Re: [Freesurfer] Task-based connectivity

[MCLAREN, Donald]

External Email - Use Caution

Hi Kazuhisa,

I believe that I included a wrapper for FSFAST to run gPPI. Please download
the toolbox and take a look. If it's not there or your having issues,
please let me know and I can help troubleshoot.

Best Regards,
Donald McLaren, PhD



On Sat, Apr 17, 2021 at 8:57 AM Kazuhisa Shibata 
wrote:

> External Email - Use Caution
>
> Hi the list,
>
> I’d like to perform task-based connectivity such as generalized PPI based
> on results obtained by GLM at freesurfer.
>
> However, at least freesurfer 5.1.0 does not support such function. Only
> resting-state connectivity analysis was allowed in freesurfer.
> *MailScanner has detected a possible fraud attempt from
> "secure-web.cisco.com" claiming to be*
> https://secure-web.cisco.com/1M3RMJC0RII7fUZhyR6iM2CJGX6YIMCfV2wf-ytbnCfVI9NKXj2hV3c0EA80m5xbUtSOLu4k4u03s7JF-m3WOmwmJaxJdFLG8JqM38KmB8Gd_MFdxicZTd_nrrQ5TrQucw7HlLx4z5OyEr-Rv_QBiXqfyuXJrupKQEEhMgCRZnNDTnESOuyLQUhx-oVdYZpHZXOvFzz2f8b40bxuY4In8WTSsDsjiuHdx5lcR4GBArtqe6Y5pBLjcn45IVDNGDoR9qH2pLbJyJh3vrx9fTWvFHw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg25136.html
> 
>
> Since then, has such function been implemented in freesurfer and fsfast?
> If so, is there any webpage that describes how to perform it?
>
> If not, it seems necessary for me to transfer freesurfer surface data to
> CONN or other software like Generalized PPI toolbox. Does anyone have
> experience for this? If so, do you know any helpful documentation for it?
> *MailScanner has detected a possible fraud attempt from
> "secure-web.cisco.com" claiming to be* 
> https://secure-web.cisco.com/1ewGXdSL6A0cqS1_xT7oOm8IkjVLmU8WY5OhyJkiUwm3Or5tazbRjj43E7sfd5033ywpgCumyJtOWgHwkWOl2nNu-DX1dlfrZBUGVrOeBEL3hfoeSZNimcWcH2Fh91QO9y-G1BmZ8jqPWmyzuflZS8ip4xJ5NySn2QGTLC66R3Gqdtb2f8VTq3SuD6HTFynWvzXc6t7RcJjULRsFQGYxtY65DG-0P3pAlW5_srQ1TxzgIGnvGuuHIyJI1m65PDkmDIO6b2fmKFZ4Bxv3spzPLpg/https%3A%2F%2Fweb.conn-toolbox.org%2Fhome
> 
> *MailScanner has detected a possible fraud attempt from
> "secure-web.cisco.com" claiming to be* 
> https://secure-web.cisco.com/1f8gSVzTGq3pxpgbGbYUp6J4e_7l2Z8zq4ukKXcEF16t05-ZKwQt5IUMItxvTMsHkEJdHiYnIIuIgCn3bf1DMVpe5yblMRQvy0rWqhmuwfiPSK5-_d8kDIreXEgPOjP6ibKuAH7V1rC2KTRFwYZklCypO6lopAG7Dh5qnbS1HKoVshuIeP6At1K7Mnhrtc0zZ_uMyY2GSsOZ3Mzlfab9-wl_rOgycH9xl3PIOWQ1QuCZ-tEWSu9KYpv5mJhtog8TII7LnNXoTasT4Q_HljM6Sow/https%3A%2F%2Fwww.nitrc.org%2Fprojects%2Fgppi
> 
>
>
> Thank you very much for your help in advance!
>
> Best,
> Kaz
> --
> Kazuhisa Shibata
>
> Team Leader
> Lab for Human Cognition and Learning
> Center for Brain Science
> RIKEN
> *MailScanner has detected a possible fraud attempt from
> "secure-web.cisco.com" claiming to be* 
> https://secure-web.cisco.com/1gKsebD1KiB1urxW4epo--yk8QU_rBhTtD0aYA0HTNxEY8Pr0cGB3MfxGjSO4P5a5Gx3d_NvDGZylsU7kKgB_kM4ag_Iv0td0Zpupyj3yGLt3s6ze-WMEpEiL3HaGD8AWm7nNLwmMDg2wzX6eRpjmUDL5k5fIM65NHzHWGo1WrpzfuaCQ04bMcHqVjWFm8scNajRu8B1Gn3w4Ad0rHs8713f_Jv07S_r04jTJKkCuOmv5ym-C8pDUo-S1f_Ir1SFcx-M6x21acbWd7NOBZjRiGg/https%3A%2F%2Fshibatalab.riken.jp%2F
> 
>
> kazuhisa.shib...@riken.jp
> kazuhisa.shib...@gmail.com
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> 

Re: [Freesurfer] GLM - covariate question

[MCLAREN, Donald]

Pedro,

Instead of saying that you want to include the covariate in the analysis,
it's better to consider why you want to include the covariate and how it
changes the interpretation. You don't necessarily want to regress out
covariates, especially when the covariate is different between groups.

DO -- Different offsets, no covariate/no slope --> the offsets are the
group means not adjusted for covariates.
DOSS -- Different offset, same slope model --> If you don't subtract the
mean, then the offsets are the group means when the covariate is 0 for all
subjects. If you subtract the mean, then the offsets are the group means
when the the covariate is the mean covariate for all subjects. The
difference in offsets won't change with mean centering the covariate.
DODS -- Different offset, different slope model --> Not possible because
the covariate for controls is collinear with the group term.

There are other models that you could construct - such as only including a
covariate for the drug group, but the interpretation will once again be
different.

The bottom line is to decide what you want to test and how you want to
interpret the results before adding covariates.
With DOSS, you will reduce/increase the group differences (depending on the
slope of the covariate) because you are interpreting the results when the
covariate is 0 in the drug group.

Best,
Donald


Best Regards,
Donald McLaren, PhD


On Sat, May 7, 2016 at 3:18 PM, Pedro Rosa  wrote:

> Dear list,
> I am running a command line group analysis, and I want to include a
> covariate that is zero for all subjects in a group, and diverse for all
> subjects in the second group (medication intake, which is null for all
> subjects in the control group).
> This generates a lack of range of that continuous variable within a class
> (control group), and thus mri_glmfit ends with errors.
> Is it possible to perform such analysis? Could demeaning procedure work
> here?
> If not, how could I "regress out" the effect of such covariate in
> between-groups thickness/area differences?
> Many thanks in advance,
> Pedro.
>
> ___
> 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


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] Minc File Error

[MCLAREN, Donald]

Zeke and others,

I recently installed Freesurfer v6 (
freesurfer-Darwin-OSX-stable-v6-beta-20151015.dmg
,
MacOS
10.9.5, XQuartz 2.7.8), and Freeview always closes whenever I try to open a
mnc file. Below is the output from the terminal after Freeview closes.

Please let me know what I need to resolve the issue. The file is in fact a
valid minc file as it can be opened by register and display.

Please let me know if additional details are needed.

Best,

Donald


Output begins here:
=

ncopen: filename "XXX.mnc": Not a netCDF file

miopen: MINC package entry point

Error opening XXX.mnc

mincRead(): error reading volume from file .mnc

dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address

  Referenced from:
/Applications/freesurfer/Freeview.app/Contents/MacOS/../Frameworks/libstdc++.6.dylib

  Expected in: /usr/lib/libSystem.B.dylib


dyld: Symbol not found: ___emutls_get_address

  Referenced from:
/Applications/freesurfer/Freeview.app/Contents/MacOS/../Frameworks/libstdc++.6.dylib

  Expected in: /usr/lib/libSystem.B.dylib


[0]PETSC ERROR:


[0]PETSC ERROR: Caught signal number 5 TRAP

[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger

[0]PETSC ERROR: or see
http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC
ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to
find memory corruption errors

[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and
run

[0]PETSC ERROR: to get more information on the crash.

[0]PETSC ERROR: - Error Message


[0]PETSC ERROR: Signal received!

[0]PETSC ERROR:


[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26
CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124

[0]PETSC ERROR: See docs/changes/index.html for recent updates.

[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.

[0]PETSC ERROR: See docs/index.html for manual pages.

[0]PETSC ERROR:


[0]PETSC ERROR: Unknown Name on a darwin12. named Belhavens-Best.local by
mclaren Wed Dec  9 14:42:45 2015

[0]PETSC ERROR: Libraries linked from
/usr/pubsw/packages/petsc/2.3.3-p13-64b/src/petsc-2.3.3-p13/lib/darwin12.2.0-c-opt

[0]PETSC ERROR: Configure run at Mon Dec 17 15:29:35 2012

[0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc
--with-fc=0 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1
--with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3
CXXOPTFLAGS=-O3 FOPTFLAGS=-O3

[0]PETSC ERROR:


[0]PETSC ERROR: User provided function() line 0 in unknown directory
unknown file

[unset]: aborting job:

application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0

[0]PETSC ERROR:


[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
probably memory access out of range

[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger

[0]PETSC ERROR: or see
http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC
ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to
find memory corruption errors

[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and
run

[0]PETSC ERROR: to get more information on the crash.

[0]PETSC ERROR: - Error Message


[0]PETSC ERROR: Signal received!

[0]PETSC ERROR:


[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26
CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124

[0]PETSC ERROR: See docs/changes/index.html for recent updates.

[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.

[0]PETSC ERROR: See docs/index.html for manual pages.

[0]PETSC ERROR:


[0]PETSC ERROR: Unknown Name on a darwin12. named Belhavens-Best.local by
mclaren Wed Dec  9 14:42:45 2015

[0]PETSC ERROR: Libraries linked from
/usr/pubsw/packages/petsc/2.3.3-p13-64b/src/petsc-2.3.3-p13/lib/darwin12.2.0-c-opt

[0]PETSC ERROR: Configure run at Mon Dec 17 15:29:35 2012

[0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc
--with-fc=0 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1
--with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3
CXXOPTFLAGS=-O3 FOPTFLAGS=-O3

[0]PETSC ERROR:

Re: [Freesurfer] Checking optseq efficiency of a custom par file.

[MCLAREN, Donald]

You need to build a wrapper that creates all possible combinations of the
three sets of par files.

Then use this to build a design matrix for each one.

Then estimate the efficiency (eff) and VRF (vrf) for the contrasts of
interest.

M = C*inv(X'*X)*C';
eff = 1/trace(M);
vrf = 1/mean(diag(M));


Hope this helps.


Best Regards,
Donald McLaren, PhD


On Fri, Oct 16, 2015 at 1:34 PM, Sam Zorowitz  wrote:

> Dear Freesurfer list,
>
> Using the optseq2 program, is it possible to calculate the efficiency of a
> custom par file? I have an fMRI task that will be split into three blocks.
> I want to calculate the overall efficiency of my overall design
> byconcatenating the best par file from optimizing each individual block. I
> have already tried doing so by concatenating the three par files (updating
> the onset times) and inputting this into optseq2 by:
>
> >> optseq2 --in new_file.par --nosearch --tr 1.75 --ntp 1080 --psdwin 0
> 3.5 1.75 --o new_dir
>
> If I do this, however, I get a "core dump" error. Does anyone know how I
> might going about doing this? I've attached the new_par file for
> convenience.
>
> Best,
> sam
>
> ___
> 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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Questions about the correction methods in Surfstat

[MCLAREN, Donald]

>The output figure is attached. In the colorbar of the figure, left
represents cluster corrected p value and right one represents the vertex
>corrected p value, right?
Right.

>So, the warm color region in the figure can be survived by the RFT vertex
correction, and the cool color region in the figure can be >survived by the
RFT cluster correction, right?
Right. RFT vertex correction is not a correct definition, it is a RFT
correction based on the maximum peak in contrast with the larger cluster
extent approach.

>If so, the regions with either warm or cool color region that can be
survived after correction. When I report the results, I can report the
>regions with warm color (vertex level correction) or report the regions
with cool color (cluster level correction), right?
Both thresholdings can be reported but I prefer peak thresholds (warm
colors) due to the lack of spatial specificity with clustering thresholds.

>In addtion, how can I understand the region overlapped by the warm and
cool color (like he postier cingulate cortex), can >simultaneously pass
double correction of vertex level and cluster level?
It is not a double corrections. The figure simply shows two different RFT
thresholding approaches.

The final question is about the RFT cluster correction method, in the SPM
or other software (like REST). Generally, on the cluster level correction,
you should be based on a voxel (vertex) uncorrected height threshold of
e.g. p<0.001 combined with a RFT-correlated cluster threshould of e.g.,
p<0.05, right? What is the detailed correction procedure in the Surfstat
software?
Exactly the same, p=0.001 for defining supra-threshold clusters and p=0.05
for RFT correction.

