[Freesurfer] Postdoctoral Fellow in Analysis of Cross-Species fMRI and/or Neurophysiology

[Thomas Yeo]

Dear All,

I am looking to hire a postdoc to develop novel tools for fMRI and/or
neurophysiology analysis. Details below.

Cheers,
Thomas

Project: Develop computational tools for discovering (1) homologies
and divergences between macaque and human brain organization using
resting-fMRI and/or (2) relationship between macaque brain network
organization revealed by fMRI versus neurophysiological recordings.

Requirements: Ph.D. in computer science, electrical engineering,
statistics, computational neuroscience or related fields. The
successful applicant will work with an interdisciplinary team of
computer scientists and neuroscientists, and must be willing to learn
some neuroscience.

Research Webpage: https://sites.google.com/site/yeoyeo02/home

Compensation: Competitive and commensurate with experience

Attraction: Perform ground-breaking research at the National
University of Singapore (NUS), while enjoying the beautiful sceneries
and cultures of South-East Asia. NUS is a research-intensive
university consistently ranked among the top 30 universities in the
world 
(http://en.wikipedia.org/wiki/National_University_of_Singapore#University_rankings).

Contact: Email BT Thomas Yeo (thomas@nus.edu.sg) with your CV.

Deadline: Whenever the position is filled.
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[Freesurfer] Postdoctoral Fellow in Human-Macaque Brain Network Organization

[Thomas Yeo]

Dear All,

I am looking to hire a postdoc in human-macaque brain organization.
Details below.

Cheers,
Thomas

Project: (1) Discover homologies and divergences between macaque and
human brain organization using resting-fMRI and/or (2) Elucidate
relationship between macaque brain network organization revealed by
fMRI versus neurophysiological recordings.

Requirements: PhD in neuroscience, psychology, cognitive science or
related fields. The successful applicant will work with an
interdisciplinary team of computer scientists and neuroscientists, and
must be willing to do some programming.

Research Webpage: https://sites.google.com/site/yeoyeo02/home

Compensation: Competitive and commensurate with experience

Attraction: The National University of Singapore (NUS) boasts one of
the few primate neurophysiology labs in the world. Perform
ground-breaking research at NUS, while enjoying the beautiful
sceneries and cultures of South-East Asia. NUS is a research-intensive
university consistently ranked among the top 30 universities in the
world 
(http://en.wikipedia.org/wiki/National_University_of_Singapore#University_rankings).

Contact: Email BT Thomas Yeo (thomas@nus.edu.sg) with your CV.

Deadline: Whenever the position is filled.
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[Freesurfer] Bus error still when trying to launch tksurfer

[Claire Morley]

Hello again Bruce,
Thanks so much for your reply. I tried uninstalling XQuartz completely and
reinstalling it, and I`m still getting the bus error. I have XQuartz`s
newest version (2.7.7) that was launched in August of this year installed
and it works with Macs 10.6 and newer.

My Mac environment is such:
Mac OS X Snow Leopard 10.6.8
Memory: 4GB 1067 MHz DDR3

Model Name:iMac
  Model Identifier:iMac10,1
  Processor Name:Intel Core 2 Duo
  Processor Speed:3.06 GHz
  Number Of Processors:1
  Total Number Of Cores:2
  L2 Cache:3 MB
  Memory:4 GB
  Bus Speed:1.07 GHz
  Boot ROM Version:IM101.00CC.B00

Any further ideas what might be going on? Do I need a newer version of OS X
in order to use Freesurfer optimally?

Thank you so much again for your time!

All the best,
Claire

On Mon, Oct 20, 2014 at 6:00 PM, 
wrote:

> Send Freesurfer mailing list submissions to
> freesurfer@nmr.mgh.harvard.edu
>
> To subscribe or unsubscribe via the World Wide Web, visit
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> or, via email, send a message with subject or body 'help' to
> freesurfer-requ...@nmr.mgh.harvard.edu
>
> You can reach the person managing the list at
> freesurfer-ow...@nmr.mgh.harvard.edu
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Freesurfer digest..."
>
>
> Today's Topics:
>
>1. GLM contrast vector for continuous variable interaction
>   (Bronwyn Overs)
>2. Bus error when trying to launch tksurfer (Claire Morley)
>3. Re: Bus error when trying to launch tksurfer (J?rgen H?nggi)
>4. Re: Bus error when trying to launch tksurfer (Bruce Fischl)
>5. Do not have 'recon edit' button! Please help! (Smaragdi A.)
>6. Re: Do not have 'recon edit' button! Please help! (Bruce Fischl)
>7. Re: Do not have 'recon edit' button! Please help! (Smaragdi A.)
>8. unpacksdcmdir (Alshikho, Mohamad J.)
>9. Re: unpacksdcmdir (Shantanu Ghosh)
>   10. Re: unpacksdcmdir (Douglas N Greve)
>   11. Re: GLM contrast vector for continuous variable   interaction
>   (Douglas N Greve)
>
>
> --
>
> Message: 1
> Date: Mon, 20 Oct 2014 09:33:13 +1100
> From: Bronwyn Overs 
> Subject: [Freesurfer] GLM contrast vector for continuous variable
> interaction
> To: Freesurfer support list 
> Message-ID: <54443c29.9000...@neura.edu.au>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear Freesurfer Mailing List,
>
> I am running a GLM in freesurfer 2 categorical variables (2 levels), and
> three continuous variables (age, prs, & sles). My fsgd file looks like
> this:
>
> GroupDescriptorFile 1
> Title GLM_sles-group-gender-age
> Class genderMale-groupControl
> Class genderFemale-groupControl
> Class genderMale-groupAtRisk
> Class genderFemale-groupAtRisk
> Variables age prs sles
> Input ID_001 genderFemale-groupAtRisk 20 21 96
> Input ID_002 genderFemale-groupControl 21 13 79
> ...
>
> I want to test for an interaction between prs and sles, while
> controlling for age, gender, and group. Can you tell me if the following
> contrast vector will correctly test for this interaction:
>
> 000000000   0 0   0   0.5
> 0.50.50.5
> 000000000.50.50.50.5 0
> 0   0   0
>
> --
>
> Kind regards,
>
> Bronwyn Overs
> Research Assistant
>
> Neuroscience Research Australia
>
> Neuroscience Research Australia
> Margarete Ainsworth Building
> Barker Street Randwick Sydney NSW 2031 Australia
> *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265
>
> neura.edu.au 
>
> Follow @neuraustralia on twitter
> Follow NeuRA on facebook
> Subscribe to the
> NeuRA Magazine 
>
> -- next part --
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[Freesurfer] Fwd: A BBVA Foundation-UPM Chair on Biomedical Imaging

[José Ángel Pineda]

   Notification of the “Isaac Peral” Program to contract one senior
researcher associated with BBVA Foundation-UPM Industry-Academia chairs for
scientific-technological research in Medical Imaging, within Marie Curie
Action COFUND.



This notice provides for a maximum of one position in the area of
scientific-technological initiatives in Biotech indicated below, in
accordance with the procedure established in the Regulatory Bases of 30
April 2009 for the ISAAC PERAL Program for Senior UPM Researchers (in the
attached document). The candidate degree may be from any
specialization in Engineering,
Physics, Mathematics, Statistics, Biology, Biochemistry, etc.


Location:

The activities will be carried out in the Campus of International
Excellence: Campus of Montegancedo at the CTB: Centre for
Biomedical Technology (www.ctb.upm.es), in Madrid, Spain.



Beneficiaries:

1. Have held a PhD for more than 10 years, effectively pursuing
uninterrupted research activity during that time.
2. Have extensive research experience in the sphere of the profile of the
contract announced, i.e. biomedical imaging.

3. Have pursued their research activity following the award of their PhD in
relevant foreign Research Centers for at least six years or have studied
the whole of the PhD and graduated in a foreign University or Research
Centre and have pursued subsequent research activity in a relevant foreign
research center for at least three years.
4. Have certified experience in the management of research groups in
university institutions or relevant research centers.

All the requirements demanded and the merits argued by candidates must have
been fulfilled prior to the date of termination of the period for the
submission of applications.



N.B.: The details of the call will be published soon, although they will be
very similar to those of the previous call (declared desert), that can be
seen at:


*http://www.upm.es/sfs/Rectorado/Vicerrectorado%20de%20Investigacion/Servicio%20de%20Investigacion/Ayudas_y_Convocatorias/Convocatorias_Propias/Convocatoria-MedImaging-Eng.pdf
*


Regulatory bases can be seen at:


http://www.upm.es/internacional/Researchers/Post_DoctoralandResearchCareerPositions/IsaacPeralProgramme


 Any questions, please feel free to contact the director of the CTB
(Francisco del Pozo Guerrero - francisco.delp...@ctb.upm.es).

[image: http://www.upm.es/sfs/Montegancedo/Noticias/imagenes/ctb.gif]

Prof. Francisco del Pozo

Director
Center for Biomedical Technology (CTB)
Universidad Politécnica de Madrid
Parque Científico y Tecnológico de la UPM
Campus de Montegancedo
28223 Pozuelo de Alarcón, Madrid, ES
Tfo: +34 913364632 (Tfo: +34 913364631)
www.ctb.upm.es



-- 

José Angel Pineda Pardo

Center of Biomedical Technology (CTB)

Parque Científico y Tecnológico de la UPM

Campus de Montegancedo

28223 Pozuelo de Alarcón, Madrid, ES
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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
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[Freesurfer] Crash on recon-all on Macbook Pro (Mavericks and Yosemite)

[Matthew Riddle]

Dear Freesurfer Team,

I recently installed Freesurfer on a new Macbook pro, which was upgraded to 
Yosemite, and I re-installed X11 after the upgrade, but I’m still experiencing 
an issue with freesurfer that I’m hoping you might have some idea about.

Just to test the install and see what my total time was to run a recon-all on 
this machine, I ran the normal recon-all on bert with the command from an X11 
terminal:

sudo –E recon-all –s bert –all

The processes crashes in a minute or two at the same place each time, and this 
is the last bit of output.

