Re: [Freesurfer] Label numbers aparc.a2009s

[Juergen Haenggi]

Dear FS experts

Please ignore my former email. 
the tool I used did not show the whole intensity range.
sorry

Cheers
Jürgen


-
University of Zurich
Dr. Jürgen Hänggi, Ph.D.
Department of Psychology
Division Neuropsychology
Binzmuehlestrasse 14, PO Box 25 
8050 Zurich, Switzerland

0041 44 635 73 97 (phone office)
0041 76 445 86 84 (phone mobile)   
0041 44 635 74 09 (fax office)
BIN 4.D.04 (office room number) 

j.haen...@psychologie.uzh.ch (email)
http://www.psychologie.uzh.ch/neuropsy/ (website)
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Am 03.06.2017 um 06:24 schrieb Juergen Haenggi:

> Dear FS experts
> 
> I have a question wrt the label numbers in FreeSurferColorLUT.txt compared 
> with those in aparc.a2009s+aseg.mgz.
> 
> I noticed that the last ctx (GM) label in FreeSurferColorLUT.txt file is 
> 12175  ctx_rh_S_temporal_transverse
> 
> whereas in the aparc.a2009s+aseg.mgz file, the highest intensity (label 
> number) is 12138.
> 
> Where this difference come from?
> 
> Thanks in advance
> Regards
> Jürgen Hänggi
> 
> 
> -
> University of Zurich
> Dr. Jürgen Hänggi, Ph.D.
> Department of Psychology
> Division Neuropsychology
> Binzmuehlestrasse 14, PO Box 25 
> 8050 Zurich, Switzerland
> 
> 0041 44 635 73 97 (phone office)
> 0041 76 445 86 84 (phone mobile)   
> 0041 44 635 74 09 (fax office)
> BIN 4.D.04 (office room number) 
> 
> j.haen...@psychologie.uzh.ch (email)
> http://www.psychologie.uzh.ch/neuropsy/ (website)
> http://www.juergenhaenggi.ch (private website)   
> 
> This e-mail (and any attachment/s) contains confidential and/or privileged
> information. If you are not the intended recipient (or have received this
> e-mail in error) please notify the sender immediately and destroy this
> e-mail. Any unauthorised copying, disclosure or distribution of the
> material in this e-mail is strictly forbidden.
> -
> 
> 
> 
> 
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[Freesurfer] Freeview overlay, positive values only

[Rita Elena Loiotile]

Hi,

Is there an easy command to only load positive values of an overlay in
Freeview.  I know in tksurfer it's truncphaseflag. Freeview does have the
"truncate" option in the surface pane of the GUI.  But, I don't see a
command line flag.  I'm hoping there's a way that's not in the help
documentation.

Thanks!
Rita
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[Freesurfer] Label numbers aparc.a2009s

[Juergen Haenggi]

Dear FS experts

I have a question wrt the label numbers in FreeSurferColorLUT.txt compared with 
those in aparc.a2009s+aseg.mgz.

I noticed that the last ctx (GM) label in FreeSurferColorLUT.txt file is 
12175  ctx_rh_S_temporal_transverse

whereas in the aparc.a2009s+aseg.mgz file, the highest intensity (label number) 
is 12138.

Where this difference come from?

Thanks in advance
Regards
Jürgen Hänggi


-
University of Zurich
Dr. Jürgen Hänggi, Ph.D.
Department of Psychology
Division Neuropsychology
Binzmuehlestrasse 14, PO Box 25 
8050 Zurich, Switzerland

0041 44 635 73 97 (phone office)
0041 76 445 86 84 (phone mobile)   
0041 44 635 74 09 (fax office)
BIN 4.D.04 (office room number) 

j.haen...@psychologie.uzh.ch (email)
http://www.psychologie.uzh.ch/neuropsy/ (website)
http://www.juergenhaenggi.ch (private website)   

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Re: [Freesurfer] running hippocampal segmentation on PING

[Bruce Fischl]

Hi Anthony
do you have any data that you have run through that version of FS? Or maybe 
you can run another dataset through it? It doesn't matter to us what 
subject it is


cheers
Bruce


On Fri, 2 Jun 2017, Anthony Dick wrote:



Hello Eugenio,

 

Thanks for responding. The PING dataset is a public use dataset but requires
direct request from PING. If I share it that would violate the data use
agreement: https://pingstudy.ucsd.edu/legal.html. You can get the data but
would need to go through the proper channels with PING, and that takes time.