Regards, Felix.

Best Regards,
Donald McLaren, PhD


On Sun, Sep 13, 2015 at 9:36 AM, chenhf_uestc  wrote:

> Dear Surfstat Users,
>
> I have a question about the RFT correction method in the Surfstat(
> http://www.math.mcgill.ca/keith/surfstat/).
> In the online manual, the command to perform RFT correction is as follows:
> [ pval, peak, clus ] = SurfStatP( slm, mask );
>
> pval.P contains P-values for peaks, and pval.C contains P-values for
> clusters. This special structure is recognised by SurfStatView which draws
> the figure in a special way:
>
> SurfStatView( pval, avsurf, 'Males-females removing age' );
>
> The output figure is attached. In the colorbar of the figure, left
> represents cluster corrected p value and right one represents the vertex
> corrected p value, right? So, the warm color region in the figure can be
> survived by the RFT vertex correction, and the cool color region in the
> figure can be survived by the RFT cluster correction, right? If so, the
> regions with either warm or cool color region that can be survived after
> correction. When I report the results, I can report the regions with warm
> color (vertex level correction) or report the regions with cool color
> (cluster level correction), right?
>
> In addtion, how can I understand the region overlapped by the warm and
> cool color (like he postier cingulate cortex), can simultaneously pass
> double correction of vertex level and cluster level?
>
> The final question is about the RFT cluster correction method, in the SPM
> or other software (like REST). Generally, on the cluster level correction,
> you should be based on a voxel (vertex) uncorrected height threshold of
> e.g. p<0.001 combined with a RFT-correlated cluster threshould of e.g.,
> p<0.05, right? What is the detailed correction procedure in the Surfstat
> software?
>
> Any help would be greatly appreciate.
>
> Best,
> Feng
>
>
>
>
>
>
> ___
> 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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] registering NHP data

[MCLAREN, Donald]

There are 2 papers the describe the atlas and method for normalization.
(1) McLaren et al. 2009. NeuroImage. A population-average MRI-based atlas
collection of the rhesus macaque.
(2) McLaren et al. 2010. Methods. Rhesus macaque brain morphometry: A
methodological comparison of voxel-wise approaches.

If you create a second image with a sphere at the electrode location, then
you can normalize the MRI and apply the parameters to the image of
electrode location spheres, then you can look up in the book which region
the electrode was located.


Best Regards,
Donald McLaren, PhD


On Wed, Aug 5, 2015 at 9:45 AM, Borzello, Mia mborze...@partners.org
wrote:

 Awesome that you guys are working a parcellation! In the meantime, if I
 wanted to try to use the atlases you suggested, how would I go about
 processing the data? Is there documentation I can follow?

 Thanks so much,
 Mia




 --
 *From:* MCLAREN, Donald [mclaren.don...@gmail.com]
 *Sent:* Tuesday, August 04, 2015 9:36 AM
 *To:* Borzello, Mia
 *Subject:* Re: [Freesurfer] registering NHP data

 Mia,

 You could use the 112RM-SL atlas for normalization and then use the
 Saleem-Logothetis Atlas for localization. Hopefully, by August, we'll have
 a parcellation on the the MR image so that localization can be done
 automatically.

 Best Regards,
 Donald McLaren, PhD


 On Mon, Aug 3, 2015 at 2:01 PM, Borzello, Mia mborze...@partners.org
 wrote:

 Hi Freesurfer experts,

 Does Freesurfer have a separate pipeline for registering NHP data? I am
 trying to register macaque data and localize the implanted electrodes, but
 the normal protocol errored. I did a google search and found this- is this
 what I should be using?:
 https://surfer.nmr.mgh.harvard.edu/fswiki/MonkeyData

 I downloaded the scripts but I'm not sure what commands I'm supposed to
 be running, etc.
 Any guidance you can give would be must appreciated!

 Thanks,
 m

 ___
 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


 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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] help with using optseq2

[MCLAREN, Donald]

This type of design is not suitable for optseq2. Furthermore, you only have
100s of task and almost 300s of scan time. This will lead to lots of empty
space. You really need more than 2 conditions per event type.

Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
=
This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
intended only for the use of the individual or entity named above. If the
reader of the e-mail is not the intended recipient or the employee or agent
responsible for delivering it to the intended recipient, you are hereby
notified that you are in possession of confidential and privileged
information. Any unauthorized use, disclosure, copying or the taking of any
action in reliance on the contents of this information is strictly
prohibited and may be unlawful. If you have received this e-mail
unintentionally, please immediately notify the sender via telephone at (773)
406-2464 or email.

On Thu, Jul 16, 2015 at 6:17 PM, Heeyoung Choo heeyoung.c...@utoronto.ca
wrote:

 Hello,

 I'm trying to create trial sequences for a slow event related fMRI
 experiment.
 I have 10 classes of stimuli, and each stimulus lasts 5 sec and repeats
 twice in a run.


 Environment: Linux 3.13.0-35-generic #62-Ubuntu SMP UTC 2014 x86_64 x86_64
 x86_64 GNU/Linux


 I ran:

 ./optseq2 --ntp 144  --tr 2.5 \
 --ev evt1 5 2 --ev evt2 5 2 --ev evt3 5 2 --ev evt4 5 2 --ev evt5 5 2 --ev
 evt6 5 2 --ev evt7 5 2 --ev evt8 5 2 --ev evt9 5 2 --ev evt10 5 2 \
 --nkeep 10 --psdwin 0 20 --o exp_video \
 --tnullmax 25 --tnullmin 7.5 \
 --nsearch 1

 Almost all of the sequences have extremely long NULL at the end of a run,
 like 82.5sec (please see one of sequences below).
 I am aware that optseq2 is for rapid event related fMRI, and wonder if the
 problem is due to specific parameters of my design, or due to a bug. I
 would appreciate any comments or help.

 Thank you very much!

 Best regards,
 Heeyoung


   0.55.000   1.  evt5
   5.07.500   1.  NULL
  12.500095.000   1.  evt9
  17.500007.500   1.  NULL
  25.35.000   1.  evt3
  30.07.500   1.  NULL
  37.5000   105.000   1. evt10
  42.50000   12.500   1.  NULL
  55.75.000   1.  evt7
  60.0   10.000   1.  NULL
  70.35.000   1.  evt3
  75.07.500   1.  NULL
  82.500045.000   1.  evt4
  87.50000   15.000   1.  NULL
 102.500065.000   1.  evt6
 107.500007.500   1.  NULL
 115.65.000   1.  evt6
 120.0   10.000   1.  NULL
 130.85.000   1.  evt8
 135.0   17.500   1.  NULL
 152.500015.000   1.  evt1
 157.500007.500   1.  NULL
 165.25.000   1.  evt2
 170.07.500   1.  NULL
 177.5000   105.000   1. evt10
 182.500007.500   1.  NULL
 190.85.000   1.  evt8
 195.07.500   1.  NULL
 202.500095.000   1.  evt9
 207.50000   12.500   1.  NULL
 220.45.000   1.  evt4
 225.07.500   1.  NULL
 232.500075.000   1.  evt7
 237.500007.500   1.  NULL
 245.15.000   1.  evt1
 250.07.500   1.  NULL
 257.500055.000   1.  evt5
 262.50000   10.000   1.  NULL
 272.500025.000   1.  evt2
 277.50000   82.500   1.  NULL
 ___
 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


The information in this e-mail is intended only for the person to whom it is
addressed. If 

Re: [Freesurfer] Dynamic causal modeling

[MCLAREN, Donald]

SPM does not make any distinction about the source of the data. For SPM to
work, all you need is .nii files for your data and you'd need a VOI.mat
that corresponds to the .nii file size.

If you take a look at the gPPI toolbox on the NITRC website, there are
commands/tools that convert FS-FAST 1st level task models to SPM 1st level
task models. The same approach could be used for setting up your DCM
analysis.

Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
=
This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
intended only for the use of the individual or entity named above. If the
reader of the e-mail is not the intended recipient or the employee or agent
responsible for delivering it to the intended recipient, you are hereby
notified that you are in possession of confidential and privileged
information. Any unauthorized use, disclosure, copying or the taking of any
action in reliance on the contents of this information is strictly
prohibited and may be unlawful. If you have received this e-mail
unintentionally, please immediately notify the sender via telephone at (773)
406-2464 or email.

On Tue, Jul 14, 2015 at 12:13 PM, std...@virgilio.it wrote:

 Hi list,

 I'm performing the functional connectivity analysis by FAST.
 Next, I'd like to perform spectral dynamic causal model analysis (SPM,
 Friston et al. 2015; Crone et al. 2015) on FS-FAST output.
 Have you any suggestion in this matter?
 Thanks,

 Stefano

 ___
 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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] finding local extrema in surface data

[MCLAREN, Donald]

Not the fastest approach, but for each vertex, you could find the neighbors
and then test if the vertex is the maximum. There are matlab functions for
getting the list of neighboring vertices.

Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
=
This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
intended only for the use of the individual or entity named above. If the
reader of the e-mail is not the intended recipient or the employee or agent
responsible for delivering it to the intended recipient, you are hereby
notified that you are in possession of confidential and privileged
information. Any unauthorized use, disclosure, copying or the taking of any
action in reliance on the contents of this information is strictly
prohibited and may be unlawful. If you have received this e-mail
unintentionally, please immediately notify the sender via telephone at (773)
406-2464 or email.

On Tue, Jun 23, 2015 at 3:49 AM, Gronenschild Ed (NP) 
ed.gronensch...@maastrichtuniversity.nl wrote:

 Hi Sabine,

 Perhaps you can transform ?h.sphere and corresponding surface data
 into a polar image in which you can try to find the local extrema.

 Cheers,
 Ed

 ___
 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


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] Label to Nii Conversion

[MCLAREN, Donald]

I have a label file on the surface, but want to be able to use it to
extract surface data that is already in nifti format (dimensions: [2737 1
6]).

Is there a way to convert a label to nifti?

Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
=
This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
intended only for the use of the individual or entity named above. If the
reader of the e-mail is not the intended recipient or the employee or agent
responsible for delivering it to the intended recipient, you are hereby
notified that you are in possession of confidential and privileged
information. Any unauthorized use, disclosure, copying or the taking of any
action in reliance on the contents of this information is strictly
prohibited and may be unlawful. If you have received this e-mail
unintentionally, please immediately notify the sender via telephone at (773)
406-2464 or email.
___
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] Brainhack EDT - Boston Updates and Registration Details

[MCLAREN, Donald]

*October 18th and 19th, Boston*


*McGovern Institute for Brain Research @ MIT - *
*http://whereis.mit.edu/?go=46* http://whereis.mit.edu/?go=46

*3rd floor Atrium *


*Doors will be locked, so we will have to let you in. If you are the door,
please call 4-3544 or (617-324-3544) or send a chat message here: *
*https://gitter.im/satra/brainhackEDT*
https://gitter.im/satra/brainhackEDT



*BRAINHACK EDT - BOSTON NEWS/UPDATES:*

·  Siemens is providing funds to help host Brainhack EDT - Boston.

·  The Brainhack EDT - Boston organizing committee is excited to
announce that we will be providing lunch to attendees who register/confirm
their attendance and food choices by 6PM on October 15th (see instructions
below; http://goo.gl/tMfwa2).

·  The Brainhack EDT - Boston organizing committee is working on
organizing a group dinner (attendee pays) on Saturday night in Cambridge.

·  Amazon will provide credits for cloud computing ($100 per person)

·  NeuroElectrics will be bringing a couple of their wireless EEG
headsets for interested parties to hack on. Please check the column if you
are interested.

·  All attendees must confirm their registration by following the
registration instructions below.

*REGISTRATION DETAILS:*

With the generous support from Siemens, we will be providing lunch to
attendees of Brainhack Boston. In order to receive lunch, you must confirm
your registration (indicate YES/NO) and food choices by Noon on October 15th,
2014.


Please click here to register: http://goo.gl/tMfwa2


When you are registering please provide us with your lunch choices along
with whether or not you plan to attend the organized dinner on Saturday
Night (attendees pay for their own dinner). If you do not provide us with
your lunch choices, you will not get free lunch.

In addition, please indicate whether you are interested in working with/on
the Neuroelectrics headset.