MRIchangeType: Building histogram
writing to /Applications/freesurfer/subjects/bert/mri/orig.mgz...
\n mri_add_xform_to_header -c 
/Applications/freesurfer/subjects/bert/mri/transforms/talairach.xfm 
/Applications/freesurfer/subjects/bert/mri/orig.mgz 
/Applications/freesurfer/subjects/bert/mri/orig.mgz \n
INFO: extension is mgz
#
#@# Talairach Thu Oct 23 07:32:53 EDT 2014
/Applications/freesurfer/subjects/bert/mri
\n mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i 
orig.mgz --o orig_nu.mgz \n
Darwin Matthews-MacBook-Pro.local 14.0.0 Darwin Kernel Version 14.0.0: Fri Sep 
19 00:26:44 PDT 2014; root:xnu-2782.1.97~2/RELEASE_X86_64 x86_64

recon-all -s bert exited with ERRORS at Thu Oct 23 07:32:55 EDT 2014


I tried this on an almost identical machine running Mavericks, and got the 
exact same problem.

>From my bugr output:

FREESURFER_HOME: /Applications/freesurfer

Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0

Kernel info: Darwin 14.0.0 x86_64



The recon-all.log file doesn’t provide any additional information, it just 
mirrors the output from the terminal.

Thanks,

-Matt


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Re: [Freesurfer] Creating an ROI mask for Cortical Thickness Analysis

[Smith, Michael]

I guess I'm not entirely sure how to do that? Are there any tutorials on how to 
extract an ROI from the aparc.stats file?

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: Wednesday, October 22, 2014 4:21 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Creating an ROI mask for Cortical Thickness Analysis


Why not just get it from the ?h.aparc.stats file?

On 10/22/2014 03:43 PM, Smith, Michael wrote:
> Hello Freesurfer's
>
> I am trying to look at the cortical thickness for a specific ROI on 
> the cortical surface (Primary Auditory Cortex: transverse temporal 
> gyri). I found a specific tutorial
> (https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness)
> however the tutorial assumes I already have an ROI mask created. I was 
> wondering if anyone had any tips on creating an ROI for the cortical 
> surface from the parcellation/annotation files. I know you can 
> "hand-draw" ROI's in tkmedit or freeview but I would prefer something 
> less subjective that doesn't rely on my untrained eye and unsteady 
> hand! Thanks in advance.
>
> Best,
>
> Michael S.
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: 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] Creating an ROI mask for Cortical Thickness Analysis

[Bruce Fischl]

Hi Michael

you can use mri_annotation2label to extract a specific label from the 
aparc file and go from there.

cheers
Bruce
On Thu, 23 Oct 2014, Smith, Michael wrote:

> I guess I'm not entirely sure how to do that? Are there any tutorials on how 
> to extract an ROI from the aparc.stats file?
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
> Sent: Wednesday, October 22, 2014 4:21 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Creating an ROI mask for Cortical Thickness Analysis
>
>
> Why not just get it from the ?h.aparc.stats file?
>
> On 10/22/2014 03:43 PM, Smith, Michael wrote:
>> Hello Freesurfer's
>>
>> I am trying to look at the cortical thickness for a specific ROI on
>> the cortical surface (Primary Auditory Cortex: transverse temporal
>> gyri). I found a specific tutorial
>> (https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness)
>> however the tutorial assumes I already have an ROI mask created. I was
>> wondering if anyone had any tips on creating an ROI for the cortical
>> surface from the parcellation/annotation files. I know you can
>> "hand-draw" ROI's in tkmedit or freeview but I would prefer something
>> less subjective that doesn't rely on my untrained eye and unsteady
>> hand! Thanks in advance.
>>
>> Best,
>>
>> Michael S.
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: 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/
>
> ___
> 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
>
>
>
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[Freesurfer] prefrontal cortex label

[Anna Jonsson]

Dear group,

Is there a way to create a prefrontal cortex label in fresurfer? if so,
please tell me the exact steps to do so, I am very confused.


Thank you,

Anna
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Crash on recon-all on Macbook Pro (Mavericks and Yosemite)

[Z K]

Matt,

Can you send me the actual recon-all.log file? It might be helpful for 
me to diagnose the issue. Thanks.

-Zeke

On 10/23/2014 07:48 AM, Matthew Riddle wrote:
> Dear Freesurfer Team,
>
> I recently installed Freesurfer on a new Macbook pro, which was upgraded
> to Yosemite, and I re-installed X11 after the upgrade, but I’m still
> experiencing an issue with freesurfer that I’m hoping you might have
> some idea about.
>
> Just to test the install and see what my total time was to run a
> recon-all on this machine, I ran the normal recon-all on bert with the
> command from an X11 terminal:
>
> sudo –E recon-all –s bert –all
>
> The processes crashes in a minute or two at the same place each time,
> and this is the last bit of output.
>
> MRIchangeType: Building histogram
> writing to /Applications/freesurfer/subjects/bert/mri/orig.mgz...
> \n mri_add_xform_to_header -c
> /Applications/freesurfer/subjects/bert/mri/transforms/talairach.xfm
> /Applications/freesurfer/subjects/bert/mri/orig.mgz
> /Applications/freesurfer/subjects/bert/mri/orig.mgz \n
> INFO: extension is mgz
> #
> #@# Talairach Thu Oct 23 07:32:53 EDT 2014
> /Applications/freesurfer/subjects/bert/mri
> \n mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50
> --no-rescale --i orig.mgz --o orig_nu.mgz \n
> Darwin Matthews-MacBook-Pro.local 14.0.0 Darwin Kernel Version 14.0.0:
> Fri Sep 19 00:26:44 PDT 2014; root:xnu-2782.1.97~2/RELEASE_X86_64 x86_64
>
> recon-all -s bert exited with ERRORS at Thu Oct 23 07:32:55 EDT 2014
>
>
> I tried this on an almost identical machine running Mavericks, and got
> the exact same problem.
>
>  From my bugr output:
>
> FREESURFER_HOME: /Applications/freesurfer
>
> Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
>
> Kernel info: Darwin 14.0.0 x86_64
>
>
>
> The recon-all.log file doesn’t provide any additional information, it
> just mirrors the output from the terminal.
>
> Thanks,
>
> -Matt
>
>
>
>
> ___
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>
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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
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Re: [Freesurfer] Bus error still when trying to launch tksurfer

[Z K]

Hello Claire,

Sorry this has been such a pain. There has been some reports that the 
newer versions of XQuartz may have broken some of the freesurfer GUIs.

Could you please try deleting XQuartz again an resinstalling XQuartz 
version 2.7.5. You can download it from this page:

http://xquartz.macosforge.org/trac/wiki/Releases

Then try again. Let me know how it goes. And please send me an exact 
copy of any error that may be produced. Thanks.

-Zeke

On 10/23/2014 06:21 AM, Claire Morley wrote:
> Hello again Bruce,
> Thanks so much for your reply. I tried uninstalling XQuartz completely
> and reinstalling it, and I`m still getting the bus error. I have
> XQuartz`s newest version (2.7.7) that was launched in August of this
> year installed and it works with Macs 10.6 and newer.
>
> My Mac environment is such:
> Mac OS X Snow Leopard 10.6.8
> Memory: 4GB 1067 MHz DDR3
>
> Model Name:iMac
>Model Identifier:iMac10,1
>Processor Name:Intel Core 2 Duo
>Processor Speed:3.06 GHz
>Number Of Processors:1
>Total Number Of Cores:2
>L2 Cache:3 MB
>Memory:4 GB
>Bus Speed:1.07 GHz
>Boot ROM Version:IM101.00CC.B00
>
> Any further ideas what might be going on? Do I need a newer version of
> OS X in order to use Freesurfer optimally?
>
> Thank you so much again for your time!
>
> All the best,
> Claire
>
> On Mon, Oct 20, 2014 at 6:00 PM,  > wrote:
>
> Send Freesurfer mailing list submissions to
> freesurfer@nmr.mgh.harvard.edu 
>
> To subscribe or unsubscribe via the World Wide Web, visit
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> or, via email, send a message with subject or body 'help' to
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> 
>
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> 
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Freesurfer digest..."
>
>
> Today's Topics:
>
> 1. GLM contrast vector for continuous variable interaction
>(Bronwyn Overs)
> 2. Bus error when trying to launch tksurfer (Claire Morley)
> 3. Re: Bus error when trying to launch tksurfer (J?rgen H?nggi)
> 4. Re: Bus error when trying to launch tksurfer (Bruce Fischl)
> 5. Do not have 'recon edit' button! Please help! (Smaragdi A.)
> 6. Re: Do not have 'recon edit' button! Please help! (Bruce Fischl)
> 7. Re: Do not have 'recon edit' button! Please help! (Smaragdi A.)
> 8. unpacksdcmdir (Alshikho, Mohamad J.)
> 9. Re: unpacksdcmdir (Shantanu Ghosh)
>10. Re: unpacksdcmdir (Douglas N Greve)
>11. Re: GLM contrast vector for continuous variable   interaction
>(Douglas N Greve)
>
>
> --
>
> Message: 1
> Date: Mon, 20 Oct 2014 09:33:13 +1100
> From: Bronwyn Overs mailto:b.ov...@neura.edu.au>>
> Subject: [Freesurfer] GLM contrast vector for continuous variable
>  interaction
> To: Freesurfer support list  >
> Message-ID: <54443c29.9000...@neura.edu.au
> >
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear Freesurfer Mailing List,
>
> I am running a GLM in freesurfer 2 categorical variables (2 levels), and
> three continuous variables (age, prs, & sles). My fsgd file looks
> like this:
>
> GroupDescriptorFile 1
> Title GLM_sles-group-gender-age
> Class genderMale-groupControl
> Class genderFemale-groupControl
> Class genderMale-groupAtRisk
> Class genderFemale-groupAtRisk
> Variables age prs sles
> Input ID_001 genderFemale-groupAtRisk 20 21 96
> Input ID_002 genderFemale-groupControl 21 13 79
> ...
>
> I want to test for an interaction between prs and sles, while
> controlling for age, gender, and group. Can you tell me if the following
> contrast vector will correctly test for this interaction:
>
> 000000000   0 0   0   0.5
> 0.50.50.5
> 000000000.50.50.50.5 0
> 0   0   0
>
> --
>
> Kind regards,
>
> Bronwyn Overs
> Research Assistant
>
> Neuroscience Research Australia
>
> Neuroscience Research Australia
> Margarete Ainsworth Building
> Barker Street Randwick Sydney NSW 2031 Australia
> *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265
>
> neura.edu.au  
>
> Follow @neuraustralia on twitter
> Follow NeuRA on facebook
>   

Re: [Freesurfer] longitudinal base template creation with one timepoint

[Martin Reuter]

Hi Tracy,

if you mean how the method works internally:

the input image is registered to it's left right flipped version and 
mapped into the midspace. this makes the image upright and straight (see 
HBM abstract
*Robust and Accurate Contralateral Registration for Pose Normalization 
and Tumor Segmentation*. M.Reuter, H.D.Rosas, B.Fischl. /Human Brain 
Mapping 2012, Beijing 
./

http://reuter.mit.edu/blue/papers/reuter-hbm12-tumor/reuter-hbm12-tumor.pdf

That new image is then taken as the base. The reasoning behind this is:
- the base image gets interpolated similarly to a regular base (with N>1 
time points)
- all other steps are identical to the longitudinal workflow (surfaces 
on the base to initialize the longitudinal time point).