 

However, I could tell you what files are in the MRI directory? Or provide
other information that might be helpful? If you know what files the
segmentation needs I could possibly just run those specific flags.

 

Anthony

 

From:  on behalf of "Iglesias
Gonzalez, Eugenio" 
Reply-To: Freesurfer support list 
Date: Friday, June 2, 2017 at 7:10 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] running hippocampal segmentation on PING

 

Dear Anthony,
Can you please send us a sample subject directory (the mri dir is enough, i
don't need the surfaces), so i can play with it and see if there's anything
we can do?
Cheers
E

Sent from my phone, please excuse brevity and typos

From: Anthony Dick
Sent: Thursday, June 1, 16:40
Subject: [Freesurfer] running hippocampal segmentation on PING
To: Freesurfer support list

Hello,

 

Our group is interested in running the hippocampal segmentation on the PING
dataset. That dataset was already Freesurfed, v4.5. When we try to just run
the –hippocampal-subfields flag (i.e., recon-all -s bert
-hippocampal-subfields-T1) it dies looking for a number of files that were
not a part of v.4.5.

 

One option is to start from scratch with v6: recon-all -all -s bert
-hippocampal-subfields-T1

 

However, this seems to be a bad option because the quality control on the
~1500 brains is already completed for the original FS run.

 

My question is, are there certain flags from –autorecon2 and –autorecon3
that we could run so we don’t have to re-freesurf everything, or would it be
better to just run –all? In other words, what are the minimum files needed
to get hippocampal-subfields-T1 to run?

 

Thanks for any suggestions!

 

Anthony

 

—

Anthony Steven Dick, Ph.D.  

Associate Professor

Director, Cognitive Neuroscience Program and Graduate Certificate in
Cognitive Neuroscience  

Department of Psychology  

Florida International University Modesto A. Maidique Campus AHC4 454  

11200 S.W. 8th Street  

Miami, FL 33199  

Ph: 305-348-4202; Lab Ph: 305-348-9055; Fx: 305-348-3879  

Email: ad...@fiu.edu

Webpage: http://myweb.fiu.edu/adick

Join the Society for the Study of Human Development:
http://www.sshdonline.org

 

 

 

 

 

 


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Re: [Freesurfer] running hippocampal segmentation on PING

[Iglesias Gonzalez, Eugenio]

Yes, please, send me a list of files. And, if you don’t mind, please send me 
aseg.mgz and wmparc.mgz, if they exist - they are segmentations, so you won’t 
be violating the agreement ;-)
Another option is sending me bert.
Cheers,
/E

Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


On 2 Jun 2017, at 14:16, Anthony Dick mailto:ad...@fiu.edu>> 
wrote:

Hello Eugenio,

Thanks for responding. The PING dataset is a public use dataset but requires 
direct request from PING. If I share it that would violate the data use 
agreement: https://pingstudy.ucsd.edu/legal.html. You can get the data but 
would need to go through the proper channels with PING, and that takes time.

However, I could tell you what files are in the MRI directory? Or provide other 
information that might be helpful? If you know what files the segmentation 
needs I could possibly just run those specific flags.