*PROJECT PROPOSALS:*

We've heard rumors of several projects for Brainhack EDT - Boston. In order
to spread the word of these projects, we request that you add your
project(s) on the following page:

http://goo.gl/fSMgc3


Project proposal introductions will be 1 minute. If you want to use a slide
to introduce your project, please send the powerpoint slide to
mclaren.donal...@t-gmail.com


*BRAINHACK EDT - BOSTON SCEHDULE:*

*Saturday, October 18, 2014*

08:30   Attendee Arrival (with coffee)

09:00   Welcome reception

09:15   Ignite Talk with icebreaker

09:45   Project Pitch

10:00   Open Hacking

12:00  Onsite Lunch (Mexicali)

13:00  Crowd Annotation Projects (Dolphin Brain)

13:45   Unconference Session

15:00   Coffee Break

15:30  Open Hacking

18:30  Organized dinner (pay your own way)

20:30  Open Hacking



*Sunday, October 19, 2014*

08:30 Attendee Arrival

09:00   Ignite Session II

09:30   Unconference Session

10:30   Open Hacking

12:30   Onsite Lunch (Mexicali)

13:30   Open Hacking

15:00  Coffee Break

15:30   Open Hacking

17:00   Project Summaries and Wrap-up

18:30   Adjournment

19:00 Optional Dinner or Open Hacking

*The Boston Brainhack Committee*


Donald G McLaren, MGH/HMS

Satra Ghosh, MIT

Matt Hutchison, Harvard University
___
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] Brainhack Eastern Standard Time - Boston October 18-19, 2014

[MCLAREN, Donald]

*Do you have a great idea for collaboration or want to collaborate on great
ideas?*

*THEN BRAINHACK IS THE PLACE FOR YOU*

Brainhack is a unique conference that convenes researchers, artists, and
members of industry from across the globe and a myriad of disciplines to
work together on innovative projects broadly related to neuroscience. Year
after year, global Brainhack events have brought together researchers to
participate in open collaboration resulting in new ideas, relationships,
and publications.

Brainhack Eastern Daylight Time (EDT; http://brainhack.org/brainhack-edt/)
will unite several regional Brainhack events during October 18  19, 2014.
Having several simultaneous events will help build a critical mass for the
regional Brainhack movement and provide opportunities for inter-Brainhack
collaboration. The Boston Brainhack will be held at the McGovern Institute
for Brain Research at MIT and is additionally supported by Siemens and
Amazon.

The Boston Brainhack aims to foster local collaborations across the diverse
neuroscience interests and institutions in the Boston area.

The three most common questions:

*Q. What happens at a brainhack?*

A. Think of it as a maker space for neuroscientists. Neuroscience is a
complex, multidisciplinary field with many unknowns. It is often the case
that no individual's expertise is enough to tackle research questions that
can encompass physics, mathematics, modeling, statistics, art, etc. These
events serve to catalyze collaboration across individuals from different
disciplines, create local connections, and promote thinking outside the
box. The events also increase awareness of new and changing technologies
around us as neuroscience move towards data and computationally intensive
approaches. Most importantly it is the social human spirit that brings
together people to share in efforts to solve problems together. If you have
a scientific problem, then the Boston Brainhack can help you solve it.
Think of it like a conference, but instead of talking about solutions,
actually sitting down and implementing them.

*Q. I am new to the field or don't know how to code, can I still come?*

A. Yes! At any level or from any discipline you can make significant
contributions. At Brainhack you will both learn and contribute. If you want
to know how to code in a specific program, please let us know and we'll do
our best to facilitate the learning process. If you are in a different
field and want to hear about neuroscience problems, come on over.

*Q. What do I need to do to prepare?*

A. Here are a few tips

1. To help us get a rough headcount, please sign up at: http://goo.gl/tMfwa2

2. Consider questions or ideas you would like to work on at Brainhack

3. Post project ideas or become a member of a project:

http://brainhack.org/brainhack-edt/

4. Bring tools, data or just enthusiasm on October 18th and 19th.

5. Start chatting at: https://gitter.im/satra/brainhackEDT/~chat#initial
https://gitter.im/satra/brainhackEDT/~chat%22%20%5Cl%20%22initial

or posting questions at: http://neurostars.org %22 (tag with
Brainhack)


We look forward to seeing everyone at the McGovern Institute.


Sincerely,


The Boston Brainhack Committee

Donald G McLaren, MGH/HMS

Satra Ghosh, MIT

Matt Hutchison, Harvard University
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Correlation coeffecient

[MCLAREN, Donald]

Lars,

Yes. You could use that equation. Here are some more conversions:
http://www.soph.uab.edu/Statgenetics/People/MBeasley/Courses/EffectSizeConversion.pdf

Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
=
This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
intended only for the use of the individual or entity named above. If the
reader of the e-mail is not the intended recipient or the employee or agent
responsible for delivering it to the intended recipient, you are hereby
notified that you are in possession of confidential and privileged
information. Any unauthorized use, disclosure, copying or the taking of any
action in reliance on the contents of this information is strictly
prohibited and may be unlawful. If you have received this e-mail
unintentionally, please immediately notify the sender via telephone at (773)
406-2464 or email.


On Sat, Jul 12, 2014 at 6:21 PM, Lars M. Rimol lari...@gmail.com wrote:

 Hi Doug,

 A naive question in regard to the issue brought up by Chris (see below):
 Could one simply use this formula (with the F from the GLM for a given
 contrast):

 r² = F/(F+df) ?


 LMR


 try this 
 oneftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fast_glm_pcc.m

 On 07/11/2014 01:51 PM, Chris Wertz wrote:
  Hi Freesurfer experts
 
  I am trying to obtain correlation coefficients for significant
  clusters and found a previous post about this,
  https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-May/023616.html
 
 
  but the MATLAB function link within this post is dead?
 
  any help is greatly appreciated
 
  thanks,
  Chris







 --
 yours,

 Lars M. Rimol, PhD
 St. Olavs Hospital
 Trondheim,
 Norway

 ___
 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


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] Surface Label to Nifti File

[MCLAREN, Donald]

I'm trying to convert a surface label to a nifti file to use with
functional surface data that is already in nifti format. The ultimate goal
is to be able to use the converted surface label as a seed in gPPI analyses
that is run in MATLAB.

I've been able to use volume based seeds for the MNI305 subcortical stream
and carryout the analysis on the surfaces already. I'm just wanting to use
cortical surface seeds now.

I think I've got the code correct, but wanted to double check that I am
using the correct command:

mri_label2label -srclabel mylabel --s fsaverage --trglabel tmplabel
--outmask test.nii --regmethod surface --hemi lh

In this case, does the target surface matter? It seems to default to white?

Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
=
This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
intended only for the use of the individual or entity named above. If the
reader of the e-mail is not the intended recipient or the employee or agent
responsible for delivering it to the intended recipient, you are hereby
notified that you are in possession of confidential and privileged
information. Any unauthorized use, disclosure, copying or the taking of any
action in reliance on the contents of this information is strictly
prohibited and may be unlawful. If you have received this e-mail
unintentionally, please immediately notify the sender via telephone at (773)
406-2464 or email.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] comparing two conditions with disproportionate number of trials

[MCLAREN, Donald]

For the contrast AB, the number of trials is not considered. When you
contrast A and B, you are assessing the mean response to trials of
condition A to the mean response to trials of condition B. You wouldn't
want to weight this by the number of trials as then the contrast would not
make sense.

The number of trials can effect the accuracy of the estimate of the mean
response to a condition. In this way, A could be stronger or weaker than it
actually is in each subject. Because of the decreased accuracy, you could
also have increased variability between subjects.

As a result of the increased variability, the mean response needed for A to
be different from 0, will be greater than that in B. However, this not
imply that A will be greater than B as the significance of A doesn't tell
you anything about AB. In fact, you could construct a case where BA and
where A0 is significant, but B0 is not significant. In A vs B, you are
using the within-subject variance and fro A or B vs 0, you are using the
variance between subjects.

Generally, you need 30-40 trials to get a stable estimate of the mean
response of each condition.

Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
=
This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
intended only for the use of the individual or entity named above. If the
reader of the e-mail is not the intended recipient or the employee or agent
responsible for delivering it to the intended recipient, you are hereby
notified that you are in possession of confidential and privileged
information. Any unauthorized use, disclosure, copying or the taking of any
action in reliance on the contents of this information is strictly
prohibited and may be unlawful. If you have received this e-mail
unintentionally, please immediately notify the sender via telephone at (773)
406-2464 or email.


On Mon, May 5, 2014 at 10:57 AM, Eryilmaz, Huseyin Hamdi 
heryil...@partners.org wrote:

   Dear FS experts,

  I have a question about the way contrasts work in an event-related
 design. I am wondering if freesurfer is doing some sort of weighing when it
 compares two different conditions with incomparable number of trials. For
 example condition A is represented by 10 trials in the paradigm file,
 whereas condition B consists of 80 trials. In that case, for the contrast
 AB does freesurfer compensate for the small number of trials in condition
 A? If so, could it lead to inflated activations? We suspected this as in
 our results, the condition with fewer trials depicted strong activations.

  Thanks very much for the tips!

  Best,
 Hamdi



  --

  Hamdi Eryilmaz, PhD

 Massachusetts General Hospital
 A.A. Martinos Center for Biomedical Imaging
 Brain Genomics Laboratory
 149 13th St, Charlestown, MA 02129
 Phone: +1 617 643 7462 %2B1%20617%20643%207462

 ___
 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


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] gPPI Toolbox Version 13.1 for SPM has now been released

[MCLAREN, Donald]

Version 13.1 of the gPPI toolbox (previously released versions were 7.12
and 13) is now available at http://www.nitrc.org/projects/gppi

Version 13.1 now supports task-models from FSFAST and can read the model
structure directly from your FSFAST analysis.

Version 13.1 now support robust weighted least squares (rWLS) - requires
your first level model to have been generated with the rWLS toolbox.

The major changes are:
(1) Integrated spm_spm and spm_spm_WB into the software, no patch
is needed. P.wb=1 will use the whole brain approach.
(2) Added ability to start with FSFAST first level models.
(3) Added ability to do rWLS, if the rWLS was used in the
first-level models.
(4) Removed dependency of gzip on java.
(5) A few other bells and whistles.
(6) Added script to pre-extract VOI timeseries
(7) Added the ability to use upsampled data or neural signal inputs


Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
=
This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
intended only for the use of the individual or entity named above. If the
reader of the e-mail is not the intended recipient or the employee or agent
responsible for delivering it to the intended recipient, you are hereby
notified that you are in possession of confidential and privileged
information. Any unauthorized use, disclosure, copying or the taking of any
action in reliance on the contents of this information is strictly
prohibited and may be unlawful. If you have received this e-mail
unintentionally, please immediately notify the sender via telephone at (773)
406-2464 or email.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] A question regarding DODS or DOSS

[MCLAREN, Donald]

You might also want to read about mean centering and same or different
slopes here:
*http://mumford http://mumford*.fmripower.org/*mean*_*centering*/

Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
=
This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
intended only for the use of the individual or entity named above. If the
reader of the e-mail is not the intended recipient or the employee or agent
responsible for delivering it to the intended recipient, you are hereby
notified that you are in possession of confidential and privileged
information. Any unauthorized use, disclosure, copying or the taking of any
action in reliance on the contents of this information is strictly
prohibited and may be unlawful. If you have received this e-mail
unintentionally, please immediately notify the sender via telephone at (773)
406-2464 or email.


On Thu, Jan 30, 2014 at 12:03 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu
 wrote:


 Technically, you are on safe ground using DODS in that I don't think a
 reviewer would object. However, I would be a little worried as to
 whether the group difference is real. Does DOSS start to look like DODS
 if you lower the threshold? Try running DODS with and without demeaning
 the covariates to see whether it changes much.

 doug

 On 01/28/2014 07:52 PM, KimMJ wrote:
 
 
  
  Dear Doug
 
  Thank you for the prompt reply.
  I want to make sure: If there is no group*age interaction, is it safe
  to report the result of group differences using DODS (1 -1 0 0 )?
  Or is it more appropriate (or mandatory) to further use DOSS to look
  for group differences (1 -1 0)?
  The reason why I ask you is that the results of group differences
  using DODS is satisfactorily significant to support my hypothesis.
 
  Sorry for bothering you again with my silly question.
  Thank you.
 
  Min J.
 
 
 
 
 
 
  Date: Tue, 28 Jan 2014 12:10:42 -0500
  From: gr...@nmr.mgh.harvard.edu
  To: freesurfer@nmr.mgh.harvard.edu
  Subject: Re: [Freesurfer] A question regarding DODS or DOSS
 
 
  On 1/28/14 7:03 AM, KimMJ wrote:
 
  Dear Doug and experts
 
  My question is about the choice of DODS or DOSS.
  I want to compare cortical thickness between 2 groups (disease
  group and control group), while controlling for the effect of age
  (nuisance covariate).
  I've already read through the mailing list about the issue of DODS
  and DOSS designs.
 
  If I understand correctly, I have to first use DODS (QDEC) in
  order to find areas of significant group*age interaction by using
  the contrast (0 0 1 -1).
  Given there is no area of interaction that survived multiple
  comparisons correction, I can go with DOSS (1 -1 0) using
  mri_glmfit (command line) to test between-group differences in
  cortical thickness, controlling for the effect of age. Am I right?
 
  Yes
 
 
  My another question is that 'MUST' I rerun DOSS model after
  confirming no group*age interaction in DODS ? Or can I directly
  use the results of DODS to look for between-group differences
  controlling for age (1 -1 0 0), since there is no group*age
  interaction ?
  Is there much difference in results between the above-mentioned
  two approaches?
 