The original publication for the longitudinal pipeline is this
*Within-Subject Template Estimation for Unbiased Longitudinal Image 
Analysis*. M.Reuter, N.J.Schmansky, H.D.Rosas, B.Fischl. /NeuroImage 
61(4):1402-1418, 2012/.


but does not describe the single time point situation, which is 
discussed in:
*Statistical Analysis of Longitudinal Neuroimage Data with Linear Mixed 
Effects Models*. J.L.Bernal-Rusiel, D.N.Greve, M.Reuter et al. 
/NeuroImage 66:249-260, 2012/.


Best, Martin

On 10/23/2014 12:17 AM, Martin Reuter wrote:

Hi Tracy,
When you call recon-all -base simply pass only the single time point -tp.
Best Martin


Sent via my smartphone, please excuse brevity.

 Original message 
From: Tracy Melzer
Date:10/22/2014 10:59 PM (GMT-05:00)
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] longitudinal base template creation with one 
timepoint


Dear FreeSurfer Experts,

I am interested in how the longitudinal stream creates a base template 
with only a single image. Could someone please explain how or point me 
to a reference as to how this is accomplished?


Thank you,
Tracy Melzer



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--
Dr. Martin Reuter

Instructor in Neurology
  Harvard Medical School
Assistant in Neuroscience
  Dept. of Radiology, Massachusetts General Hospital
  Dept. of Neurology, Massachusetts General Hospital
Research Affiliate
  Computer Science and Artificial Intelligence Lab,
  Dept. of Electrical Engineering and Computer Science,
  Massachusetts Institute of Technology

A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129

Phone: +1-617-724-5652
Email:
   mreu...@nmr.mgh.harvard.edu
   reu...@mit.edu
Web  : http://reuter.mit.edu

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Re: [Freesurfer] Creating an ROI mask for Cortical Thickness Analysis

[Douglas N Greve]

It is just a text file, so you can just look in it. You can also run 
aparcstats2table to extract all ROIs or a particular ROI for a group of 
subjects.
doug

On 10/23/2014 09:00 AM, Smith, Michael wrote:
> I guess I'm not entirely sure how to do that? Are there any tutorials on how 
> to extract an ROI from the aparc.stats file?
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
> Sent: Wednesday, October 22, 2014 4:21 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Creating an ROI mask for Cortical Thickness Analysis
>
>
> Why not just get it from the ?h.aparc.stats file?
>
> On 10/22/2014 03:43 PM, Smith, Michael wrote:
>> Hello Freesurfer's
>>
>> I am trying to look at the cortical thickness for a specific ROI on
>> the cortical surface (Primary Auditory Cortex: transverse temporal
>> gyri). I found a specific tutorial
>> (https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness)
>> however the tutorial assumes I already have an ROI mask created. I was
>> wondering if anyone had any tips on creating an ROI for the cortical
>> surface from the parcellation/annotation files. I know you can
>> "hand-draw" ROI's in tkmedit or freeview but I would prefer something
>> less subjective that doesn't rely on my untrained eye and unsteady
>> hand! Thanks in advance.
>>
>> Best,
>>
>> Michael S.
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: 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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> at http://www.partners.org/complianceline . If the e-mail was sent to you in 
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>
>
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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
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Re: [Freesurfer] Crash on recon-all on Macbook Pro (Mavericks and Yosemite)

[Matthew Riddle]

Hi Zeke,

So I may have solved the issue. Since /applications is write protected by 
default, I had to run the recon-all with sudo. But it seems like the 
subroutines of recon-all don't inherit the permissions, so I moved my Subjects 
directory to Documents, and then I can run recon-all without the initial crash, 
since permissions are no longer an issue. Hopefully it will run all the way 
through. 

Best 

-Matt 

Sent from my iPhone

> On Oct 23, 2014, at 10:34 AM, "Z K"  wrote:
> 
> Matt,
> 
> Can you send me the actual recon-all.log file? It might be helpful for 
> me to diagnose the issue. Thanks.
> 
> -Zeke
> 
>> On 10/23/2014 07:48 AM, Matthew Riddle wrote:
>> Dear Freesurfer Team,
>> 
>> I recently installed Freesurfer on a new Macbook pro, which was upgraded
>> to Yosemite, and I re-installed X11 after the upgrade, but I’m still
>> experiencing an issue with freesurfer that I’m hoping you might have
>> some idea about.
>> 
>> Just to test the install and see what my total time was to run a
>> recon-all on this machine, I ran the normal recon-all on bert with the
>> command from an X11 terminal:
>> 
>> sudo –E recon-all –s bert –all
>> 
>> The processes crashes in a minute or two at the same place each time,
>> and this is the last bit of output.
>> 
>> MRIchangeType: Building histogram
>> writing to /Applications/freesurfer/subjects/bert/mri/orig.mgz...
>> \n mri_add_xform_to_header -c
>> /Applications/freesurfer/subjects/bert/mri/transforms/talairach.xfm
>> /Applications/freesurfer/subjects/bert/mri/orig.mgz
>> /Applications/freesurfer/subjects/bert/mri/orig.mgz \n
>> INFO: extension is mgz
>> #
>> #@# Talairach Thu Oct 23 07:32:53 EDT 2014
>> /Applications/freesurfer/subjects/bert/mri
>> \n mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50
>> --no-rescale --i orig.mgz --o orig_nu.mgz \n
>> Darwin Matthews-MacBook-Pro.local 14.0.0 Darwin Kernel Version 14.0.0:
>> Fri Sep 19 00:26:44 PDT 2014; root:xnu-2782.1.97~2/RELEASE_X86_64 x86_64
>> 
>> recon-all -s bert exited with ERRORS at Thu Oct 23 07:32:55 EDT 2014
>> 
>> 
>> I tried this on an almost identical machine running Mavericks, and got
>> the exact same problem.
>> 
>> From my bugr output:
>> 
>> FREESURFER_HOME: /Applications/freesurfer
>> 
>> Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
>> 
>> Kernel info: Darwin 14.0.0 x86_64
>> 
>> 
>> 
>> The recon-all.log file doesn’t provide any additional information, it
>> just mirrors the output from the terminal.
>> 
>> Thanks,
>> 
>> -Matt
>> 
>> 
>> 
>> 
>> ___
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> 
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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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Re: [Freesurfer] prefrontal cortex label

[Douglas N Greve]

You can use mri_annotation2label to break up the annotation into 
individual labels, then use mris_label2annot to recombine selected 
labels into an annotation or use mri_merge_label to merge them into a 
single label. All you have to do is decide with labels define prefontal
doug


On 10/23/2014 10:25 AM, Anna Jonsson wrote:
> Dear group,
>
> Is there a way to create a prefrontal cortex label in fresurfer? if 
> so, please tell me the exact steps to do so, I am very confused.
>
>
> Thank you,
>
> Anna
>
>
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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
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Re: [Freesurfer] Crash on recon-all on Macbook Pro (Mavericks and Yosemite)

[Z K]

Interesting. Ive never encountered that issue before but Ive also never 
conducted an install test on subject bert on Mavericks or Yosemite. Ill 
take a look. Thanks for the update.

-Zeke

On 10/23/2014 12:03 PM, Matthew Riddle wrote:
> Hi Zeke,
>
> So I may have solved the issue. Since /applications is write protected by 
> default, I had to run the recon-all with sudo. But it seems like the 
> subroutines of recon-all don't inherit the permissions, so I moved my 
> Subjects directory to Documents, and then I can run recon-all without the 
> initial crash, since permissions are no longer an issue. Hopefully it will 
> run all the way through.
>
> Best
>
> -Matt
>
> Sent from my iPhone
>
>> On Oct 23, 2014, at 10:34 AM, "Z K"  wrote:
>>
>> Matt,
>>
>> Can you send me the actual recon-all.log file? It might be helpful for
>> me to diagnose the issue. Thanks.
>>
>> -Zeke
>>
>>> On 10/23/2014 07:48 AM, Matthew Riddle wrote:
>>> Dear Freesurfer Team,
>>>
>>> I recently installed Freesurfer on a new Macbook pro, which was upgraded
>>> to Yosemite, and I re-installed X11 after the upgrade, but I’m still
>>> experiencing an issue with freesurfer that I’m hoping you might have
>>> some idea about.
>>>
>>> Just to test the install and see what my total time was to run a
>>> recon-all on this machine, I ran the normal recon-all on bert with the
>>> command from an X11 terminal:
>>>
>>> sudo –E recon-all –s bert –all
>>>
>>> The processes crashes in a minute or two at the same place each time,
>>> and this is the last bit of output.
>>>
>>> MRIchangeType: Building histogram
>>> writing to /Applications/freesurfer/subjects/bert/mri/orig.mgz...
>>> \n mri_add_xform_to_header -c
>>> /Applications/freesurfer/subjects/bert/mri/transforms/talairach.xfm
>>> /Applications/freesurfer/subjects/bert/mri/orig.mgz
>>> /Applications/freesurfer/subjects/bert/mri/orig.mgz \n
>>> INFO: extension is mgz
>>> #
>>> #@# Talairach Thu Oct 23 07:32:53 EDT 2014
>>> /Applications/freesurfer/subjects/bert/mri
>>> \n mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50
>>> --no-rescale --i orig.mgz --o orig_nu.mgz \n
>>> Darwin Matthews-MacBook-Pro.local 14.0.0 Darwin Kernel Version 14.0.0:
>>> Fri Sep 19 00:26:44 PDT 2014; root:xnu-2782.1.97~2/RELEASE_X86_64 x86_64
>>>
>>> recon-all -s bert exited with ERRORS at Thu Oct 23 07:32:55 EDT 2014
>>>
>>>
>>> I tried this on an almost identical machine running Mavericks, and got
>>> the exact same problem.
>>>
>>>  From my bugr output:
>>>
>>> FREESURFER_HOME: /Applications/freesurfer
>>>
>>> Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
>>>
>>> Kernel info: Darwin 14.0.0 x86_64
>>>
>>>
>>>
>>> The recon-all.log file doesn’t provide any additional information, it
>>> just mirrors the output from the terminal.
>>>
>>> Thanks,
>>>
>>> -Matt
>>>
>>>
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> ___
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>> 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.
>>
>
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Re: [Freesurfer] Crash on recon-all on Macbook Pro (Mavericks and Yosemite)

