N Greve 
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote:

Hi Yang, I've computed a matrix that should do the trick. If you are in
matlab, then

M = [0.9975   -0.00730.0176   -0.0429
 0.01461.0009   -0.00241.5496
-0.0130   -0.00930.99711.1840
  0 0 01.]
P305 = [MNI305x MNI305y MNI305z 1]';
P152 = M*P305

Can you give this a shot and see if it makes sense? It will probably be
hard to tell since the matrix is pretty close to identity.

doug




On 09/10/2013 05:17 PM, Yang, Daniel wrote:
Thanks, Doug. I am really hoping to get MNI152 (because I also use
fsl). Are MNI305 and MNI152 the same? How can I obtain MNI152 coordinates?

Best,
Daniel

--
Yung-Jui Daniel Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454

On 9/10/13 5:14 PM, Douglas N Greve 
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu%3E wrote:


 It is an estimate of Tal coords from the MNI305. See

 http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach

 If you want MNI305, run mri_surfcluster with --nofixmni

 doug



 On 09/10/2013 05:08 PM, Yang, Daniel wrote:

 Hi all,

 The output of mri_surfcluster --sum shows TalX TalY TalZ. I am
 wondering if they are based on the Talairach system or some
 sort of
 MNI-Talairach system. If the latter, can you tell me something
 more
 about it? Like a webpage that describes its relationship
 between the
 MNI152 or the Talairach system?

 I find it confusing because mri_surfcluster said: INFO:
 fixing MNI
 talairach coordinates

 Thanks!
 Daniel

 --
 Yung-Jui Daniel Yang, PhD
 Postdoctoral Researcher
 Yale Child Study Center
 New Haven, CT
 (203) 737-5454


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Re: [Freesurfer] TALx coordinates

[Yang, Daniel]

Thanks, Doug!! That sounds good.

I think if FreeSurfer can include MNI152 output option in its next release, 
that would be awesome!

Best,
Daniel

On Sep 15, 2013, at 3:54 PM, Douglas Greve 
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote:

That converts from MNI305 to MNI152 without going through the talairach itself. 
When FS computes Tal coords, it does so nonlinearly.
doug


On 9/11/13 12:08 PM, Yang, Daniel wrote:
Hi Doug,

It's pretty awesome. So accordingly,

MNI152x = (0.9975) MNI305x + (-0.0073) MNI305y + (0.0176) MNI305z + (-0.0429) * 
1
MNI152y = (0.0146) MNI305x + (1.0009) MNI305y + (-0.0024) MNI305z + (1.5496) * 1
MNI152z = (-0.0130) MNI305 + (-0.0093) MNI305y + (0.9971) MNI305z + (1.1840) * 1

The last row of the M (i.e., [-0.0429 1.5496 1.1840]') looks like some sort of 
offset to me, correct?

In other words, we are obtaining MNI305 first, Freesurfer convert that to TAL 
by default (question: is it done linearly or non-linearly?), and then we can 
manually convert it to MNI152 also.

Thanks so much!
Daniel

--
Yung-Jui Daniel Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454

On 9/10/13 6:52 PM, Douglas N Greve 
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote:

Hi Yang, I've computed a matrix that should do the trick. If you are in
matlab, then

M = [0.9975   -0.00730.0176   -0.0429
 0.01461.0009   -0.00241.5496
-0.0130   -0.00930.99711.1840
  0 0 01.]
P305 = [MNI305x MNI305y MNI305z 1]';
P152 = M*P305

Can you give this a shot and see if it makes sense? It will probably be
hard to tell since the matrix is pretty close to identity.

doug




On 09/10/2013 05:17 PM, Yang, Daniel wrote:
Thanks, Doug. I am really hoping to get MNI152 (because I also use
fsl). Are MNI305 and MNI152 the same? How can I obtain MNI152 coordinates?

Best,
Daniel

--
Yung-Jui Daniel Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454

On 9/10/13 5:14 PM, Douglas N Greve 
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu%3E wrote:


 It is an estimate of Tal coords from the MNI305. See

 http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach

 If you want MNI305, run mri_surfcluster with --nofixmni

 doug



 On 09/10/2013 05:08 PM, Yang, Daniel wrote:

 Hi all,

 The output of mri_surfcluster --sum shows TalX TalY TalZ. I am
 wondering if they are based on the Talairach system or some
 sort of
 MNI-Talairach system. If the latter, can you tell me something
 more
 about it? Like a webpage that describes its relationship
 between the
 MNI152 or the Talairach system?