  Technically, yes, though the results will be different. How different,
  no one knows. The reason I like going to DODS is that there are no
  issues with the slopes being slightly different. It does not take much
  time to re-run it.
 
  I've found a reply by Doug from the mailing list: If there is no
  interaction, then either DODS or DOSS is appropriate. DOSS will be
  more powerful and a little more interpretable
  (
 http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg33418.html
  
 http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg33418.html
 ).
  From this context, what does the 'powerful' mean? Does DOSS yield
  higher statistical values than DODS?
 
  It means that you will have a higher degrees of freedom. All other
  things being equal, it means more significant p values.
  doug
 
 
  Apology for the beginner's questions.
  Thank you in advance for your help.
 
  MJ
 
 
  ___
  Freesurfer mailing list
  Freesurfer@nmr.mgh.harvard.edu  mailto:
 Freesurfer@nmr.mgh.harvard.edu
  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 
 
 
  ___ Freesurfer mailing
  list Freesurfer@nmr.mgh.harvard.edu
  

Re: [Freesurfer] Power analysis for Qdec

[MCLAREN, Donald]

One comment on power calculations. You cannot do the power calculations
after you have completed the study. Any reviewer/referee asking you to
compute the power should be politely informed that post-hoc power analyses
are not valid and are biased (because you would be computing the power of
the observed effect).

What you want to do is to compute the power of the experiment before you
conduct the experiment. You want to be able to say that to compare an
effect of X, we have have Y% power to detect the effect with N subjects.

G*Power is an excellent program to compute power - although it doesn't do
it on the entire image.

Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
=
This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
intended only for the use of the individual or entity named above. If the
reader of the e-mail is not the intended recipient or the employee or agent
responsible for delivering it to the intended recipient, you are hereby
notified that you are in possession of confidential and privileged
information. Any unauthorized use, disclosure, copying or the taking of any
action in reliance on the contents of this information is strictly
prohibited and may be unlawful. If you have received this e-mail
unintentionally, please immediately notify the sender via telephone at (773)
406-2464 or email.


On Tue, Oct 29, 2013 at 10:25 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu
 wrote:


 We don't have a way to do a power analysis directly from QDEC. I have
 some matlab code that does it for univariate analysis.

 In the QDEC output folder, you will see a glm folder. In that there will
 be folders for each contrast. In the contrast folder, you will see an
 F.mgh file which will be the F-values. You can convert this to a t =
 sign(gamma.mgh)*sqrt(F)

 doug


 On 10/28/2013 07:27 AM, amirhossein manzouri wrote:
  Hi
  Would you please let me know if it is possible to calculate the power
 for a group comparison in cortical thickness? Also, a referee is requesting
 F-values and T map , are they generated by q-dec?
  That would be great if I can get an answer in more detail since I have
  seen the post in FAQ, just need more information in detail regarding
  calculating the power !
  --
  Best regards,
  Amirhossein Manzouri
 
 

 --
 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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Power analysis for Qdec

[MCLAREN, Donald]

For anyone who wants G*Power, here is a link to the download page. It is
free for all users.

http://www.psycho.uni-duesseldorf.de/abteilungen/aap/gpower3/

Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
=
This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
intended only for the use of the individual or entity named above. If the
reader of the e-mail is not the intended recipient or the employee or agent
responsible for delivering it to the intended recipient, you are hereby
notified that you are in possession of confidential and privileged
information. Any unauthorized use, disclosure, copying or the taking of any
action in reliance on the contents of this information is strictly
prohibited and may be unlawful. If you have received this e-mail
unintentionally, please immediately notify the sender via telephone at (773)
406-2464 or email.


On Tue, Oct 29, 2013 at 10:40 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu
 wrote:

 Good point Donald. Where can one get G*Power?
 doug



 On 10/29/2013 10:38 AM, MCLAREN, Donald wrote:

 One comment on power calculations. You cannot do the power calculations
 after you have completed the study. Any reviewer/referee asking you to
 compute the power should be politely informed that post-hoc power analyses
 are not valid and are biased (because you would be computing the power of
 the observed effect).

 What you want to do is to compute the power of the experiment before you
 conduct the experiment. You want to be able to say that to compare an
 effect of X, we have have Y% power to detect the effect with N subjects.

 G*Power is an excellent program to compute power - although it doesn't do
 it on the entire image.

 Best Regards, Donald McLaren
 =
 D.G. McLaren, Ph.D.
 Research Fellow, Department of Neurology, Massachusetts General Hospital
 and
 Harvard Medical School
 Postdoctoral Research Fellow, GRECC, Bedford VA
 Website: 
 http://www.martinos.org/~**mclarenhttp://www.martinos.org/~mclaren
 http://www.martinos.org/%**7Emclaren http://www.martinos.org/%7Emclaren
 

 Office: (773) 406-2464
 =
 This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
 HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
 intended only for the use of the individual or entity named above. If the
 reader of the e-mail is not the intended recipient or the employee or
 agent
 responsible for delivering it to the intended recipient, you are hereby
 notified that you are in possession of confidential and privileged
 information. Any unauthorized use, disclosure, copying or the taking of
 any
 action in reliance on the contents of this information is strictly
 prohibited and may be unlawful. If you have received this e-mail
 unintentionally, please immediately notify the sender via telephone at
 (773)
 406-2464 or email.


 On Tue, Oct 29, 2013 at 10:25 AM, Douglas N Greve 
 gr...@nmr.mgh.harvard.edu 
 mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu
 wrote:


 We don't have a way to do a power analysis directly from QDEC. I have
 some matlab code that does it for univariate analysis.

 In the QDEC output folder, you will see a glm folder. In that
 there will
 be folders for each contrast. In the contrast folder, you will see an
 F.mgh file which will be the F-values. You can convert this to a t =
 sign(gamma.mgh)*sqrt(F)

 doug


 On 10/28/2013 07:27 AM, amirhossein manzouri wrote:
  Hi
  Would you please let me know if it is possible to calculate the
 power for a group comparison in cortical thickness? Also, a
 referee is requesting F-values and T map , are they generated by
 q-dec?
  That would be great if I can get an answer in more detail since
 I have
  seen the post in FAQ, just need more information in detail regarding
  calculating the power !
  --
  Best regards,
  Amirhossein Manzouri
 
 

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

 Bugs: 
 surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 
 http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 
 FileDrop: 
 https://gate.nmr.mgh.harvard.**edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2
 
 www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop

[Freesurfer] Brainhack 2013 Stipend Program (DEADLINE TO APPLY: 11:59PM EST OCTOBER 3rd, 2013)

[MCLAREN, Donald]

Dear Colleagues,

The Neurobureau is excited to announce a stipend program for Brainhack
2013. The stipend program was created following a generous grant from
Siemens Healthcare to assist young investigators in attending Brainhack
2013. Without their support, the stipend program would not exist.

The stipend program will provide at least 6 stipends for partial or full
registration fees [if 24 attendees apply, you have a 25% chance of getting
a stipend]. The exact breakdown of stipends provided will depend on the
number of applicants and the cost of attending the conference for those
applicants.

The application for stipend requires:
(1) A poster abstract
(2) A 1-2 page Brainhack project proposal (pdf format)
(3) NIH Biosketch/CV (pdf format)

The Brainhack 2013 Organizing Committee will decide which applications
will receive stipends based on their abstract and proposed brainhack
projects.

The deadline to apply for one of the stipends is 11:59PM EST on THURSDAY
OCTOBER 3rd. All decisions will be made by October 6th and must be accepted
within 24 hours of being awarded. Registration and payment will be
completed by the organizing committee.

Please mail the above application materials to mclaren.don...@gmail.com to
apply.

Good luck.





Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
=
This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
intended only for the use of the individual or entity named above. If the
reader of the e-mail is not the intended recipient or the employee or agent
responsible for delivering it to the intended recipient, you are hereby
notified that you are in possession of confidential and privileged
information. Any unauthorized use, disclosure, copying or the taking of any
action in reliance on the contents of this information is strictly
prohibited and may be unlawful. If you have received this e-mail
unintentionally, please immediately notify the sender via telephone at (773)
406-2464 or email.
___
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] UPDATES on Brainhack 2013 (including stipend application extension)

[MCLAREN, Donald]

Dear All,

Brainhack 2013 will be taking place in just under a month outside of Paris,
France. A welcome reception will be held on the evening of October 23rd to
be followed by the hackathon on October 24th, 25th, and 26th.

Brainhack 2013 will be highlighted by Ignite talks by:

   - *Yves Burnod,
PhD,http://www.imed.jussieu.fr/en/outils/affiche_personne.php?pers_id=217
INSERM
   (French national Institute for Health)*
   - *Jean Daunizeau,
PhD,https://sites.google.com/site/jeandaunizeauswebsite/l’Institut
   du Cerveau et de la Moelle épinière*
   - *Martin Lindquist, PhD, http://www.biostat.jhsph.edu/~mlindqui/
Department
   of Biostatistics of the Johns Hopkins University Bloomberg School of Public
   Health.*
   - *Ziad Saad,
PhD,http://intramural.nimh.nih.gov/research/clinicians/sc_saad_z.html
US
   National Institutes of Mental Health Statistical and Scientific Computing
   Core*
   - *Gaël Varoquaux, PhD, http://gael-varoquaux.info/ INRIA at the
   Neurospin*
   - *Xinian Zuo, PhD, http://lfcd.psych.ac.cn/ Institute of Psychology,
   Chinese Academy of Science*

UPDATES:
We have four important updates about Brainhack 2013:
(1) Brainhack.org back online after being offline at the end of last week
and over the weekend. Details about Brainhack 2013 can now be found there.

(2) Due to the technical problems last week, we've extend the stipend
application deadline to 11:59 PM EST on Thursday October 3rd. See
brainhack.org for details on how to apply.

(3) Attendees can now complete their registration by paying the
registration fees at: http://dr01.azur-colloque.cnrs.fr Instructions on
this process can be found here: http://www.brainhack.org/?page_id=5425. The
deadline for registering is October 15th and payment must be received by
October 16th.

(4) If you want to have your poster abstract appear in the Brainhack 2013
Program, please submit your abstract online at brainhack.org. Posters will
be presented electronically during the welcome reception.

Hope to see you next Month.


 Please let Donald McLaren know if you have any questions. He can be
 reached via email: mclaren.don...@gmail.com

___
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] Brainhack Registration and Payment

[MCLAREN, Donald]

Brainhack.org is currently offline due to technical issues. We hope to have
the website back up and running shortly.

Here are the details to register (if you have not already) and to complete
the payment process (if you pre-registered). The cost for the entire
workshop and lodging for 4 nights is 450 Euros. The cost for the conference
alone is about 200 Euros.

*
First step* :

Here is the website :
http://dr01.azur-colloque.cnrs.fr.http://dr01.azur-colloque.cnrs.fr

-  Choose your language
-  Choose our “event” : Brain Hack 2013
-  Click on “Pre-registration”
-  Fill the form (as you have already done for the Brainhack.org website).
The standard “Tarification” you must check is “Researcher”.

*Second step* :

- After this “Pre-registration” (*and our validation*), you will receive an
email “Confirm a pre-registration”. This message will invite you to
payon-line. Please follow the link you will receive.

- Several pages need to be validated :

   - 1st page – “Please enter your information” : to get logged, please
enter the information previously used.
   - 2nd page – “Personal information” : fill the form
   - 3rd page – “Organization (origin)” : just click on “next step”
  - 4th page – “Payment” : If your university or other institution
will paythe fee for you, please check the second option “Someone
else...” and fill
the form.
  - 5th page – “Invoice” : just validate.
  - 6th page – “Invoice details”. Two options:

Credit Card: simple, fast and best payment option.

Transfer: Please do not take into account the message in red “only from
French public organizations” – you do have the right to use this option,
even if you're living in a foreign country. Moreover, once the
paymenttransfered, you will receive a confirmation only several days
after – do
not panic, this is only a delay due to this option.

I apologise for the lateness but our website is down.

Please, let me know if you have problem or questions.

Sincerely yours,

Marlène Etienne

Please let Donald McLaren know if you have any questions. He can be reached
via email: mclaren.don...@gmail.com
___
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] Fwd: Brainhack 2013 Stipend Program (DEADLINE TO APPLY: 11:59PM EST TONIGHT)

[MCLAREN, Donald]

Dear Colleagues,

The Neurobureau is excited to announce a stipend program for Brainhack
2013. The stipend program was created following a generous grant from
Siemens Healthcare to assist young investigators in attending Brainhack
2013. Without their support, the stipend program would not exist.

The stipend program will provide at least 6 stipends for partial or full
registration fees [if 24 attendees apply, you have a 25% chance of getting
a stipend]. The exact breakdown of stipends provided will depend on the
number of applicants and the cost of attending the conference for those
applicants.