[Matthew Riddle]

I tried to run a recon-all on a brand new subject and ran into the same issue, 
so I just moved the subjects directory on a hunch. I'm used to running 
Freesurfer on a CentOS system, so I'd never really considered OSX being as 
picky as it seems to be about write permissions. Bert's recon has been running 
for a couple of hours now without an issue, so let's hope it keeps going. I'll 
get back to you after it (hopefully) completes and let you know if it solves 
the issue. 

-Matt 

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Z K
Sent: Thursday, October 23, 2014 12:08 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Crash on recon-all on Macbook Pro (Mavericks and 
Yosemite)

Interesting. Ive never encountered that issue before but Ive also never 
conducted an install test on subject bert on Mavericks or Yosemite. Ill take a 
look. Thanks for the update.

-Zeke

On 10/23/2014 12:03 PM, Matthew Riddle wrote:
> Hi Zeke,
>
> So I may have solved the issue. Since /applications is write protected by 
> default, I had to run the recon-all with sudo. But it seems like the 
> subroutines of recon-all don't inherit the permissions, so I moved my 
> Subjects directory to Documents, and then I can run recon-all without the 
> initial crash, since permissions are no longer an issue. Hopefully it will 
> run all the way through.
>
> Best
>
> -Matt
>
> Sent from my iPhone
>
>> On Oct 23, 2014, at 10:34 AM, "Z K"  wrote:
>>
>> Matt,
>>
>> Can you send me the actual recon-all.log file? It might be helpful 
>> for me to diagnose the issue. Thanks.
>>
>> -Zeke
>>
>>> On 10/23/2014 07:48 AM, Matthew Riddle wrote:
>>> Dear Freesurfer Team,
>>>
>>> I recently installed Freesurfer on a new Macbook pro, which was 
>>> upgraded to Yosemite, and I re-installed X11 after the upgrade, but 
>>> I'm still experiencing an issue with freesurfer that I'm hoping you 
>>> might have some idea about.
>>>
>>> Just to test the install and see what my total time was to run a 
>>> recon-all on this machine, I ran the normal recon-all on bert with 
>>> the command from an X11 terminal:
>>>
>>> sudo -E recon-all -s bert -all
>>>
>>> The processes crashes in a minute or two at the same place each 
>>> time, and this is the last bit of output.
>>>
>>> MRIchangeType: Building histogram
>>> writing to /Applications/freesurfer/subjects/bert/mri/orig.mgz...
>>> \n mri_add_xform_to_header -c
>>> /Applications/freesurfer/subjects/bert/mri/transforms/talairach.xfm
>>> /Applications/freesurfer/subjects/bert/mri/orig.mgz
>>> /Applications/freesurfer/subjects/bert/mri/orig.mgz \n
>>> INFO: extension is mgz
>>> #
>>> #@# Talairach Thu Oct 23 07:32:53 EDT 2014 
>>> /Applications/freesurfer/subjects/bert/mri
>>> \n mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 
>>> --no-rescale --i orig.mgz --o orig_nu.mgz \n Darwin 
>>> Matthews-MacBook-Pro.local 14.0.0 Darwin Kernel Version 14.0.0:
>>> Fri Sep 19 00:26:44 PDT 2014; root:xnu-2782.1.97~2/RELEASE_X86_64 
>>> x86_64
>>>
>>> recon-all -s bert exited with ERRORS at Thu Oct 23 07:32:55 EDT 2014
>>>
>>>
>>> I tried this on an almost identical machine running Mavericks, and 
>>> got the exact same problem.
>>>
>>>  From my bugr output:
>>>
>>> FREESURFER_HOME: /Applications/freesurfer
>>>
>>> Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
>>>
>>> Kernel info: Darwin 14.0.0 x86_64
>>>
>>>
>>>
>>> The recon-all.log file doesn't provide any additional information, 
>>> it just mirrors the output from the terminal.
>>>
>>> Thanks,
>>>
>>> -Matt
>>>
>>>
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> ___
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>> 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.
>>
>
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Re: [Freesurfer] Sulcal CSF Volume

[Douglas N Greve]

No, not currently. This is quite a hard problem even if you have a T2. 
The pulse sequences are usually low enough bandwidth that fat from the 
scalp and skull marrow shift into the CSF spaces making it impossible to 
properly segment that area as CSF. If you wanted an approximate value, 
you could create a binary mask from the aparc+aseg.mgz, dilated it by 3 
or 4 voxels, then erode it by the same amount, then remove the original 
mask. The remaining voxels will be something like the sulcal CSF.

doug


On 10/22/2014 04:50 PM, Mohammed Goryawala wrote:
> Hello FreeSurfer Experts,
>
> Is it possible to estimate the sulcal CSF volume in Freesurfer 
> processing? If not directly are there any indirect means that can give 
> me an estimate?
>
> Thank you
>
> Mohammed Goryawala, PhD
> Department of Radiology
> Miller School of Medicine, University of Miami
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] Sulcal CSF Volume

[Mohammed Goryawala]

Thanks Doug.

I was looking at a paper  "ARANGO, C., MCMAHON, R. P., LEFKOWITZ, D. M.,
PEARLSON, G., KIRKPATRICK, B. & BUCHANAN, R. W. 2008. Patterns of cranial,
brain and sulcal CSF volumes in male and female deficit and nondeficit
patients with schizophrenia. Psychiatry Research: Neuroimaging, 162,
91-100.", which estimates sulcal CSF volume as
2.4.4. Sulcal CSF (sCSF)

The sCSF was derived by subtracting T
​otal ​
B
​rain ​
V
​olume ​
and V
​entricular  ​
V
​olume​
from T
​otal ​
C
​ranial ​
V
olume​
.

​Can such a strategy be explored using FreeSurfer​ output ?

​Thanks for your advice

Mohammed​


On Thu, Oct 23, 2014 at 12:16 PM, Douglas N Greve  wrote:

>
> No, not currently. This is quite a hard problem even if you have a T2.
> The pulse sequences are usually low enough bandwidth that fat from the
> scalp and skull marrow shift into the CSF spaces making it impossible to
> properly segment that area as CSF. If you wanted an approximate value,
> you could create a binary mask from the aparc+aseg.mgz, dilated it by 3
> or 4 voxels, then erode it by the same amount, then remove the original
> mask. The remaining voxels will be something like the sulcal CSF.
>
> doug
>
>
> On 10/22/2014 04:50 PM, Mohammed Goryawala wrote:
> > Hello FreeSurfer Experts,
> >
> > Is it possible to estimate the sulcal CSF volume in Freesurfer
> > processing? If not directly are there any indirect means that can give
> > me an estimate?
> >
> > Thank you
> >
> > Mohammed Goryawala, PhD
> > Department of Radiology
> > Miller School of Medicine, University of Miami
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: 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 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
> properly
> dispose of the e-mail.
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Re: [Freesurfer] Sulcal CSF Volume

[Douglas N Greve]

In theory that works, but remember the FS total cranial volume is only 
an estimate based on the talairach transform. It is not counting voxels 
that are inside the skull.

On 10/23/2014 12:30 PM, Mohammed Goryawala wrote:
> Thanks Doug.
>
> I was looking at a paper "ARANGO, C., MCMAHON, R. P., LEFKOWITZ, D. 
> M., PEARLSON, G., KIRKPATRICK, B. & BUCHANAN, R. W. 2008. Patterns of 
> cranial, brain and sulcal CSF volumes in male and female deficit and 
> nondeficit patients with schizophrenia. Psychiatry Research: 
> Neuroimaging, 162, 91-100.", which estimates sulcal CSF volume as
>
>
> 2.4.4. Sulcal CSF (sCSF)
>
> The sCSF was derived by subtracting T
>
> ​otal ​
> B
> ​ rain ​
> V
> ​ olume ​
> and V
> ​ entricular ​
> V
> ​ olume​
> from T
> ​ otal ​
> C
> ​ ranial ​
> V
> olume ​
> .
> ​Can such a strategy be explored using FreeSurfer​ output ?
>
> ​Thanks for your advice
> Mohammed​
>
>
> On Thu, Oct 23, 2014 at 12:16 PM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
>
> No, not currently. This is quite a hard problem even if you have a T2.
> The pulse sequences are usually low enough bandwidth that fat from the
> scalp and skull marrow shift into the CSF spaces making it
> impossible to
> properly segment that area as CSF. If you wanted an approximate value,
> you could create a binary mask from the aparc+aseg.mgz, dilated it
> by 3
> or 4 voxels, then erode it by the same amount, then remove the
> original
> mask. The remaining voxels will be something like the sulcal CSF.
>
> doug
>
>
> On 10/22/2014 04:50 PM, Mohammed Goryawala wrote:
> > Hello FreeSurfer Experts,
> >
> > Is it possible to estimate the sulcal CSF volume in Freesurfer
> > processing? If not directly are there any indirect means that
> can give
> > me an estimate?
> >
> > Thank you
> >
> > Mohammed Goryawala, PhD
> > Department of Radiology
> > Miller School of Medicine, University of Miami
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> 
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu 
> Phone Number: 617-724-2358 
> Fax: 617-726-7422 
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> 
> FileDrop: 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/
>
> ___
> 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