 I find it confusing because mri_surfcluster said: INFO:
 fixing MNI
 talairach coordinates

 Thanks!
 Daniel

 --
 Yung-Jui Daniel Yang, PhD
 Postdoctoral Researcher
 Yale Child Study Center
 New Haven, CT
 (203) 737-5454


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[Freesurfer] Maximum significance

[Yang, Daniel]

Hi all,

I performed cluster analyses and obtained several clusters, which are indicated 
by the corresponding maximum significance levels. For example, cluster one -- 
4.00, and cluster two -- 4.00.

Then I did a conjunction analysis to see their overlap, and then did a 
mri_surfcluster to get the clusters from the overlap. 

Then I observed that I have TalX TalY TalZ for each cluster in the overlap -- 
my question is, how does mri_surfcluster determine those coordinates? Since the 
whole cluster might have the same significance level everywhere?

Thanks,
Daniel
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Re: [Freesurfer] z-scores versus raw_age for correction in GLM_FIT or qdec

[Yang, Daniel]

Just my two cents:

I think the age should be mean-centered; otherwise, the meaning of the other 
variables need to be interpreted as age = 0 (rather than mean age = 0).

In general, I believe in qdec or mri_glmfit, the effects of Class variable are 
interpreted as 0 on the continuous/nuisance variables.

Best,
Daniel

--
Yung-Jui Daniel Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454

On 9/11/13 1:13 PM, Erik Lindberg 
erikoloflindb...@gmail.commailto:erikoloflindb...@gmail.com wrote:

Dear Douglas,
attached you´ll find the two y.fsgd file from the analysis run in GLM_FIT. the 
results are completely different (the z-score converted age produces a 
believable result, while the result correcting with raw age scores seems 
completely wrong.

best regards

Olof


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Re: [Freesurfer] Interpretation of red/blue clusters in group analysis

[Yang, Daniel]

you can refer to this post:

http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg31297.html

--
Yung-Jui Daniel Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454

On 9/12/13 9:04 AM, Anita van Loenhoud 
acvanloenh...@gmail.commailto:acvanloenh...@gmail.com wrote:

Hi FreeSurfers,

I'm doing an analysis with two groups: patients and controls. When I look at 
Does the average thickness differ between 1 (patients) and 2 (controls)?, I 
can see blue (negative) and red (positive) correlations. I know that it means 
that in some cases, the patients have a higher cortical thickness compared to 
the controls, and in others it's the other way around. But which is which?

Since most of the clusters are blue, I assume that blue means: patients have a 
lower cortical thickness compared to controls, and red means: patients have a 
higher cortical thickness compared to controls. Is this correct?

How does FreeSurfer decide which group to use as the 'reference group' (i.e. 
the group to which the other group is compared)?

Thanks,

Anita
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[Freesurfer] mri_annotation2annotation?

[Yang, Daniel]

Hi all,

I know I can use mri_label2label and then mris_anatomical_stats -l to obtain 
the label-based cortical thickness for each individual subject.

I also know that there is a tool called mri_annotation2label.

But is there a way to convert annotation to each individual subject, so that I 
can use mris_anatomical_stats -a to obtain the annotation-based cortical 
thickness for each individual subject?

Many thanks!
Daniel

--
Yung-Jui Daniel Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454
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Re: [Freesurfer] TALx coordinates

[Yang, Daniel]

Hi Doug,

It's pretty awesome. So accordingly,

MNI152x = (0.9975) MNI305x + (-0.0073) MNI305y + (0.0176) MNI305z + (-0.0429) * 
1
MNI152y = (0.0146) MNI305x + (1.0009) MNI305y + (-0.0024) MNI305z + (1.5496) * 1
MNI152z = (-0.0130) MNI305 + (-0.0093) MNI305y + (0.9971) MNI305z + (1.1840) * 1

The last row of the M (i.e., [-0.0429 1.5496 1.1840]') looks like some sort of 
offset to me, correct?

In other words, we are obtaining MNI305 first, Freesurfer convert that to TAL 
by default (question: is it done linearly or non-linearly?), and then we can 
manually convert it to MNI152 also.