The application for stipend requires:
(1) A poster abstract
(2) A 1-2 page Brainhack project proposal (pdf format)
(3) NIH Biosketch/CV (pdf format)

The Brainhack 2013 Organizing Committee will decide which applications
will receive stipends based on their abstract and proposed brainhack
projects.

The deadline to apply for one of the stipends is 11:59PM EST on September
27th. All decisions will be made by October 3rd and must be accepted within
24 hours of being awarded.

To submit the application. Please email the 3 documents above to Donald
McLaren (mclaren.don...@gmail.com) by 11:59 PM EST tonight.

Good luck.
___
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] Fwd: Brainhack 2013 Stipend Program (DEADLINE TO APPLY: 11:59PM EST SEPTEMBER 27, 2013)

[MCLAREN, Donald]

Dear Colleagues,

The Neurobureau is excited to announce a stipend program for Brainhack
2013. The stipend program was created following a generous grant from
Siemens Healthcare to assist young investigators in attending Brainhack
2013. Without their support, the stipend program would not exist.

The stipend program will provide at least 6 stipends for partial or full
registration fees [if 24 attendees apply, you have a 25% chance of getting
a stipend]. The exact breakdown of stipends provided will depend on the
number of applicants and the cost of attending the conference for those
applicants.

The application for stipend requires:
(1) A poster abstract
(2) A 1-2 page Brainhack project proposal (pdf format)
(3) NIH Biosketch/CV (pdf format)

To apply, please send the above details to Donald McLaren (
mclaren.don...@gmail.com). This change is being made due to technical
difficulties of the website. I will email everyone on Saturday morning to
confirm that their application is being considered. If you do not receive
and email on Saturday morning, please resend your application.

The Brainhack 2013 Organizing Committee will decide which applications
will receive stipends based on their abstract and proposed brainhack
projects.

The deadline to apply for one of the stipends is 11:59PM EST on September
27th. All decisions will be made by October 3rd and must be accepted within
24 hours of being awarded.

Good luck.





Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
=
This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
intended only for the use of the individual or entity named above. If the
reader of the e-mail is not the intended recipient or the employee or agent
responsible for delivering it to the intended recipient, you are hereby
notified that you are in possession of confidential and privileged
information. Any unauthorized use, disclosure, copying or the taking of any
action in reliance on the contents of this information is strictly
prohibited and may be unlawful. If you have received this e-mail
unintentionally, please immediately notify the sender via telephone at (773)
406-2464 or email.
___
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] Fwd: Brainhack 2013 Stipend Program (DEADLINE TO APPLY: 11:59PM EST SEPTEMBER 27, 2013)

[MCLAREN, Donald]

Dear Colleagues,

The Neurobureau http://www.neurobureau.org is excited to announce a
stipend program for Brainhack 2013 http://www.brainhack.org (October
23-26 in Sevres, France (just outside of Paris). The stipend program was
created following a generous grant from Siemens Healthcare to assist young
investigators in attending Brainhack 2013. Without their support, the
stipend program would not exist.

The stipend program will provide at least 6 stipends for partial or full
registration fees [if 24 attendees apply, you have a 25% chance of getting
a stipend]. The exact breakdown of stipends provided will depend on the
number of applicants and the cost of attending the conference for those
applicants.

The application for stipend requires:
(1) A poster abstract
(2) A 1-2 page Brainhack project proposal (pdf format)
(3) NIH Biosketch/CV (pdf format)

The Brainhack 2013 Organizing Committee will decide which applications
will receive stipends based on their abstract and proposed brainhack
projects.

Details on Brainhack 2013 can be found
herehttp://www.brainhack.org/?page_id=27784
.

The deadline to apply for one of the stipends is 11:59PM EST on September
27th. All decisions will be made by October 3rd and must be accepted within
24 hours of being awarded.

If you have any questions please contact myself (mclaren.don...@gmail.com)
or one of the organizers.

Click here to apply. http://www.brainhack.org/?page_id=40668

Good luck.

Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
=
This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
intended only for the use of the individual or entity named above. If the
reader of the e-mail is not the intended recipient or the employee or agent
responsible for delivering it to the intended recipient, you are hereby
notified that you are in possession of confidential and privileged
information. Any unauthorized use, disclosure, copying or the taking of any
action in reliance on the contents of this information is strictly
prohibited and may be unlawful. If you have received this e-mail
unintentionally, please immediately notify the sender via telephone at (773)
406-2464 or email.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Ploting convolved stimuli with actual stimuli

[MCLAREN, Donald]

Aser,

If you you put your custom sequence into SPM, you can get the graphs above.
The key variables are:
SPM.Sess.U.u, time variable is
0:TR/#oftimebins:TR/#oftimebins*size(SPM.Sess.U.u,1)
SPM.xX.X, time variable is 0:TR:TR*size(SPM.xX.X,1), this is the convolved
data., this is the stick function or stimulus on times

** Sess will need to be index for each run (e.g. Sess(1).U)
** U will need to be indexed for each condition (e.g. U(1).u, U(2).u)

Hope this helps.

Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
=
This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
intended only for the use of the individual or entity named above. If the
reader of the e-mail is not the intended recipient or the employee or agent
responsible for delivering it to the intended recipient, you are hereby
notified that you are in possession of confidential and privileged
information. Any unauthorized use, disclosure, copying or the taking of any
action in reliance on the contents of this information is strictly
prohibited and may be unlawful. If you have received this e-mail
unintentionally, please immediately notify the sender via telephone at (773)
406-2464 or email.


On Sun, Sep 15, 2013 at 6:14 PM, Aser A fmri2...@gmail.com wrote:

 Hi all,

 Using the output from OptSeq, is there a possible ( easy ^u^ ) way of
 plotting in the same graph the presentation of stimuli with their
 convolution?

 So basically, I created my design using OptSeq. To make it nicer, I want
 to plot this. I am not aware of freesufer and I use SPM. In SPM it just
 shows the convolved stimuli without showing sticks of the stimuli.

 I have attached a picture taken from the genetic program that helps
 creating or optimizing fMRI designs just to show you what I mean or I want.


 I have also attached an excel file contains the output from OptSeq.

 Thanks

 Aser



 ___
 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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Getting around a design matrix with zero columns

[MCLAREN, Donald]

Ye,

If you use the DOSS model as Doug suggested, you have will not have a
column of 0s in the matrix. However, the group columns become the
covariate-adjusted thickness in each group  (e.g. thickness at the mean
years of meditation across everyone) - which doesn't make sense as
non-meditators will always have 0 years.

What I would suggest is to mean center the covariate based on the two
meditator groups and keep the the non-meditator group at 0. This will then
make the meditator group means be at the mean years of the two groups and
compare to the non-meditator group. This should work as I presume that you
are adding the covariate to account for the differences in years of
meditating.

Hope this helps.

Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
=
This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
intended only for the use of the individual or entity named above. If the
reader of the e-mail is not the intended recipient or the employee or agent
responsible for delivering it to the intended recipient, you are hereby
notified that you are in possession of confidential and privileged
information. Any unauthorized use, disclosure, copying or the taking of any
action in reliance on the contents of this information is strictly
prohibited and may be unlawful. If you have received this e-mail
unintentionally, please immediately notify the sender via telephone at (773)
406-2464 or email.


On Sun, Sep 15, 2013 at 5:42 PM, ye tian tianye...@gmail.com wrote:

 Dear Doug,

 I am afraid that I don't see a difference between fsgd file and customized
 design matrix in this case. If I were to set up my own design, the matrix
 would still have a column of zero's -- unless there is a trick that I don't
 know?

 Thank you very much for your patience.

 Sincerely,
 Ye


 On Sun, Sep 15, 2013 at 2:28 PM, Douglas Greve 
 gr...@nmr.mgh.harvard.eduwrote:


 There is not a way to do this using an FSGD and a DODS model. It will
 work if you change it to DOSS (if that is appropriate). Otherwise, you will
 need to create your own design matrix and feed it to mri_glmfit with --X
 doug



 On 9/13/13 10:21 PM, ye tian wrote:

  Dear Freesurfers,

 I am studying how the practice of meditation affects cortical
 thickness. I have two types of meditations, and I also know for how many
 years each mediator has meditated. Therefore, ideally I would like my
 categorical factor to be meditation (control, meditation1 and meditation2),
 and continuous factor to be the number of years of meditation. This design,
 of course, has a problematic column of zeros, which corresponds to the
 slope of the control (a non-meditator has meditated for 0 years).

 Does freesurfer has a way out of this problem? For example, I have came
 across pseudoinverse methods in literature?

 Any suggestion is highly appreciated.

 Thank you very much!
  Sincerely,
 Ye


 ___
 Freesurfer mailing 
 listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



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


 The information in this e-mail is intended only for the person to whom it
 is
 addressed. If you believe this e-mail was sent to you in error and the
 e-mail
 contains patient information, please contact the Partners Compliance
 HelpLine at
 http://www.partners.org/complianceline . If the e-mail was sent to you
 in error
 but does not contain patient information, please contact the sender and
 properly
 dispose of the e-mail.



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


 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


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

Re: [Freesurfer] [martinos-tech]

[MCLAREN, Donald]

Suzanne,

p0.005 is the same whether its voxels or vertices.
The liberal nature of 20 voxels is vague to begin with as there is two
things contributing to how liberal 20 voxels are: (1) voxel size - 20 1mm
isotropic voxels is quite different from 20 3mm isotropic voxels; (2) The
number of voxels you are testing -- testing 100 voxels and finding 20 that
are significant is quite different than testing 10 voxels and finding
20 that are significant.

Thus, trying to compare voxels to surface area is quite difficult. I am not
sure if there is a way to equate the surface area to voxels given points #1
and #2. It's hard to equate the number of voxels to the surface area
because voxels occur outside of the surface as well. You'd have to
constrain your analysis to only grey matter and p 0.005 in 20 voxels to be
testing the same measurements. Even then, the tests wouldn't quite be the
same number or areas.


Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
=
This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
intended only for the use of the individual or entity named above. If the
reader of the e-mail is not the intended recipient or the employee or agent
responsible for delivering it to the intended recipient, you are hereby
notified that you are in possession of confidential and privileged
information. Any unauthorized use, disclosure, copying or the taking of any
action in reliance on the contents of this information is strictly
prohibited and may be unlawful. If you have received this e-mail
unintentionally, please immediately notify the sender via telephone at (773)
406-2464 or email.


On Wed, Sep 11, 2013 at 4:20 AM, Suzanne Oosterwijk 
suzanne.oosterw...@gmail.com wrote:

 Hi Doug,

 Thanks for your reply. I know how to run mri_glmfit-sim. What I'd like to
 do is to apply a more liberal threshold to my data to examine the clusters
 that fall outside of the MC-corrected threshold. To do this I applied the
 mri_surfcluster command with a vertex-wise threshold of p  .005, and a
 minarea of 50 mm2. My question is how I should interpret the minarea flag.
 I want to have some insight in whether this threshold is more liberal than
 a threshold of 20 continuous voxels with a p-value of .005 (p  .005; k 
 20) or whether this threshold is more conservative.

 Thanks,
 Suzanne


 On Wed, Sep 11, 2013 at 12:08 AM, Douglas N Greve 
 gr...@nmr.mgh.harvard.edu wrote:

 Hi Suzanne, I'll cc the FS list so others can benefit ...


 On 09/09/2013 06:02 AM, Suzanne Oosterwijk wrote:

 Hi Doug,

 I have two follow-up questions to enhance my own understanding of
 Freesurfer. I know that MC simulations take into account the smoothness of
 the data. I noticed that the smoothing factor of my surface maps is quite
 high (around 8/9 fwhm), even though I applied a smoothing factor of 5
 during pre-processing. Can you explain to me why the final maps have such a
 high fwhm? Is this because of the transformations that are necessary to
 create the surfaces?


 The final measured FWHM is a composite of the smoothing you applied plus
 any smoothness that may already be in the data. Eg, when the surfaces are
 created, there is a smoothness constraint that can cause smoothness in the
 surfaces. The gyrification index has very high smoothenss. For fMRI, there
 is already natural smoothness in the data plus smoothness added due to
 interpolation when sampling to the surface.



 Another question concerns the relationship between voxels and vertices.
 Does one voxel corresponds to one vertex, or is the relationship different?
 This may be a very stupid question, but I thoroughly searched the wiki and
 the web without finding a straightforward answer.

 Vertices and voxels are different entities. A voxel is a 3D box, a vertex
 is essentially a 2D triangle on the surface. The surface is made from a
 volume, of course. Initially, the square face of a voxel is divided into
 two triangles of equal size. The location of the vertices are then adjusted
 to get a better fit. Oftentimes, we use the term voxel and vertex
 interchangeably because each just represents a data point either on the
 surface or in the volume.


  The next question is, if I want to apply a liberal threshold to my data
 that is similar to say p  .005; k  20, then how do I produce this using
 the minarea flag in the mri_surfcluster command?