-- 
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
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Re: [Freesurfer] Sulcal CSF Volume

[Mohammed Goryawala]

Thanks

On Thu, Oct 23, 2014 at 12:34 PM, Douglas N Greve  wrote:

>
> In theory that works, but remember the FS total cranial volume is only
> an estimate based on the talairach transform. It is not counting voxels
> that are inside the skull.
>
> On 10/23/2014 12:30 PM, Mohammed Goryawala wrote:
> > Thanks Doug.
> >
> > I was looking at a paper "ARANGO, C., MCMAHON, R. P., LEFKOWITZ, D.
> > M., PEARLSON, G., KIRKPATRICK, B. & BUCHANAN, R. W. 2008. Patterns of
> > cranial, brain and sulcal CSF volumes in male and female deficit and
> > nondeficit patients with schizophrenia. Psychiatry Research:
> > Neuroimaging, 162, 91-100.", which estimates sulcal CSF volume as
> >
> >
> > 2.4.4. Sulcal CSF (sCSF)
> >
> > The sCSF was derived by subtracting T
> >
> > ​otal ​
> > B
> > ​ rain ​
> > V
> > ​ olume ​
> > and V
> > ​ entricular ​
> > V
> > ​ olume​
> > from T
> > ​ otal ​
> > C
> > ​ ranial ​
> > V
> > olume ​
> > .
> > ​Can such a strategy be explored using FreeSurfer​ output ?
> >
> > ​Thanks for your advice
> > Mohammed​
> >
> >
> > On Thu, Oct 23, 2014 at 12:16 PM, Douglas N Greve
> > mailto:gr...@nmr.mgh.harvard.edu>> wrote:
> >
> >
> > No, not currently. This is quite a hard problem even if you have a
> T2.
> > The pulse sequences are usually low enough bandwidth that fat from
> the
> > scalp and skull marrow shift into the CSF spaces making it
> > impossible to
> > properly segment that area as CSF. If you wanted an approximate
> value,
> > you could create a binary mask from the aparc+aseg.mgz, dilated it
> > by 3
> > or 4 voxels, then erode it by the same amount, then remove the
> > original
> > mask. The remaining voxels will be something like the sulcal CSF.
> >
> > doug
> >
> >
> > On 10/22/2014 04:50 PM, Mohammed Goryawala wrote:
> > > Hello FreeSurfer Experts,
> > >
> > > Is it possible to estimate the sulcal CSF volume in Freesurfer
> > > processing? If not directly are there any indirect means that
> > can give
> > > me an estimate?
> > >
> > > Thank you
> > >
> > > Mohammed Goryawala, PhD
> > > Department of Radiology
> > > Miller School of Medicine, University of Miami
> > >
> > >
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > 
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > gr...@nmr.mgh.harvard.edu 
> > Phone Number: 617-724-2358 
> > Fax: 617-726-7422 
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > 
> > FileDrop: 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/
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu  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
>
> --
> 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/
>
> ___
> Freesurfer mailing list
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Re: [Freesurfer] strange artefact in T1 - stripe pattern

[Bruce Fischl]

Hi Corinna

it's hard to say. It's quite noisy, but you should give it a try

Bruce
On Thu, 23 
Oct 2014, Corinna Bauer wrote:

> Hello,
> I am analysing some structural data for collaborators and one of the
> datasets has a strange artefact in it. Is there any way to adjust for the
> intensity bands or is this a lost cause?
> 
> Thanks,
> 
> Corinna
> 
>
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Re: [Freesurfer] strange artefact in T1 - stripe pattern

[Corinna Bauer]

We actually ran it through the processing stream and only the middle of the
brain made it into the wm.mgz and the surfaces.

On Thu, Oct 23, 2014 at 12:49 PM, Bruce Fischl 
wrote:

> Hi Corinna
>
> it's hard to say. It's quite noisy, but you should give it a try
>
> Bruce
> On Thu, 23
> Oct 2014, Corinna Bauer wrote:
>
> > Hello,
> > I am analysing some structural data for collaborators and one of the
> > datasets has a strange artefact in it. Is there any way to adjust for the
> > intensity bands or is this a lost cause?
> >
> > Thanks,
> >
> > Corinna
> >
> >
> ___
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> 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
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> but does not contain patient information, please contact the sender and
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Re: [Freesurfer] strange artefact in T1 - stripe pattern

[Bruce Fischl]

you may need to add some control points
On Thu, 23 Oct 2014, Corinna Bauer 
wrote:

> We actually ran it through the processing stream and only the middle of the
> brain made it into the wm.mgz and the surfaces.
> 
> On Thu, Oct 23, 2014 at 12:49 PM, Bruce Fischl 
> wrote:
>   Hi Corinna
>
>   it's hard to say. It's quite noisy, but you should give it a try
>
>   Bruce
>   On Thu, 23
>   Oct 2014, Corinna Bauer wrote:
>
>   > Hello,
>   > I am analysing some structural data for collaborators and one
>   of the
>   > datasets has a strange artefact in it. Is there any way to
>   adjust for the
>   > intensity bands or is this a lost cause?
>   >
>   > Thanks,
>   >
>   > Corinna
>   >
>   >
> ___
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> 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.
> 
> 
> 
>
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Re: [Freesurfer] using mri_convert with multiframe dicom

[Flavin, John]

Hi Timothy

you should be able to. You can use the -nth  switch to convert
each frame individually

cheers

Bruce


On Mon, 11 Jul 2011, Timothy Brown wrote:

> Hi All,
>
> Can mri_convert be used with multiframe dicom?



Is this advice still valid? I tried converting a multi frame DICOM (176 frames 
in one file) using the -nth flag in mri_convert in Freesurfer 5.3 and it did 
not work as I expected.

$ $FREESURFER_HOME/bin/mri_convert -i RAW/301/foo.dcm -o 
PROCESSED/subj/mri/orig/001.mgz -nth 0
/path/to/bin/mri_convert -i RAW/301/foo.dcm -o PROCESSED/subj/mri/orig/001.mgz 
-nth 0
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from RAW/301/foo.dcm...
Starting DICOMRead2()
dcmfile = RAW/301/foo.dcm
dcmdir = RAW/301
WARNING: tag image orientation not found in RAW/301/foo.dcm
Ref Series No = 301
Found 3 files, checking for dicoms
WARNING: tag image orientation not found in RAW/301/foo.dcm
Found 1 dicom files in series.
WARNING: tag image orientation not found in RAW/301/foo.dcm
First Sorting
Computing Slice Direction


 WARNING: it appears that the image position for all slices is the same.
 This is a problem with the DICOM file. Using direction cosines from col and row
 to compute slice direction, but the output may be misoriented.

Vs: 0 0 0
Vs: -nan -nan -nan
Second Sorting
Counting frames
nframes = 1
nslices = 1
ndcmfiles = 1
PE Dir = UNKNOWN (dicom read)
/usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qr::solve() 
: matrix is rank-deficient by 2
/usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qr::solve() 
: matrix is rank-deficient by 2
/usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qr::solve() 
: matrix is rank-deficient by 2
/usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qr::solve() 
: matrix is rank-deficient by 2
TransferSyntaxUID: --1.2.840.10008.1.2.1--
Loading pixel data
/usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qr::solve() 
: matrix is rank-deficient by 2
/usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qr::solve() 
: matrix is rank-deficient by 2
/usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qr::solve() 
: matrix is rank-deficient by 2
/usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qr::solve() 
: matrix is rank-deficient by 2
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0, -0, 0)
j_ras = (-0, -0, 0)
k_ras = (nan, nan, -nan)
Reslicing using trilinear interpolation
/usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qr::solve() 
: matrix is rank-deficient by 2
/usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qr::solve() 
: matrix is rank-deficient by 2
/usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qr::solve() 
: matrix is rank-deficient by 2
/usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qr::solve() 
: matrix is rank-deficient by 2
MRIresample(): error inverting matrix; determinant is -nan, matrix is:
-0.000  -0.000   nan   nan;
-0.000  -0.000   nan   nan;
 0.000   0.000  -nan  -nan;
 0.000   0.000   0.000   1.000;


I get the exact same output running with -nth 0 as I do not using the -nth flag 
at all. If I try using -nth 1 (or -nth i for any integer i > 0) I get

mri_read(): start frame (1) is out of range (1 frames in volume)


mri_convert reports nframes = 1. I can look in the DICOM headers of the file 
and find

(0028, 0008) Number of FramesIS: ‘176’

and

(2001, 1018) [Number of Slices MR]   SL: 176


Anything I can do to tell mri_convert the correct number of frames?


Flavin




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Re: [Freesurfer] using mri_convert with multiframe dicom

[Douglas N Greve]

I doubt that it will work. I've never actually seen a multi-frame dicom 
myself. Can you upload one to me? It should be of a phantom, not a 
human, so we can avoid privacy issues.
doug