Thanks so much!
Daniel

--
Yung-Jui Daniel Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454

On 9/10/13 6:52 PM, Douglas N Greve 
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote:

Hi Yang, I've computed a matrix that should do the trick. If you are in
matlab, then

M = [0.9975   -0.00730.0176   -0.0429
 0.01461.0009   -0.00241.5496
-0.0130   -0.00930.99711.1840
  0 0 01.]
P305 = [MNI305x MNI305y MNI305z 1]';
P152 = M*P305

Can you give this a shot and see if it makes sense? It will probably be
hard to tell since the matrix is pretty close to identity.

doug




On 09/10/2013 05:17 PM, Yang, Daniel wrote:
Thanks, Doug. I am really hoping to get MNI152 (because I also use
fsl). Are MNI305 and MNI152 the same? How can I obtain MNI152 coordinates?

Best,
Daniel

--
Yung-Jui Daniel Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454

On 9/10/13 5:14 PM, Douglas N Greve 
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu wrote:


 It is an estimate of Tal coords from the MNI305. See

 http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach

 If you want MNI305, run mri_surfcluster with --nofixmni

 doug



 On 09/10/2013 05:08 PM, Yang, Daniel wrote:

 Hi all,

 The output of mri_surfcluster --sum shows TalX TalY TalZ. I am
 wondering if they are based on the Talairach system or some
 sort of
 MNI-Talairach system. If the latter, can you tell me something
 more
 about it? Like a webpage that describes its relationship
 between the
 MNI152 or the Talairach system?

 I find it confusing because mri_surfcluster said: INFO:
 fixing MNI
 talairach coordinates

 Thanks!
 Daniel

 --
 Yung-Jui Daniel Yang, PhD
 Postdoctoral Researcher
 Yale Child Study Center
 New Haven, CT
 (203) 737-5454


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 --
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 MGH-NMR Center
 gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu 
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 Phone Number: 617-724-2358
 Fax: 617-726-7422

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Fax: 617-726-7422

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Re: [Freesurfer] convert .mgh to .label?

[Yang, Daniel]

Gotcha, so you mean run mri_concat --conjunct on the original .mgh files first, 
and then use mri_surfcluster to extract labels from the finalized .mgh.

By the way, mri_annotation2label works like a charm!

--
Yung-Jui Daniel Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454

On 9/9/13 6:40 PM, Douglas N Greve 
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote:

You cannot. You will have to do the conjunction on the cluster sig
files, then extract a label from that.


On 09/09/2013 06:30 PM, Yang, Daniel wrote:
Thanks so much! I used the cluster analysis, I will look for the .annot there.

I am also performing a conjunction analysis. One question I have is that can I 
perform mri_concat on those label files? I wanted to obtain the thickness value 
from the regions from the conjunction analysis.

Thanks!
Daniel

On Sep 9, 2013, at 3:08 PM, Douglas N Greve 
gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote:

If you have run the correction for multiple comparisons, there should be
an annotation (.annot) file in the QDEC output directory (in the
contrast folder). You can convert that into labels using
mri_annotation2label. Otherwise use Gari's suggestion.
doug



On 09/09/2013 03:00 PM, Garikoitz Lerma-Usabiaga wrote:
Hi Daniel,
you can use mri_surfcluster.
br,
Gari


On Mon, Sep 9, 2013 at 8:25 PM, Yang, Daniel 
yung-jui.y...@yale.edumailto:yung-jui.y...@yale.edu
mailto:yung-jui.y...@yale.edu wrote:

 Dear all,

 Is there a way to convert .mgh to .label? My .mgh is a ROI file
 from qdec-based group analysis and I don't want to draw the ROIs
 manually.

 Thanks!
 Daniel
 --
 Yung-Jui Daniel Yang, PhD
 Postdoctoral Researcher
 Yale Child Study Center
 New Haven, CT
 (203) 737-5454

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Fax: 617-726-7422

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[Freesurfer] TALx coordinates

[Yang, Daniel]

Hi all,

The output of mri_surfcluster --sum shows TalX TalY TalZ. I am wondering if 
they are based on the Talairach system or some sort of MNI-Talairach system. If 
the latter, can you tell me something more about it? Like a webpage that 
describes its relationship between the MNI152 or the Talairach system?

I find it confusing because mri_surfcluster said: INFO: fixing MNI talairach 
coordinates

Thanks!
Daniel

--
Yung-Jui Daniel Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454
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