 I'm not sure what you mean by p  .005. Is that a vertex-wise threshold
 (ie, the cluster-forming threshold) or cluster-wise? What is k? If you want
 to correct for multiple comparisons, then you can run mri_glmfit-sim. Once
 you select a cluster-wise and cluster-forming thresholds (and given the
 

[Freesurfer] Brainhack 2013 Update - Registration is open, Stipend program announced

[MCLAREN, Donald]

Dear colleagues,

I wanted to draw your attention on the upcoming Brainhack 2013, which is
being held from October 23-26 at the Centre International d'Études
Pédagogiques, Sèvres, France (just outside of Paris).

Registration is limited, please register to guarantee a spot (http://www.
brainhack.org/?page_id=27743)
* The registration page has now been separated from the abstract submission
to allow for registration in advance of abstract submission. Register today
while space is still available.

*NEW TO BRAINHACK 2013:*
(1) Abstract book listing all presented abstracts - please submit your
abstract online for inclusion after you register
(2) Stipend program to help defray registration fees (
http://www.brainhack.org/?page_id=40668)


We have also confirmed the following IGNITE
speakershttp://www.brainhack.org/?page_id=40630
:
*Yves Burnod, 
PhD,http://www.imed.jussieu.fr/en/outils/affiche_personne.php?pers_id=217
INSERM
(French national Institute for Health)
**Jean Daunizeau,
PhD,https://sites.google.com/site/jeandaunizeauswebsite/l’Institut
du Cerveau et de la Moelle épinière
**Martin Lindquist, PhD, http://www.biostat.jhsph.edu/~mlindqui/ Department
of Biostatistics of the Johns Hopkins University Bloomberg School of Public
Health.
**Ziad Saad, 
PhD,http://intramural.nimh.nih.gov/research/clinicians/sc_saad_z.html
US
National Institutes of Mental Health Statistical and Scientific Computing
Core
**Gaël Varoquaux, PhD, http://gael-varoquaux.info/ INRIA at the Neurospin
**Xinian Zuo, PhD, http://lfcd.psych.ac.cn/ Institute of Psychology,
Chinese Academy of Science*

Brainhack 2013 is a unique workshop with the goals of fostering
interdisciplinary collaboration and open neuroscience. The structure builds
from the concepts of an unconference and hackathon: The term “unconference”
refers to the fact that most of the content will be dynamically created by
the participants — a hackathon is an event where participants collaborate
intensively on projects.

Participants interested in neuroimaging from any discipline are welcome.
Ideal participants span in range from graduate students to professors
across any disciplines willing to contribute (e.g., mathematics, computer
science, engineering, neuroscience, psychology, psychiatry, neurology,
medicine, art, etc…). The primary requirement is a desire to work in close
collaborations with people outside of your specialization in order to
address neuroscience questions that are beyond the expertise of a single
discipline.

One should come to brainhack ready to engage into collaborative projects,
and with some material (slides, ideas, data, tools) ready to start a
project or a discussion panel. Brainhack will build on the successful
techniques used in other unconferences to keep the meeting focused and
productive. It is possible to start a project and build a team as early as
today. Please have a look at the website for information on the conference
and a sample of projects (from Brainhack 2012): http://www.brainhack.org

The Preliminary Schedule for Brainhack 2013 is available online: http://www.
brainhack.org/?page_id=27753

Registration is now open: http://www.brainhack.org/?page_id=27743

Abstract Submission is now open: http://www.brainhack.org/?page_id=40661

Stipend Application is now open: http://www.brainhack.org/?page_id=40668

Please share this with your friends and colleagues.

Please do not hesitate to contact one of the members of the organizing
committee if you have any questions.

We look forward to seeing you in Paris.
Sincerely,

The Neuro Bureau
___
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] Brainhack 2013 Invitation and Registration Link

[MCLAREN, Donald]

Dear colleagues,

I wanted to draw your attention on the upcoming Brainhack 2013, which is
being held from October 23-26 at the Centre International d'Études
Pédagogiques, Sèvres, France (just outside of Paris).

Brainhack 2013 is a unique workshop with the goals of fostering
interdisciplinary collaboration and open neuroscience. The structure builds
from the concepts of an unconference and hackathon: The term “unconference”
refers to the fact that most of the content will be dynamically created by
the participants — a hackathon is an event where participants collaborate
intensively on projects.

Participants interested in neuroimaging from any discipline are welcome.
Ideal participants span in range from graduate students to professors
across any disciplines willing to contribute (e.g., mathematics, computer
science, engineering, neuroscience, psychology, psychiatry, neurology,
medicine, art, etc…). The primary requirement is a desire to work in close
collaborations with people outside of your specialization in order to
address neuroscience questions that are beyond the expertise of a single
discipline.

One should come to brainhack ready to engage into collaborative projects,
and with some material (slides, ideas, data, tools) ready to start a
project or a discussion panel. Brainhack will build on the successful
techniques used in other unconferences to keep the meeting focused and
productive. It is possible to start a project and build a team as early as
today. Please have a look at the website for information on the conference
and a sample of projects (from Brainhack 2012): http://www.brainhack.org

The Preliminary Schedule for Brainhack 2013 is available online:
http://www.brainhack.org/?page_id=27753

***NEW*** We will be accepting and publishing Brainhack 2013 abstracts.
Abstracts should be submitted when you register.

Registration is now open: http://www.brainhack.org/?page_id=27743

Please share this with your friends and colleagues.
Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
=
This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
intended only for the use of the individual or entity named above. If the
reader of the e-mail is not the intended recipient or the employee or agent
responsible for delivering it to the intended recipient, you are hereby
notified that you are in possession of confidential and privileged
information. Any unauthorized use, disclosure, copying or the taking of any
action in reliance on the contents of this information is strictly
prohibited and may be unlawful. If you have received this e-mail
unintentionally, please immediately notify the sender via telephone at (773)
406-2464 or email.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Differences on baseline volumes within subject cross-sectional vs longitudinal processing

[MCLAREN, Donald]

This raises an interesting question.

Given that the longitudinal process is more reliable, if we collect 2 scans
on the same day, should we average those scans and then submit to
Freesurfer or apply Freesurfer first and then create an average of the
metrics from the longitudinal pipeline?

Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
=
This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
intended only for the use of the individual or entity named above. If the
reader of the e-mail is not the intended recipient or the employee or agent
responsible for delivering it to the intended recipient, you are hereby
notified that you are in possession of confidential and privileged
information. Any unauthorized use, disclosure, copying or the taking of any
action in reliance on the contents of this information is strictly
prohibited and may be unlawful. If you have received this e-mail
unintentionally, please immediately notify the sender via telephone at (773)
406-2464 or email.


On Tue, Jun 25, 2013 at 2:00 PM, Martin Reuter
mreu...@nmr.mgh.harvard.eduwrote:

  Hi Cedric,

 this is as expected, the data changes when using the longitudinal stream
 (it will become more reliable, removing some of the variance you get in the
 independent processing). Becuase of the different processing approaches,
 the results from independent processing (cross) and long will not be
 directly comparable.

 Cheers, Martin



 On 06/25/2013 04:02 AM, Koolschijn, Cédric wrote:

 Hi FreeSurfers,

  I ran the longitudinal processing pipeline on my subjects, FS 5.0.
 Following the tutorial, first independently, then base, then long
 etc. Everything works well,  no problems there.

  Out of curiosity I compared the asegstats  aparcstats within subject at
 baseline (i.e. The same timepoint): so the independent fsid vs the
 same_fsid.long.same_fsid_template, and there are (large) differences
 between all volumes/thicknesses. The independent measures are in almost all
 brain areas larger compared to those derived from the longi-stream. Except
 for the IC, which is completely the same, but of course, this measure is
 based on the Buckner method and calculated differently.

  Overall this seems a bit strange to me, because I believe there
 shouldn't be differences within subject on the same time-point.
 Is this the result of the within-subject template use for the longitudinal
 data or is something else going wrong, or is this normal?

  Many thanks!

  Cheers,
 Cédric

  
 P.C.M.P. Koolschijn (Cédric), PhD
 Dutch Autism  ADHD Research Center
 Brain and Cognition
 Amsterdam, The Netherlands
 *E *p.c.m.p.koolsch...@uva.nl
 *W *http://www.dutcharc.nl



 ___
 Freesurfer mailing 
 listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


 --
 Martin Reuter, Ph.D.
 Assistant in Neuroscience - Massachusetts General Hospital
 Instructor in Neurology   - Harvard Medical School
 MGH / HMS / MIT

 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


 ___
 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


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] Mean Regional Thickness

[MCLAREN, Donald]

Has anyone published the mean cortical thickness of healthy older adults
for all the Freesurfer ROI? I've only been able to find papers that report
a of subset of the ROIs.

Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
=
This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
intended only for the use of the individual or entity named above. If the
reader of the e-mail is not the intended recipient or the employee or agent
responsible for delivering it to the intended recipient, you are hereby
notified that you are in possession of confidential and privileged
information. Any unauthorized use, disclosure, copying or the taking of any
action in reliance on the contents of this information is strictly
prohibited and may be unlawful. If you have received this e-mail
unintentionally, please immediately notify the sender via telephone at (773)
406-2464 or email.
___
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] Cross-sectional v5.1 vs. Longitudinal v4.4

[MCLAREN, Donald]

Dear All,

If I had to choose between longitudinal processing v4.4 or cross-sectional
processing v5.1 for analyzing longitudinal data, what processing stream
should I choose?

Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
=
This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
intended only for the use of the individual or entity named above. If the
reader of the e-mail is not the intended recipient or the employee or agent
responsible for delivering it to the intended recipient, you are hereby
notified that you are in possession of confidential and privileged
information. Any unauthorized use, disclosure, copying or the taking of any
action in reliance on the contents of this information is strictly
prohibited and may be unlawful. If you have received this e-mail
unintentionally, please immediately notify the sender via telephone at (773)
406-2464 or email.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] p-value visualization

[MCLAREN, Donald]

Here is an example regionaldata file. (File with script and dependency is
being held for moderator approval)

Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
=
This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
intended only for the use of the individual or entity named above. If the
reader of the e-mail is not the intended recipient or the employee or agent
responsible for delivering it to the intended recipient, you are hereby
notified that you are in possession of confidential and privileged
information. Any unauthorized use, disclosure, copying or the taking of any
action in reliance on the contents of this information is strictly
prohibited and may be unlawful. If you have received this e-mail
unintentionally, please immediately notify the sender via telephone at (773)
406-2464 or email.


On Fri, May 24, 2013 at 10:54 AM, Ludovici, Katharine (NIH/NIMH) [F] 
katharine.ludov...@nih.gov wrote:

 Hello,

 We are attempting to compare surface area for 46 regions of interest in
 subjects versus controls. We've created a list of p-values for each ROI
 using R Studio to compare the two groups. Is there any way to visualize
 these p-values mapped on to the ROI's?

 Thanks very much,

 Katie Ludovici
 Postbaccalaureate IRTA
 National Institute of Mental Health
 Child Psychiatry Branch
 301-435-5557

 ___
 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.




pp_leftright_20120210.mat
Description: Binary data
___
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] T2/FLAIR images longitudinal stream

[MCLAREN, Donald]

Martin and others,

As the T2/FLAIR image is only available for cross-sectional
processing; if we are doing a longitudinal study, is there any
advantage of using the T2/FLAIR image? Will the improved pial surface
can transferred to the base and long surfaces?

Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
=
This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
intended only for the use of the individual or entity named above. If the
reader of the e-mail is not the intended recipient or the employee or agent
responsible for delivering it to the intended recipient, you are hereby
notified that you are in possession of confidential and privileged
information. Any unauthorized use, disclosure, copying or the taking of any
action in reliance on the contents of this information is strictly
prohibited and may be unlawful. If you have received this e-mail
unintentionally, please immediately notify the sender via telephone at (773)
406-2464 or email.
___
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] Fwd: [FSL] Neuro Bureau Announces the BRAIN-ART COMPETITION 2013

[MCLAREN, Donald]

In order to recognize the beauty and creativity of artistic renderings
emerging from the neuroimaging community, we are launching the third annual
Brain-Art Competition.

Countless hours are devoted to the creation of informative visualizations
for communicating neuroscientific findings. The Brain-Art Competition aims
to recognize this often unappreciated aspect of the publication process,
and highlight the artistic creativity of our community.

We are inviting researchers to submit their favorite unpublished works for
entry. Both team and single-person entries are welcomed. The competition
will have five award categories:

– Best Representation of the Human Connectome
– Best Abstract Brain Illustration
– Best Humorous Brain Illustration
– Best Video Illustration of the Brain
– Special Topic: Best Visualization of Probabilistic Connectivity

The 'Special Topic' is a new addition to this year’s competition that
highlights an important challenge in current connectomics research:
visualizing the uncertainty of 3D connections in tractography and
functional connectivity data.

Submission Deadline: 11:59PM CDT, Wednesday, June 5th, 2013

Award Notification: June 17th during the Neuro Bureau gala event, held at
the OHBM Annual Meeting in Seattle.