On 10/23/2014 01:07 PM, Flavin, John wrote:
>
>> Hi Timothy
>>
>> you should be able to. You can use the -nth  switch to convert
>> each frame individually
>> cheers
>> Bruce
>>
>>
>> On Mon, 11 Jul 2011, Timothy Brown wrote:
>>
>> > Hi All,
>> >
>> > Can mri_convert be used with multiframe dicom?
>
>
> Is this advice still valid? I tried converting a multi frame DICOM 
> (176 frames in one file) using the -nth flag in mri_convert in 
> Freesurfer 5.3 and it did not work as I expected.
>
>> $ $FREESURFER_HOME/bin/mri_convert -i RAW/301/foo.dcm -o 
>> PROCESSED/subj/mri/orig/001.mgz -nth 0
>> /path/to/bin/mri_convert -i RAW/301/foo.dcm -o 
>> PROCESSED/subj/mri/orig/001.mgz -nth 0
>> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
>> reading from RAW/301/foo.dcm...
>> Starting DICOMRead2()
>> dcmfile = RAW/301/foo.dcm
>> dcmdir = RAW/301
>> WARNING: tag image orientation not found in RAW/301/foo.dcm
>> Ref Series No = 301
>> Found 3 files, checking for dicoms
>> WARNING: tag image orientation not found in RAW/301/foo.dcm
>> Found 1 dicom files in series.
>> WARNING: tag image orientation not found in RAW/301/foo.dcm
>> First Sorting
>> Computing Slice Direction
>>
>>
>> WARNING: it appears that the image position for all slices is the same.
>> This is a problem with the DICOM file. Using direction cosines from 
>> col and row
>> to compute slice direction, but the output may be misoriented.
>>
>> Vs: 0 0 0
>> Vs: -nan -nan -nan
>> Second Sorting
>> Counting frames
>> nframes = 1
>> nslices = 1
>> ndcmfiles = 1
>> PE Dir = UNKNOWN (dicom read)
>> /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: 
>> vnl_qr::solve() : matrix is rank-deficient by 2
>> /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: 
>> vnl_qr::solve() : matrix is rank-deficient by 2
>> /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: 
>> vnl_qr::solve() : matrix is rank-deficient by 2
>> /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: 
>> vnl_qr::solve() : matrix is rank-deficient by 2
>> TransferSyntaxUID: --1.2.840.10008.1.2.1--
>> Loading pixel data
>> /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: 
>> vnl_qr::solve() : matrix is rank-deficient by 2
>> /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: 
>> vnl_qr::solve() : matrix is rank-deficient by 2
>> /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: 
>> vnl_qr::solve() : matrix is rank-deficient by 2
>> /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: 
>> vnl_qr::solve() : matrix is rank-deficient by 2
>> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
>> i_ras = (-0, -0, 0)
>> j_ras = (-0, -0, 0)
>> k_ras = (nan, nan, -nan)
>> Reslicing using trilinear interpolation
>> /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: 
>> vnl_qr::solve() : matrix is rank-deficient by 2
>> /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: 
>> vnl_qr::solve() : matrix is rank-deficient by 2
>> /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: 
>> vnl_qr::solve() : matrix is rank-deficient by 2
>> /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: 
>> vnl_qr::solve() : matrix is rank-deficient by 2
>> MRIresample(): error inverting matrix; determinant is -nan, matrix is:
>> -0.000 -0.000 nan nan;
>> -0.000 -0.000 nan nan;
>> 0.000 0.000 -nan -nan;
>> 0.000 0.000 0.000 1.000;
>
> I get the exact same output running with -nth 0 as I do not using the -nth 
> flag at all. If I try using -nth 1 (or -nth i for any integer i > 0) I get
>> mri_read(): start frame (1) is out of range (1 frames in volume)
>
> mri_convert reports nframes = 1. I can look in the DICOM headers of the file 
> and find
>> (0028, 0008) Number of Frames IS: ‘176’
> and
>> (2001, 1018) [Number of Slices MR] SL: 176
>
> Anything I can do to tell mri_convert the correct number of frames?
>
> Flavin
>
>
> 
>
> The material in this message is private and may contain Protected 
> Healthcare Information (PHI). If you are not the intended recipient, 
> be advised that any unauthorized use, disclosure, copying or the 
> taking of any action in reliance on the contents of this information 
> is strictly prohibited. If you have received this email in error, 
> please immediately notify the sender via telephone or return mail.
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facil

Re: [Freesurfer] Longitudinal prediction

[Alex Hanganu]

Hi Martin,
thanks for confirming. I duplicated the parameter and got good results in qdec.
I also tried to repeat the analysis with mri_glmfit but I can't manage to come 
to an end.In order to analyse the correlation between pc1 and parameter 'A', it 
seems that I have to construct an fsgd file, that is different from the .qdec 
file included in the "long_mris_slopes" command. Nevertheless, after doing so 
(presumably all "Inputs" were attibuted to subject.long.base-time1 and 
subject.long.base-time2) I thought that a contrast is needed, yet the "--C" and 
the "--osgm" flags cannot be used together.- How can the correlation between 
-pc1 and parameter 'A' be performed in this case ?
Additionally, after performing the "mri_glmfit" described in the 2-stage-model 
page, in the tksurfer  how can I see the plot ? The y.fsgd file wasn't created. 
Is there another method ?
Thanks,Alex
 
   

  Le mardi 21 octobre 2014 16h40, Martin Reuter  a 
écrit :
   

  Hi Alex,
 
 you have to duplicate the parameter (it is basically fixed across time). If 
you put 0 for tp2, it will average the two values, which is not what you want. 
Otherwise I think it is the correct approach.
 
 Best, Martin
 
 
 On 10/21/2014 04:31 PM, Alex Hanganu wrote:
  
  Dear Martin, 
  thank you very much for your answer ! and thanks for all the details ! - yes, 
we have exactly 2 time points in all subjects and the parameter is a single 
number. 
  In qdec - it seems that qdec table has to include the parameter 'A' both at 
time 1 and at time 2 in order for "long_qdec_table" command to create the 
"cross" file. I put a zero at time 2. In qdec design we analyzed parameter 'A' 
with -pc1 and -spc. I'm not sure that this is the correct approach.
  
  I'll continue with LME and mri_glmfit.

  Sincerely, Alex 

   Le mardi 21 octobre 2014 9h19, Martin Reuter 
 a écrit :
   
 
Hi Alex,
 
 the parameter is a single number that happens to be measured at time 1 right, 
eg baseline age? Lets call that parameter 'A' for the discussion below.  Also 
you have exactly 2 time points in all subjects?
 
 There is two alternatives:
 
 1. Simple approach (2-stage-model): You compute the atrophy rate (e.g. percent 
thickness change) on the cortex (long_mris_slopes) for each subject. At this 
point you have 1 measure per subject and work cross-sectionally. You can use 
qdec or mri_glmfit to  correlate 'A' (independent parameter) with the thickness 
change (dependent variable). This is OK if you have the same number of time 
points and the same time distance in all subjects. Details here:
 https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel 
 
 2. Better approach: use Linear Mixed Effects models (we have matlab tools for 
that). This model is more flexible (different manycolumn of ones, time points, 
different time intervals, even subjects with a single time point can be added). 
You'd setup a  system like 
 Y_ij = beta_0 + b_i + beta_1 * A_i + beta_2 t_ij + beta_3 A_i * tij + error_ij
 where  Y_ij is the thickness of subject i at time point j (known)
 t_ij is the time from baseline of the j measurement in subject i (known),
 A_i is the variable you measure at baseline in subject i (known),
 the model will estimate the following:
 b_i (a random effect) is the subject specific intercept (offset from the 
global intercept beta_0)
 beta_1 another intercept offset caused by A
 beta_2 the slope with respect to time (fixed effect, so it will be the same 
for all subjects, can also be modelled as a mixed effect)
 beta_3 the interaction of A and time (<- you are interested in this)
 Testing if the interaction beta_3 is different from zero will show you where A 
has an effect on the slope.
 For the model above the X matrix would have 4 columns:
 1 A T (A.*T) 
 where 1 is a column of 1's, A the A_ij (Ai repeated j times for each subject), 
T=t_ij and the coordinate wise product of A and T. Contast [ 0 0 0 1] tests the 
interaction. You'd tell the function that you want the intercept to be a random 
effect by passing  [ 1] (selecting the first column). If you also want to have 
t_ij as a random, you can pass [1 3 ] . Details here:
 https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels
 
 Best, Martin
 
 
 On 10/20/2014 03:20 PM, Alexandru Hanganu wrote:
  
 Dear FreeSurfer Experts,
 
 How could the longitudinal analysis be performed in order to show whether a 
parameter at time 1 is predictive of changes in cortical thickness over time ? 
and can the corresponding regions be shown in FreeSurfer ?
 
 In a statistical analysis, as we see it, we must perform the  correlation 
between the parameter at time 1 and the cortical thickness difference (or ROI) 
time 2-time 1, yet in this case we cannot see it on the cortex.
 
 Thank you,
 Alex
  
  
 



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The information in this

[Freesurfer] FS-FAST par file ?

[dgw]

If I have events which precede the first MR volume, can I input
negative values in my par file?

I understand my power, and the advantage of doing this will be
minimal, but I wanted to inquire if FS-FAST is capable of handling
this case.

Thanks,
Dan
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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 you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Longitudinal prediction

[Martin Reuter]

Hi Alex,

you are not looking at a "one sample group mean" (osgd) so don't pass 
that flag. Your design is probably something like

1 A other_co_vars_to_regress_out
(these are column vectors).

so contrast in that case would be [ 0 1 0... ]

That should create all outputs. All of this is really cross sectional 
analysis where the depending variable is simply the 'change in 
thickness' instead of thickness itself. Take a look at the glm tutorial 
on the wiki, which describes the process.


Best, Martin


On 10/23/2014 02:40 PM, Alex Hanganu wrote:

Hi Martin,

thanks for confirming. I duplicated the parameter and got good results 
in qdec.


I also tried to repeat the analysis with mri_glmfit but I can't manage 
to come to an end.
In order to analyse the correlation between pc1 and parameter 'A', it 
seems that I have to construct an fsgd file, that is different from 
the .qdec file included in the "long_mris_slopes" command. 
Nevertheless, after doing so (presumably all "Inputs" were attibuted 
to subject.long.base-time1 and subject.long.base-time2) I thought that 
a contrast is needed, yet the "--C" and the "--osgm" flags cannot be 
used together.
- How can the correlation between -pc1 and parameter 'A' be performed 
in this case ?


Additionally, after performing the "mri_glmfit" described in the 
2-stage-model page, in the tksurfer  how can I see the plot ? The 
y.fsgd file wasn't created. Is there another method ?


Thanks,
Alex




Le mardi 21 octobre 2014 16h40, Martin Reuter 
 a écrit :



Hi Alex,

you have to duplicate the parameter (it is basically fixed across 
time). If you put 0 for tp2, it will average the two values, which is 
not what you want. Otherwise I think it is the correct approach.


Best, Martin


On 10/21/2014 04:31 PM, Alex Hanganu wrote:

Dear Martin,

thank you very much for your answer ! and thanks for all the details !
- yes, we have exactly 2 time points in all subjects and the 
parameter is a single number.


In qdec - it seems that qdec table has to include the parameter 'A' 
both at time 1 and at time 2 in order for "long_qdec_table" command 
to create the "cross" file. I put a zero at time 2. In qdec design we 
analyzed parameter 'A' with -pc1 and -spc. I'm not sure that this is 
the correct approach.