Anthony

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of "Iglesias Gonzalez, Eugenio" 
mailto:e.igles...@ucl.ac.uk>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Friday, June 2, 2017 at 7:10 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] running hippocampal segmentation on PING


Dear Anthony,
Can you please send us a sample subject directory (the mri dir is enough, i 
don't need the surfaces), so i can play with it and see if there's anything we 
can do?
Cheers
E

Sent from my phone, please excuse brevity and typos

From: Anthony Dick
Sent: Thursday, June 1, 16:40
Subject: [Freesurfer] running hippocampal segmentation on PING
To: Freesurfer support list

Hello,



Our group is interested in running the hippocampal segmentation on the PING 
dataset. That dataset was already Freesurfed, v4.5. When we try to just run the 
–hippocampal-subfields flag (i.e., recon-all -s bert -hippocampal-subfields-T1) 
it dies looking for a number of files that were not a part of v.4.5.



One option is to start from scratch with v6: recon-all -all -s bert 
-hippocampal-subfields-T1



However, this seems to be a bad option because the quality control on the ~1500 
brains is already completed for the original FS run.



My question is, are there certain flags from –autorecon2 and –autorecon3 that 
we could run so we don’t have to re-freesurf everything, or would it be better 
to just run –all? In other words, what are the minimum files needed to get 
hippocampal-subfields-T1 to run?



Thanks for any suggestions!



Anthony



—

Anthony Steven Dick, Ph.D.

Associate Professor

Director, Cognitive Neuroscience Program and Graduate Certificate in Cognitive 
Neuroscience

Department of Psychology

Florida International University Modesto A. Maidique Campus AHC4 454

11200 S.W. 8th Street

Miami, FL 33199

Ph: 305-348-4202; Lab Ph: 305-348-9055; Fx: 305-348-3879

Email: ad...@fiu.edu

Webpage: http://myweb.fiu.edu/adick

Join the Society for the Study of Human Development: http://www.sshdonline.org













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Re: [Freesurfer] running hippocampal segmentation on PING

[Anthony Dick]

Hello Eugenio,

Thanks for responding. The PING dataset is a public use dataset but requires 
direct request from PING. If I share it that would violate the data use 
agreement: https://pingstudy.ucsd.edu/legal.html. You can get the data but 
would need to go through the proper channels with PING, and that takes time.

However, I could tell you what files are in the MRI directory? Or provide other 
information that might be helpful? If you know what files the segmentation 
needs I could possibly just run those specific flags.

Anthony

From:  on behalf of "Iglesias Gonzalez, 
Eugenio" 
Reply-To: Freesurfer support list 
Date: Friday, June 2, 2017 at 7:10 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] running hippocampal segmentation on PING


Dear Anthony,
Can you please send us a sample subject directory (the mri dir is enough, i 
don't need the surfaces), so i can play with it and see if there's anything we 
can do?
Cheers
E

Sent from my phone, please excuse brevity and typos

From: Anthony Dick
Sent: Thursday, June 1, 16:40
Subject: [Freesurfer] running hippocampal segmentation on PING
To: Freesurfer support list

Hello,



Our group is interested in running the hippocampal segmentation on the PING 
dataset. That dataset was already Freesurfed, v4.5. When we try to just run the 
–hippocampal-subfields flag (i.e., recon-all -s bert -hippocampal-subfields-T1) 
it dies looking for a number of files that were not a part of v.4.5.



One option is to start from scratch with v6: recon-all -all -s bert 
-hippocampal-subfields-T1



However, this seems to be a bad option because the quality control on the ~1500 
brains is already completed for the original FS run.



My question is, are there certain flags from –autorecon2 and –autorecon3 that 
we could run so we don’t have to re-freesurf everything, or would it be better 
to just run –all? In other words, what are the minimum files needed to get 
hippocampal-subfields-T1 to run?



Thanks for any suggestions!



Anthony



—

Anthony Steven Dick, Ph.D.