For more information, check out the competition details and submission form
at: www.neurobureau.org
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Permutation doubts

[MCLAREN, Donald]

An alternative approach would be to use bootstrapping to determine the
significance as was done by Gross et al. 2012. *Cortical signatures of
cognition and their relationship to Alzheimer's disease.*

Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
=
This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
intended only for the use of the individual or entity named above. If the
reader of the e-mail is not the intended recipient or the employee or agent
responsible for delivering it to the intended recipient, you are hereby
notified that you are in possession of confidential and privileged
information. Any unauthorized use, disclosure, copying or the taking of any
action in reliance on the contents of this information is strictly
prohibited and may be unlawful. If you have received this e-mail
unintentionally, please immediately notify the sender via telephone at (773)
406-2464 or email.


On Thu, Apr 4, 2013 at 12:16 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:

 Correct, you cannot do a permutation test with continuous variables (or
 with any non-orthogonal design matrix). If you use the --perm-force, it
 will do the permutation test as normal (by randomly swapping the rows),
 but technically the test is not legal. Having said that, I suspect that
 LOTS of people do exactly that.
 doug



 On 04/04/2013 10:03 AM, Gabriel Gonzalez Escamilla wrote:
 
  Dear Freesurfer experts,
 
 
  I'm having troubles when setting a permutation test, I'm making group
  comparisons, but I'm introducing the Age, and cortical thickness as
  niusance variables (as previously recommended).
 
  It seems that permutations only work for orthogonal matrices, does
  this means that I cannot set any niusance variable?
 
 
  If so, this is telling me that I can run the command with the flag
  --perm-force, and I'm wondering, which would be the implications of
  force to run the permutations with niusance variables?
 
 
  Many thanks in advance,
  Gabriel
 
 
  ___
  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: 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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] How to get surface-based AAL template {Disarmed}

[MCLAREN, Donald]

I believe that someone has created the AAL labels on the Colin 27 brain.
These should be able to be transformed to the fsaverage brain.

I've contacted the person who said they had the files and will let you know
if I get the files and am able to transform the files.

Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
=
This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
intended only for the use of the individual or entity named above. If the
reader of the e-mail is not the intended recipient or the employee or agent
responsible for delivering it to the intended recipient, you are hereby
notified that you are in possession of confidential and privileged
information. Any unauthorized use, disclosure, copying or the taking of any
action in reliance on the contents of this information is strictly
prohibited and may be unlawful. If you have received this e-mail
unintentionally, please immediately notify the sender via telephone at (773)
406-2464 or email.


On Mon, Apr 1, 2013 at 6:52 AM, Jürgen Hänggi
j.haen...@psychologie.uzh.chwrote:

  Hi Zhiliang

 You can use

 mris_make_face_parcellation

 Or

 mris_divide_parcellation

 directly in FreeSurfer to produce your own parcellation scheme

 Cheers
 Jürgen


 On [DATE], ZhiLiangLong [ADDRESS] wrote:

 Hi Thomas:
  There are no special reasons why i need the surface-based aal
 template. my goal is to parcellate surface into thousands of small brain
 areas, and construct large-scale cortical network. I have no idea how to
 segment the surface  directly in FS. But i know the way to segment AAL
 template to the specific parcellation level (e.g. AAL-1024 ) i want. that
 is why i do this.

   Best.
 zhiliang




 At 2013-04-01 12:55:03,Thomas Yeo ytho...@csail.mit.edu wrote:
 Hi Zhi Liang,
 
 Out of curiosity, why not just use the FreeSurfer parcellations, so
 you don't end up with holes in the sulci/gyri?
 
 --Thomas
 
 On Sun, Mar 31, 2013 at 8:28 PM, Martijn Steenwijk
 martijnsteenw...@gmail.com wrote:
  I faced this problem a while ago. Both MNI to fsaverage, MNI itself and
  Colin27 didn’t work sufficiently for sampling the labels, all had
 problems
  with the registration causing holes in the sulci and gyri ending up in
 the
  wrong label. (That might be ‘good’ since AAL is a volumetric atlas; but
  might also be bad, since you often don’t want to look at an in complete
  label). I ended up making my own gcs fom a training set with
 mris_ca_train.
  Now I can segment surfaces just by calling mris_ca_label which works
  flawlessly and consistent throughout subjects.
 
 
 
  Best,
 
  Martijn
 
 
 
  Van: freesurfer-boun...@nmr.mgh.harvard.edu
  [mailto:freesurfer-boun...@nmr.mgh.harvard.edufreesurfer-boun...@nmr.mgh.harvard.edu]
 Namens ZhiLiangLong

  Verzonden: zaterdag 30 maart 2013 16:25
  Aan: Garikoitz Lerma-Usabiaga
  CC: Freesurfer
  Onderwerp: Re: [Freesurfer] How to get surface-based AAL template
 
 
 
  Dear Gari:
 
  Thank you for give me suggestions patiently. i figured it out as you
  suggested. it works well. I have one more question: Do you know there
 are
  published papers which use the surface-based aal template (or something
 like
  this) to do research (e.g. cortical network analysis based on this
  template)?
 
 
 
  Best wishes.
 
  zhiliang
 
  At 2013-03-29 15:34:02,Garikoitz Lerma-Usabiaga gariko...@gmail.com
  wrote:
 
  Hi Zhiliang,
 
  1- well, I just recon-all-ed their subject again with the newest
 version.
  Recon-all -s Colin -all
 
  2- maybe Doug or some other will answer this question better. I don't
 know
  the exact differences between fs mni305 and fs mnicolin27. What I know
 is
  that going the fsaverage path I couldn't obtain reliable
 transformations of
  the AAL labels. I think this was because fsaverage is very smoothed.
  Spm_register and vol2surf weren't working well.
 
 
 
  The thing is, for group analysis, you can use Colin (or any other), as I
  understood it. When you use -qcache your data goes to fsaverage, but
 you can
  do it manually and specify that you want Colin instead (maybe someone
 can
  confirm it). If you are going to use just the AAL average CTs, then you
 just
  need to use surf2surf or label2label and you won't need fsaverage at
 all.
 
 
 
  3- well, the spm single subject and Colin from Surfrend are the same
 subject
  but not exactly the same image. You do bbregister to them and obtain
 your
  register.dat matrix (you name it), and it goes from 2mm to 1mm and has
 some
  minimal translation. If you see both T1-s with tkregister you will see
 that
  they are almost the same (the spm version a little bit blurred, because
 of
  the resolution). You 

Re: [Freesurfer] slice timing

[MCLAREN, Donald]

If you are using ASL, you do not want to use Slice timing. You must compute
the CBF maps and keep the slice timing intact.

Removing the time delay between slices will lead to the wrong CBF values as
the CBF equations have the time delay in the equation.

Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
=
This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
intended only for the use of the individual or entity named above. If the
reader of the e-mail is not the intended recipient or the employee or agent
responsible for delivering it to the intended recipient, you are hereby
notified that you are in possession of confidential and privileged
information. Any unauthorized use, disclosure, copying or the taking of any
action in reliance on the contents of this information is strictly
prohibited and may be unlawful. If you have received this e-mail
unintentionally, please immediately notify the sender via telephone at (773)
406-2464 or email.


On Fri, Mar 29, 2013 at 1:08 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:

 what are you using to do STC? I think by default FSL will move it to the
 middle slice, but there is probably a way to make take into account the
 fact that the slices are not uniform over the TR. You should contact the
 list of the software you are using to get a definative answer.
 doug


 On 03/29/2013 11:37 AM, Meryem Ayse Yucel wrote:
  Hi,
 
  I am running a pASL sequence with a TR = 3 sec and TI2 = 1.8. I am
  wondering when I do slice time correction does that move all slices to
 the
  mid of TR that is 1.5 s prior in time or, it moves them to the timing of
  the mid slice, which would be the mid of image acquisition aorund 0.6 sec
  prior in time with respect to the end of TR.
 
  Thank you,
 
  Meryem
  ___
  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: 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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Correlation with cortical thickness

[MCLAREN, Donald]

It was brought to my attention that the previous link was broken. Here is a
corrected link:
http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2656.2002.00618.x/abstract

The paper reference is:
On the misuse of residuals in ecology: regression of residuals vs. multiple
regression

   1. Robert P. Freckleton*

Article first published online: 8 MAY 2002

DOI: 10.1046/j.1365-2656.2002.00618.x

Issue
[image: Journal of Animal Ecology]
Journal of Animal Ecology

Volume 71, Issue 3,
http://onlinelibrary.wiley.com/doi/10./jae.2002.71.issue-3/issuetocpages
542–545, May 2002











Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
=
This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
intended only for the use of the individual or entity named above. If the
reader of the e-mail is not the intended recipient or the employee or agent
responsible for delivering it to the intended recipient, you are hereby
notified that you are in possession of confidential and privileged
information. Any unauthorized use, disclosure, copying or the taking of any
action in reliance on the contents of this information is strictly
prohibited and may be unlawful. If you have received this e-mail
unintentionally, please immediately notify the sender via telephone at (773)
406-2464 or email.


On Wed, Mar 27, 2013 at 3:46 PM, MCLAREN, Donald
mclaren.don...@gmail.comwrote:

 Here is a link describing the difference in the methods:

 http://onlinelibrary.wiley.com/store/10.1046/j.1365-2656.2002.00618.x/asset/j.1365-2656.2002.00618.x.pdf?v=1t=heswinwbs=dce1a222e16e861d105340fd919c65fb43dc39ac

 Best Regards, Donald McLaren
 =
 D.G. McLaren, Ph.D.
 Research Fellow, Department of Neurology, Massachusetts General Hospital
 and
 Harvard Medical School
 Postdoctoral Research Fellow, GRECC, Bedford VA
 Website: http://www.martinos.org/~mclaren
 Office: (773) 406-2464
 =
 This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
 HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
 intended only for the use of the individual or entity named above. If the
 reader of the e-mail is not the intended recipient or the employee or agent
 responsible for delivering it to the intended recipient, you are hereby
 notified that you are in possession of confidential and privileged
 information. Any unauthorized use, disclosure, copying or the taking of any
 action in reliance on the contents of this information is strictly
 prohibited and may be unlawful. If you have received this e-mail
 unintentionally, please immediately notify the sender via telephone at
 (773)
 406-2464 or email.


 On Wed, Mar 27, 2013 at 3:39 PM, Douglas N Greve 
 gr...@nmr.mgh.harvard.edu wrote:


 In the 2nd option, age and weight (and other variables) are
 simultaneously fit to the data. Most people refer to this as regressing
 out the effect of one variable when looking at the other. But it is not
 regressing out age and then looking at the correlation of age with the
 residual.
 doug


 On 03/27/2013 07:02 AM, Martijn Steenwijk wrote:
  Dear all,
 
  I've a question regarding computing correlations with cortical
  thicknesses on the surface; Suppose I have two variables for each
  subject: (age and weight) and I want to compute the correlation
  between cortical thickness and weight, corrected for age.
 
  Option 1:
  Fsgd contains: Variables weight
  Contrast file contains: 0 1
 
  Option 2:
  Fsgd contains: Variables age weight
  Contrast file contains: 0 0 1
 
  Is it true that the effect of age is regressed out in the second
  option; and it computes the correlation between CT and weight after
  correcting for age?
 
  Best,
  Martijn
 
 
 
  ___
  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: 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

Re: [Freesurfer] Linear Mixed modal

[MCLAREN, Donald]

Contrast creation is the same in all programs. It is based on the design
matrix.

Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
=
This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
intended only for the use of the individual or entity named above. If the
reader of the e-mail is not the intended recipient or the employee or agent
responsible for delivering it to the intended recipient, you are hereby
notified that you are in possession of confidential and privileged
information. Any unauthorized use, disclosure, copying or the taking of any
action in reliance on the contents of this information is strictly
prohibited and may be unlawful. If you have received this e-mail
unintentionally, please immediately notify the sender via telephone at (773)
406-2464 or email.


On Mon, Mar 25, 2013 at 11:50 PM, xiangbo_2010 xiangbo_2...@126.com wrote:

 Dear experts

 Whether can the design of contrast in freesurfer 5.2 the same as SPM? it
 is difficult to make the contrast in freesurfer if the categorical
 variables were much more, specifically compute the interaction or F-test in
 study. Thanks！



 Bo Xiang




 ___
 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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] contrast matrix

[MCLAREN, Donald]

On Wed, Mar 27, 2013 at 2:53 AM, xiangbo_2010 xiangbo_2...@126.com wrote:

 Dear Prof Donald McLaren

 I am sorry to disturb you! I have four discrete variables {factor 1(A,B),
 factor 2(C,D), factor 3(G,H), and gender(M,F)} and a continuous variable
 (age), I want to use the GLM to analysis the result of the interaction
 among  factor 1(A,B), factor 2(C,D) and factor 3(E,F)
 regressing out the effect of gender and age, and I have 16 classes:
 MACG,MACH, MADG, MADH, MBCG, MBCH, MBDG, MBDH, FACG,FACH, FADG, FADH,
 FBCG, FBCH, FBDG, FBDH, so I design the contrast is following:
 1 -1 -1 1 -1 1 1 -1 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 1 -1 -1 1 -1 1 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0


IF - and this is a big if -- the columns are as you have described in this
order, then the contrast should be:
1 -1 -1 1 -1 1 1 -1 1 -1 -1 1 -1 1 1 -1

To create any contrast, you need to start with the null hypothesis and then
you can build up the contrast from its smaller elements:
This is for a design with 18 subjects in group 1, 9 subjects in group
2, 2 group terms and 7 conditions: Start with the simpliest element,
single subject in a single condition, build its contrast, repeat for
all subjects and conditions, and then combine the ones you want.