I'll continue with LME and mri_glmfit.

Sincerely,
Alex


Le mardi 21 octobre 2014 9h19, Martin Reuter 
  a 
écrit :



Hi Alex,

the parameter is a single number that happens to be measured at time 
1 right, eg baseline age? Lets call that parameter 'A' for the 
discussion below.  Also you have exactly 2 time points in all subjects?


There is two alternatives:

1. Simple approach (2-stage-model): You compute the atrophy rate 
(e.g. percent thickness change) on the cortex (long_mris_slopes) for 
each subject. At this point you have 1 measure per subject and work 
cross-sectionally. You can use qdec or mri_glmfit to correlate 'A' 
(independent parameter) with the thickness change (dependent 
variable). This is OK if you have the same number of time points and 
the same time distance in all subjects. Details here:

https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel

2. Better approach: use Linear Mixed Effects models (we have matlab 
tools for that). This model is more flexible (different manycolumn of 
ones, time points, different time intervals, even subjects with a 
single time point can be added). You'd setup a system like
Y_ij = beta_0 + b_i + beta_1 * A_i + beta_2 t_ij + beta_3 A_i * tij + 
error_ij

where  Y_ij is the thickness of subject i at time point j (known)
t_ij is the time from baseline of the j measurement in subject i (known),
A_i is the variable you measure at baseline in subject i (known),
the model will estimate the following:
b_i (a random effect) is the subject specific intercept (offset from 
the global intercept beta_0)

beta_1 another intercept offset caused by A
beta_2 the slope with respect to time (fixed effect, so it will be 
the same for all subjects, can also be modelled as a mixed effect)

beta_3 the interaction of A and time (<- you are interested in this)
Testing if the interaction beta_3 is different from zero will show 
you where A has an effect on the slope.

For the model above the X matrix would have 4 columns:
1 A T (A.*T)
where 1 is a column of 1's, A the A_ij (Ai repeated j times for each 
subject), T=t_ij and the coordinate wise product of A and T. Contast 
[ 0 0 0 1] tests the interaction. You'd tell the function that you 
want the intercept to be a random effect by passing [ 1] (selecting 
the first column). If you also want to have t_ij as a random, you can 
pass [1 3 ] . Details here:

https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels

Best, Martin


On 10/20/2014 03:20 PM, Alexandru Hanganu wrote:

Dear FreeSurfer Experts,

How could the longitudinal analysis be performed in order to show 
whether a parameter at time 1 is predictive of changes in cortical 

Re: [Freesurfer] FS-FAST par file ?

[Douglas N Greve]

yes
On 10/23/2014 02:48 PM, dgw wrote:
> If I have events which precede the first MR volume, can I input
> negative values in my par file?
>
> I understand my power, and the advantage of doing this will be
> minimal, but I wanted to inquire if FS-FAST is capable of handling
> this case.
>
> Thanks,
> Dan
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: 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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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
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Re: [Freesurfer] using mri_convert with multiframe dicom

[Flavin, John]

We only have a few examples of the multi frame dicom, and they’re all of 
humans. We can anonymize one and email it to you directly.

Flavin

On Oct 23, 2014, at 1:18 PM, Douglas N Greve 
mailto:gr...@nmr.mgh.harvard.edu>> wrote:


I doubt that it will work. I've never actually seen a multi-frame dicom
myself. Can you upload one to me? It should be of a phantom, not a
human, so we can avoid privacy issues.
doug


On 10/23/2014 01:07 PM, Flavin, John wrote:

Hi Timothy

you should be able to. You can use the -nth  switch to convert
each frame individually
cheers
Bruce


On Mon, 11 Jul 2011, Timothy Brown wrote:

Hi All,

Can mri_convert be used with multiframe dicom?


Is this advice still valid? I tried converting a multi frame DICOM
(176 frames in one file) using the -nth flag in mri_convert in
Freesurfer 5.3 and it did not work as I expected.

$ $FREESURFER_HOME/bin/mri_convert -i RAW/301/foo.dcm -o
PROCESSED/subj/mri/orig/001.mgz -nth 0
/path/to/bin/mri_convert -i RAW/301/foo.dcm -o
PROCESSED/subj/mri/orig/001.mgz -nth 0
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from RAW/301/foo.dcm...
Starting DICOMRead2()
dcmfile = RAW/301/foo.dcm
dcmdir = RAW/301
WARNING: tag image orientation not found in RAW/301/foo.dcm
Ref Series No = 301
Found 3 files, checking for dicoms
WARNING: tag image orientation not found in RAW/301/foo.dcm
Found 1 dicom files in series.
WARNING: tag image orientation not found in RAW/301/foo.dcm
First Sorting
Computing Slice Direction


WARNING: it appears that the image position for all slices is the same.
This is a problem with the DICOM file. Using direction cosines from
col and row
to compute slice direction, but the output may be misoriented.

Vs: 0 0 0
Vs: -nan -nan -nan
Second Sorting
Counting frames
nframes = 1
nslices = 1
ndcmfiles = 1
PE Dir = UNKNOWN (dicom read)
/usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx:
vnl_qr::solve() : matrix is rank-deficient by 2
/usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx:
vnl_qr::solve() : matrix is rank-deficient by 2
/usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx:
vnl_qr::solve() : matrix is rank-deficient by 2
/usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx:
vnl_qr::solve() : matrix is rank-deficient by 2
TransferSyntaxUID: --1.2.840.10008.1.2.1--
Loading pixel data
/usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx:
vnl_qr::solve() : matrix is rank-deficient by 2
/usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx:
vnl_qr::solve() : matrix is rank-deficient by 2
/usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx:
vnl_qr::solve() : matrix is rank-deficient by 2
/usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx:
vnl_qr::solve() : matrix is rank-deficient by 2
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0, -0, 0)
j_ras = (-0, -0, 0)
k_ras = (nan, nan, -nan)
Reslicing using trilinear interpolation
/usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx:
vnl_qr::solve() : matrix is rank-deficient by 2
/usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx:
vnl_qr::solve() : matrix is rank-deficient by 2
/usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx:
vnl_qr::solve() : matrix is rank-deficient by 2
/usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx:
vnl_qr::solve() : matrix is rank-deficient by 2
MRIresample(): error inverting matrix; determinant is -nan, matrix is:
-0.000 -0.000 nan nan;
-0.000 -0.000 nan nan;
0.000 0.000 -nan -nan;
0.000 0.000 0.000 1.000;

I get the exact same output running with -nth 0 as I do not using the -nth flag 
at all. If I try using -nth 1 (or -nth i for any integer i > 0) I get
mri_read(): start frame (1) is out of range (1 frames in volume)

mri_convert reports nframes = 1. I can look in the DICOM headers of the file 
and find
(0028, 0008) Number of Frames IS: ‘176’
and
(2001, 1018) [Number of Slices MR] SL: 176

Anything I can do to tell mri_convert the correct number of frames?

Flavin




The material in this message is private and may contain Protected
Healthcare Information (PHI). If you are not the intended recipient,
be advised that any unauthorized use, disclosure, copying or the
taking of any action in reliance on the contents of this information
is strictly prohibited. If you have received this email in error,
please immediately notify the sender via telephone or return mail.


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

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

Bugs: 
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2

Re: [Freesurfer] using mri_convert with multiframe dicom

[Douglas N Greve]

Yea, that should work. Use the filedrop at the end of this email
On 10/23/2014 04:13 PM, Flavin, John wrote:
> We only have a few examples of the multi frame dicom, and they’re all 
> of humans. We can anonymize one and email it to you directly.
>
> Flavin
>
>> On Oct 23, 2014, at 1:18 PM, Douglas N Greve 
>> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>>
>>
>> I doubt that it will work. I've never actually seen a multi-frame dicom
>> myself. Can you upload one to me? It should be of a phantom, not a
>> human, so we can avoid privacy issues.
>> doug
>>
>>
>> On 10/23/2014 01:07 PM, Flavin, John wrote:
>>>
 Hi Timothy

 you should be able to. You can use the -nth  switch to convert
 each frame individually
 cheers
 Bruce


 On Mon, 11 Jul 2011, Timothy Brown wrote:

> Hi All,
>
> Can mri_convert be used with multiframe dicom?
>>>
>>>
>>> Is this advice still valid? I tried converting a multi frame DICOM
>>> (176 frames in one file) using the -nth flag in mri_convert in
>>> Freesurfer 5.3 and it did not work as I expected.
>>>
 $ $FREESURFER_HOME/bin/mri_convert -i RAW/301/foo.dcm -o
 PROCESSED/subj/mri/orig/001.mgz -nth 0
 /path/to/bin/mri_convert -i RAW/301/foo.dcm -o
 PROCESSED/subj/mri/orig/001.mgz -nth 0
 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
 reading from RAW/301/foo.dcm...
 Starting DICOMRead2()
 dcmfile = RAW/301/foo.dcm
 dcmdir = RAW/301
 WARNING: tag image orientation not found in RAW/301/foo.dcm
 Ref Series No = 301
 Found 3 files, checking for dicoms
 WARNING: tag image orientation not found in RAW/301/foo.dcm
 Found 1 dicom files in series.
 WARNING: tag image orientation not found in RAW/301/foo.dcm
 First Sorting
 Computing Slice Direction


 WARNING: it appears that the image position for all slices is the same.
 This is a problem with the DICOM file. Using direction cosines from
 col and row
 to compute slice direction, but the output may be misoriented.