Associate Professor

Director, Cognitive Neuroscience Program and Graduate Certificate in Cognitive 
Neuroscience

Department of Psychology

Florida International University Modesto A. Maidique Campus AHC4 454

11200 S.W. 8th Street

Miami, FL 33199

Ph: 305-348-4202; Lab Ph: 305-348-9055; Fx: 305-348-3879

Email: ad...@fiu.edu

Webpage: http://myweb.fiu.edu/adick

Join the Society for the Study of Human Development: http://www.sshdonline.org












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Re: [Freesurfer] running hippocampal segmentation on PING

[Iglesias Gonzalez, Eugenio]

Dear Anthony,
Can you please send us a sample subject directory (the mri dir is enough, i 
don't need the surfaces), so i can play with it and see if there's anything we 
can do?
Cheers
E

Sent from my phone, please excuse brevity and typos

From: Anthony Dick
Sent: Thursday, June 1, 16:40
Subject: [Freesurfer] running hippocampal segmentation on PING
To: Freesurfer support list

Hello,



Our group is interested in running the hippocampal segmentation on the PING 
dataset. That dataset was already Freesurfed, v4.5. When we try to just run the 
–hippocampal-subfields flag (i.e., recon-all -s bert -hippocampal-subfields-T1) 
it dies looking for a number of files that were not a part of v.4.5.



One option is to start from scratch with v6: recon-all -all -s bert 
-hippocampal-subfields-T1



However, this seems to be a bad option because the quality control on the ~1500 
brains is already completed for the original FS run.



My question is, are there certain flags from –autorecon2 and –autorecon3 that 
we could run so we don’t have to re-freesurf everything, or would it be better 
to just run –all? In other words, what are the minimum files needed to get 
hippocampal-subfields-T1 to run?



Thanks for any suggestions!



Anthony



—

Anthony Steven Dick, Ph.D.

Associate Professor

Director, Cognitive Neuroscience Program and Graduate Certificate in Cognitive 
Neuroscience

Department of Psychology

Florida International University Modesto A. Maidique Campus AHC4 454

11200 S.W. 8th Street

Miami, FL 33199

Ph: 305-348-4202; Lab Ph: 305-348-9055; Fx: 305-348-3879

Email: ad...@fiu.edu

Webpage: http://myweb.fiu.edu/adick

Join the Society for the Study of Human Development: http://www.sshdonline.org













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[Freesurfer] register.dat file between fMRI runs?

[Maria Hakonen]

Dear Freesurfer experts,

I have used fslregister to register fMRI data to anatomical data.
However, now I would like to register all fMRI runs to the fMRI run that I
have registered to the anatomical data.

Could someone please let me know how to get a register.dat file between
fMRI runs?

Many thanks already in advance!

Best,
Maria
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Re: [Freesurfer] Creating age-adjusted z score maps against a control group

[Elijah Mak]

Hi Freesurfer team,

Sorry for reposting. The previous email might have slipped through the cracks.

I was wondering if anyone know how to create subject-level Z score maps of 
thickness (against a set of healthy controls) after regressing out various 
covariates such as age / education ?

Thank you.

Best Wishes,
Elijah

Dr. Elijah Mak, Research Associate
Department of Psychiatry,  Old Age Psychiatry Group
University of Cambridge
Trinity College, CB21TQ, UK
http://www.neuroscience.cam.ac.uk/directory/profile.php?fkm24


On 23 May 2017 at 09:21:24, Elijah Mak (fk...@medschl.cam.ac.uk) wrote:

Hi Doug,

I have used fscalc to create subject-level Z score maps of cortical thickness 
against a set of healthy controls. 

fscalc $i/surf/lh.fsaverage.mgh sub
group_mean_control_lh.mgh div group_std_control_lh.mgh --o
$i/surf/lh.Z.thickness.fsaverage.mgh; done

Beyond this, is there a way to adjust the Z score maps for age, and then 
produce an age-adjusted Z score map?

Thanks for your help.

Best Wishes,
Elijah



Dr. Elijah Mak, Research Associate
Department of Psychiatry,  Old Age Psychiatry Group
University of Cambridge
Trinity College, CB21TQ, UK
http://www.neuroscience.cam.ac.uk/directory/profile.php?fkm24 

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