 Vs: 0 0 0
 Vs: -nan -nan -nan
 Second Sorting
 Counting frames
 nframes = 1
 nslices = 1
 ndcmfiles = 1
 PE Dir = UNKNOWN (dicom read)
 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx:
 vnl_qr::solve() : matrix is rank-deficient by 2
 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx:
 vnl_qr::solve() : matrix is rank-deficient by 2
 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx:
 vnl_qr::solve() : matrix is rank-deficient by 2
 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx:
 vnl_qr::solve() : matrix is rank-deficient by 2
 TransferSyntaxUID: --1.2.840.10008.1.2.1--
 Loading pixel data
 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx:
 vnl_qr::solve() : matrix is rank-deficient by 2
 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx:
 vnl_qr::solve() : matrix is rank-deficient by 2
 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx:
 vnl_qr::solve() : matrix is rank-deficient by 2
 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx:
 vnl_qr::solve() : matrix is rank-deficient by 2
 TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
 i_ras = (-0, -0, 0)
 j_ras = (-0, -0, 0)
 k_ras = (nan, nan, -nan)
 Reslicing using trilinear interpolation
 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx:
 vnl_qr::solve() : matrix is rank-deficient by 2
 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx:
 vnl_qr::solve() : matrix is rank-deficient by 2
 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx:
 vnl_qr::solve() : matrix is rank-deficient by 2
 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx:
 vnl_qr::solve() : matrix is rank-deficient by 2
 MRIresample(): error inverting matrix; determinant is -nan, matrix is:
 -0.000 -0.000 nan nan;
 -0.000 -0.000 nan nan;
 0.000 0.000 -nan -nan;
 0.000 0.000 0.000 1.000;
>>>
>>> I get the exact same output running with -nth 0 as I do not using 
>>> the -nth flag at all. If I try using -nth 1 (or -nth i for any 
>>> integer i > 0) I get
 mri_read(): start frame (1) is out of range (1 frames in volume)
>>>
>>> mri_convert reports nframes = 1. I can look in the DICOM headers of 
>>> the file and find
 (0028, 0008) Number of Frames IS: ‘176’
>>> and
 (2001, 1018) [Number of Slices MR] SL: 176
>>>
>>> Anything I can do to tell mri_convert the correct number of frames?
>>>
>>> Flavin
>>>
>>>
>>> 
>>>
>>> The material in this message is private and may contain Protected
>>> Healthcare Information (PHI). If you are not the intended recipient,
>>> be advised that any unauthorized use, disclosure, copying or the
>>> taking of any action in reliance on the contents of this i

[Freesurfer] Research Assistant I position in Neuroimaging

[Dana DeMaster]

Position: Research Assistant I (full-time research assistant position in
Brain Research Analysis in Neurodevelopment (BRAIN) Laboratory)

Location: University of Texas-Health Science Center at Houston

Apply at: jobs.uth.tmc.edu/applicants/Central?quickFind=100904



A full-time research assistant position in Brain Research Analysis in
Neurodevelopment (BRAIN) Laboratory, at the Children's Learning Institute.
Our laboratory uses neuroimaging techniques to investigate the neural
systems underlying a variety of developmental disorders. The BRAIN Lab is a
lively, collaborative, supportive intellectual environment.  Duties will
include assisting with all aspects of neuroimaging data collection
including, but not limited to, running the MRI scanner, organizing
structural and functional data, basic processing of structural and
functional data, and coordinating lab activities.



Departmental Requirements/Preferences

- BA/BS in Psychology, Cognitive Science, Neuroscience or other related
scientific field
- Fluent or nearly fluent Spanish speaker
- Strong computer skills
- An ability to solve technical problems independently
- Strong organization skills
- Detail oriented
- Prior research experience
- Experience working with elementary school aged children
- Flexible schedule with willingness to work nights and weekends.

This would be an excellent position for an individual desiring to hone
their research skills before continuing on to postgraduate study. Applications
must be submitted at jobs.uth.tmc.edu/applicants/Central?quickFind=100904

-- 
Dana DeMaster
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[Freesurfer] Trouble specifying contrast vectors

[Bronwyn Overs]

Dear Freesurfer Mailing List,

I wish to run a GLM in freesurfer with 3 categorical variables 
(haplotype-2levels, gender-2levels, group-2levels), and 1 continuous 
variables (age). Unfortunately, the MRI images I am using come from five 
different testing sites, so I also need to account for the potentially 
confounding effects of using different scanners. So my fsgd file like this:


GroupDescriptorFile 1
Title GLM_SiteGender
Class siteBrisbane-numRiskNoRisk-genderMale-groupCase
Class siteBrisbane-numRiskNoRisk-genderFemale-groupCase
Class siteBrisbane-numRiskNoRisk-genderMale-groupControl
Class siteBrisbane-numRiskNoRisk-genderFemale-groupControl
Class siteBrisbane-numRiskanyRisk-genderMale-groupCase
Class siteBrisbane-numRiskanyRisk-genderFemale-groupCase
Class siteBrisbane-numRiskanyRisk-genderMale-groupControl
Class siteBrisbane-numRiskanyRisk-genderFemale-groupControl
Class siteMelbourne-numRiskNoRisk-genderMale-groupCase
Class siteMelbourne-numRiskNoRisk-genderFemale-groupCase
Class siteMelbourne-numRiskNoRisk-genderMale-groupControl
Class siteMelbourne-numRiskNoRisk-genderFemale-groupControl
Class siteMelbourne-numRiskanyRisk-genderMale-groupCase
Class siteMelbourne-numRiskanyRisk-genderFemale-groupCase
Class siteMelbourne-numRiskanyRisk-genderMale-groupControl
Class siteMelbourne-numRiskanyRisk-genderFemale-groupControl
Class siteNewcastle-numRiskNoRisk-genderMale-groupCase
Class siteNewcastle-numRiskNoRisk-genderFemale-groupCase
Class siteNewcastle-numRiskNoRisk-genderMale-groupControl
Class siteNewcastle-numRiskNoRisk-genderFemale-groupControl
Class siteNewcastle-numRiskanyRisk-genderMale-groupCase
Class siteNewcastle-numRiskanyRisk-genderFemale-groupCase
Class siteNewcastle-numRiskanyRisk-genderMale-groupControl
Class siteNewcastle-numRiskanyRisk-genderFemale-groupControl
Class sitePerth-numRiskNoRisk-genderMale-groupCase
Class sitePerth-numRiskNoRisk-genderFemale-groupCase
Class sitePerth-numRiskNoRisk-genderMale-groupControl
Class sitePerth-numRiskNoRisk-genderFemale-groupControl
Class sitePerth-numRiskanyRisk-genderMale-groupCase
Class sitePerth-numRiskanyRisk-genderFemale-groupCase
Class sitePerth-numRiskanyRisk-genderMale-groupControl
Class sitePerth-numRiskanyRisk-genderFemale-groupControl
Class siteSydney-numRiskNoRisk-genderMale-groupCase
Class siteSydney-numRiskNoRisk-genderFemale-groupCase
Class siteSydney-numRiskNoRisk-genderMale-groupControl
Class siteSydney-numRiskNoRisk-genderFemale-groupControl
Class siteSydney-numRiskanyRisk-genderMale-groupCase
Class siteSydney-numRiskanyRisk-genderFemale-groupCase
Class siteSydney-numRiskanyRisk-genderMale-groupControl
Class siteSydney-numRiskanyRisk-genderFemale-groupControl
Variables age
Input 100105SA sitePerth-anyRiskAnyRisk-genderMale-groupCase 23
...

As the number of categorical variables really complicates the 
specification of contrast vectors, I was wondering if you could confirm 
whether these vectors are correct:


Main effect for haplotype (Risk vs No Risk):
0.5 	0.5 	0.5 	0.5 	-0.5 	-0.5 	-0.5 	-0.5 	0.5 	0.5 	0.5 	0.5 	-0.5 
-0.5 	-0.5 	-0.5 	0.5 	0.5 	0.5 	0.5 	-0.5 	-0.5 	-0.5 	-0.5 	0.5 
0.5 	0.5 	0.5 	-0.5 	-0.5 	-0.5 	-0.5 	0.5 	0.5 	0.5 	0.5 	-0.5 
-0.5 	-0.5 	-0.5 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 
0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0



Main effect for gender (Male vs Female):
0.5 	-0.5 	0.5 	-0.5 	0.5 	-0.5 	0.5 	-0.5 	0.5 	-0.5 	0.5 	-0.5 
0.5 	-0.5 	0.5 	-0.5 	0.5 	-0.5 	0.5 	-0.5 	0.5 	-0.5 	0.5 	-0.5 
0.5 	-0.5 	0.5 	-0.5 	0.5 	-0.5 	0.5 	-0.5 	0.5 	-0.5 	0.5 	-0.5 
0.5 	-0.5 	0.5 	-0.5 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 
0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 
0 	0 	0 	0



Main effect for group (Case vs Control):
0.5 	0.5 	-0.5 	-0.5 	0.5 	0.5 	-0.5 	-0.5 	0.5 	0.5 	-0.5 	-0.5 
0.5 	0.5 	-0.5 	-0.5 	0.5 	0.5 	-0.5 	-0.5 	0.5 	0.5 	-0.5 	-0.5 
0.5 	0.5 	-0.5 	-0.5 	0.5 	0.5 	-0.5 	-0.5 	0.5 	0.5 	-0.5 	-0.5 
0.5 	0.5 	-0.5 	-0.5 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 
0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 
0 	0 	0 	0



Interaction between gender & group:
0.5 	-0.5 	-0.5 	0.5 	0.5 	-0.5 	-0.5 	0.5 	0.5 	-0.5 	-0.5 	0.5 
0.5 	-0.5 	-0.5 	0.5 	0.5 	-0.5 	-0.5 	0.5 	0.5 	-0.5 	-0.5 	0.5 
0.5 	-0.5 	-0.5 	0.5 	0.5 	-0.5 	-0.5 	0.5 	0.5 	-0.5 	-0.5 	0.5 
0.5 	-0.5 	-0.5 	0.5 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 
0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 
0 	0 	0 	0



Interaction between gender & haplotype:
0.5 	-0.5 	0.5 	-0.5 	-0.5 	0.5 	-0.5 	0.5 	0.5 	-0.5 	0.5 	-0.5 
-0.5 	0.5 	-0.5 	0.5 	0.5 	-0.5 	0.5 	-0.5 	-0.5 	0.5 	-0.5 	0.5 
0.5 	-0.5 	0.5 	-0.5 	-0.5 	0.5 	-0.5 	0.5 	0.5 	-0.5 	0.5 	-0.5 
-0.5 	0.5 	-0.5 	0.5 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 
0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 	0 
0 	0 	0 	0



Interaction between group & haplotype:
0.5 	0.5 	-0.5 	-0.5 	-0.5 	-0.5 	0.5 	0.5 	0.5 	0.5 	-0.5 	-0.5 	-0.5 
-0.5 	0.5 	0.5 	0.5 	0.5 	-0.5