S1G1C1=[1 zeros(1,26) 1 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0]
S1G1C2=[1 zeros(1,26) 1 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0]

Now average your G1C1 and by summing and dividing by the number of
subjects, you'd get
G1C1=[ones(1,18)/18 zeros(1,9) 1 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0
0]
and
G1C2=[ones(1,18)/18 zeros(1,9) 1 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0
0]
and
G2C1=[zeros(1,18) ones(1,9)/9 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0]
and
G2C2=[zeros(1,18) ones(1,9)/9 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0]

Now subtract G1C1-G1C2 AND G2C2-G2C1
G1C1-G1C2=[zeros(1,27) 0 0 1 -1 0 0 0 0 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0]
and
G2C1-G2C2=[zeros(1,27) 0 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 1 -1 0 0 0 0 0]

Now subtract these two:
Interaction contrast=[zeros(1,27) 0 0 0 0 0 0 0 0 0 1 -1 0 0 0 0 0 -1
1 0 0 0 0 0]

In your case, if you start with G-H for Males in group A/C:
1 -1 0 0 0 0...

Then Males in group A/D:
0 0 1 -1 0 0

Subtracting these gives you the interaction of factor 2 and 3 for A males.

1 -1 -1 1 0 0 0 0 0...

You can repeat for A females.

0 0 0 0 0 0 0 0 1 -1 -1 1 0 0 0 0

Now you can do the same for B males and B females:
0 0 0 0 1 -1 -1 1 0 0 0 0 0 0 0 0 and 0 0 0 0 0 0 0 0 0 0 0 0 1 -1 -1 1

Now subtract A from B after adding males and females:
1 -1 -1 1 -1 1 1 -1 1 -1 -1 1 -1 1 1 -1

This will work for any contrast that you ever want to make.





 is correct? thank you very much!

 look forward for your reply!


 Bo Xiang






 At 2012-11-21 04:07:37,MCLAREN, Donald mclaren.don...@gmail.com
  wrote:
 On Tue, Nov 20, 2012 at 12:56 PM, Douglas N Greve
 gr...@nmr.mgh.harvard.edu wrote:
  Thanks Donald. Is this the standard way to do this? I had used 8 rows
  instead of 4 with the difference being that 8 rows gives you an opportunity
  to look for an effect in males OR females.
 
 Yes. Having 8 rows would tell you if you have an interaction between
 factor 1 and 2 in either males or females. My 4 rows only tell you if
 the interaction exists. Technically speaking, one would run the
 three-way interaction first. If nothing existed then you do the
 two-way interaction as I suggested. If there is a three-way
 interaction, then you would use Doug's approach of the interaction in
 either males or females.
 
 If there is an effect in both
  males and females but the effects go in opposite directions, then the 4 row
  implementation will resolve to 0 (no effect). Or am I misunderstanding
  something (again:)?
 
 Nope. You are right. If the male and female effects are different,
 then they could cancel each other out. If you suspect this to be the
 case, then you should be able to demonstrate a three-way interaction.
 
  thanks!
  doug
 
 
  On 11/20/2012 01:50 PM, MCLAREN, Donald wrote:
 
  Bo,
 
  Doug asked me to chime in on your issue. Here are some points that you
  (and others) will hopefully find useful.
 
  (1) Inferences are two-step process. First, you create and estimate
  the design matrix. Every column in the design matrix accounts can
  account for some of the variance in the data. Second, you have
  contrasts that allow you to infer specific effects. Because the model
  contains your covariates, you are always controlling for the
  covariates and by extension any factor/covariate not in the contrast.
 
  (2) Forming contrasts is often the most difficult thing to do. I
  assume that your three factors (1, 2, and gender) are all
  between-subject factors. If one of them is a within-subject factor
  please let me know and disregard the rest of the email. The final
  F-contrast will have 4 rows (factor 1 levels-1)*(factor 2 levels
  -1)=(3-1)*(3-1)=2*2=4
 
  The following is an outline for creating

Re: [Freesurfer] Correlation with cortical thickness

[MCLAREN, Donald]

Here is a link describing the difference in the methods:
http://onlinelibrary.wiley.com/store/10.1046/j.1365-2656.2002.00618.x/asset/j.1365-2656.2002.00618.x.pdf?v=1t=heswinwbs=dce1a222e16e861d105340fd919c65fb43dc39ac

Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
=
This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
intended only for the use of the individual or entity named above. If the
reader of the e-mail is not the intended recipient or the employee or agent
responsible for delivering it to the intended recipient, you are hereby
notified that you are in possession of confidential and privileged
information. Any unauthorized use, disclosure, copying or the taking of any
action in reliance on the contents of this information is strictly
prohibited and may be unlawful. If you have received this e-mail
unintentionally, please immediately notify the sender via telephone at (773)
406-2464 or email.


On Wed, Mar 27, 2013 at 3:39 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:


 In the 2nd option, age and weight (and other variables) are
 simultaneously fit to the data. Most people refer to this as regressing
 out the effect of one variable when looking at the other. But it is not
 regressing out age and then looking at the correlation of age with the
 residual.
 doug


 On 03/27/2013 07:02 AM, Martijn Steenwijk wrote:
  Dear all,
 
  I've a question regarding computing correlations with cortical
  thicknesses on the surface; Suppose I have two variables for each
  subject: (age and weight) and I want to compute the correlation
  between cortical thickness and weight, corrected for age.
 
  Option 1:
  Fsgd contains: Variables weight
  Contrast file contains: 0 1
 
  Option 2:
  Fsgd contains: Variables age weight
  Contrast file contains: 0 0 1
 
  Is it true that the effect of age is regressed out in the second
  option; and it computes the correlation between CT and weight after
  correcting for age?
 
  Best,
  Martijn
 
 
 
  ___
  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: 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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] help with contrasts

[MCLAREN, Donald]

On Thu, Mar 21, 2013 at 8:59 PM, Laura M. Tully
tully.la...@googlemail.comwrote:

 oops sorry! (I also miscalculated the # of regressors - there's actually
  12 (not 10 as previously noted). Here is the list of column labels:
 Grp1male  Grp1female Grp2male Grp2female Grp1maleVar1 Grp1femaleVar1
 Grp1maleVar2 Grp1femaleVar2 Grp2maleVar1 Grp2femaleVar1 Grp2maleVar2
 Grp2femaleVar2

 And what I think is actually an F test looking for group x var 1
 interaction OR group x variable 2 interaction whilst accounting for gender.
 .5 .5 -.5 -.5 0 0 0 0 0 0
 0 0 0 0 0 0 .5 .5 -.5 -.5


The Contrast for group*var1 would be: 0 0 0 0 .5 .5 0 0 -.5 -.5 0 0
The Contrast for group*var2 would be: 0 0 0 0 0 0 .5 .5 0 0 -.5 -.5




 But what I actually WANT to test is a  multiple regression style model -
 i.e. if I put var 1 AND 2 into the model together do they explain more
 variance than either variable alone, AND does this vary by group (is this
 even a sensible contrast to make?). Which I *think* would look something
 like this...

 0 0 0 0 .125 .125 .125 .125 .125 .125 .125 .125


People generally don't ask that question.  The answer is when you add more
variables, you will explain more variance. Tests about overall model fits
are generally assessed with the AIC, BIC, etc. metrics. I'm not sure if
there is anyway in regression to say that the amount of variance explained
is different by group unless you run 2 separate models. If you think this
might be a valid question, I'd consult a statistician - which I am not.



 Laura.



 On Thu, Mar 21, 2013 at 5:51 PM, MCLAREN, Donald mclaren.don...@gmail.com
  wrote:

 Please include the list of the column labels.

 Best Regards, Donald McLaren
 =
 D.G. McLaren, Ph.D.
 Research Fellow, Department of Neurology, Massachusetts General Hospital
 and
 Harvard Medical School
 Postdoctoral Research Fellow, GRECC, Bedford VA
 Website: http://www.martinos.org/~mclaren
 Office: (773) 406-2464
 =
 This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
 HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
 intended only for the use of the individual or entity named above. If the
 reader of the e-mail is not the intended recipient or the employee or
 agent
 responsible for delivering it to the intended recipient, you are hereby
 notified that you are in possession of confidential and privileged
 information. Any unauthorized use, disclosure, copying or the taking of
 any
 action in reliance on the contents of this information is strictly
 prohibited and may be unlawful. If you have received this e-mail
 unintentionally, please immediately notify the sender via telephone at
 (773)
 406-2464 or email.


 On Thu, Mar 21, 2013 at 6:43 PM, Laura M. Tully 
 tully.la...@googlemail.com wrote:

 hi Experts,

 I'm struggling to conceptualize the appropriate contrasts for my
 cortical thickness analysis. I have four classes [two groups; two levels
 (patients,controls; male,female) and two behavioral variables. I want to
 see if together the two variables account significant proportion of the
 variance in y (thickness) and if this differs by group whilst regressing
 out gender. - i.e. if I enter both behavioral variables into the model does
 it account for more variance than either variable on their own (after
 controlling for gender)? What I have is this:

 .5 .5 -.5 -.5 0 0 0 0
 0 0 0 0 .5 .5 -.5 -.5

 Does this look right?

 Thanks!

 Laura.




 --
 --
 Laura M. Tully, MA
 Social Neuroscience  Psychopathology, Harvard University
 Center for the Assessment and Prevention of Prodromal States, UCLA Semel
 Institute of Neuroscience
 ltu...@mednet.ucla.edu
 ltu...@fas.harvard.edu
 310-267-0170
 --
 My musings as a young clinical scientist:
 http://theclinicalbrain.blogspot.com/
 Follow me on Twitter: @tully_laura

 ___
 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.





 --
 --
 Laura M. Tully, MA
 Social Neuroscience  Psychopathology, Harvard University
 Center for the Assessment and Prevention of Prodromal States, UCLA Semel
 Institute of Neuroscience
 ltu...@mednet.ucla.edu
 ltu...@fas.harvard.edu
 310-267-0170
 --
 My musings as a young clinical scientist:
 http://theclinicalbrain.blogspot.com/
 Follow me on Twitter: @tully_laura

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

Re: [Freesurfer] help with contrasts

[MCLAREN, Donald]

You'd want an F test with 2 rows. One for the F-test of var 1 and one for
the F-test of var2. A significant F-test won't tell you if your
significantly better though than the F-test of var 1 only in the model.

However, this sounds more like a model fitting question, which would be
best addressed using AIC, BIC, etc. metrics of the overall model fit.

Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
=
This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
intended only for the use of the individual or entity named above. If the
reader of the e-mail is not the intended recipient or the employee or agent
responsible for delivering it to the intended recipient, you are hereby
notified that you are in possession of confidential and privileged
information. Any unauthorized use, disclosure, copying or the taking of any
action in reliance on the contents of this information is strictly
prohibited and may be unlawful. If you have received this e-mail
unintentionally, please immediately notify the sender via telephone at (773)
406-2464 or email.


On Fri, Mar 22, 2013 at 11:38 AM, Laura M. Tully tully.la...@googlemail.com
 wrote:

 Thanks Donald for your help. One final question - putting the does the
 amount of variance explained vary by group? question aside, if I wanted to
 run a multiple regression style model within one group looking at the
 contribution of the two behavioral variables together, does it make sense
 to weight the two variables as part of the same chunk of variance e.g. 0 0
 0 0 .125 .125 .125 .125 .125 .125 .125 .125 (which I think will run a
 model looking at the contribution of variables 1  2 together regardless of
 group or gender).  If so, I'm assuming I could adjust the model and run
 separate GLMs within each group, as you suggested - I just want to make
 sure I am understanding the weights correctly first...

 LT


 On Fri, Mar 22, 2013 at 8:23 AM, MCLAREN, Donald mclaren.don...@gmail.com
  wrote:


 On Thu, Mar 21, 2013 at 8:59 PM, Laura M. Tully 
 tully.la...@googlemail.com wrote:

 oops sorry! (I also miscalculated the # of regressors - there's actually
  12 (not 10 as previously noted). Here is the list of column labels:
 Grp1male  Grp1female Grp2male Grp2female Grp1maleVar1 Grp1femaleVar1
 Grp1maleVar2 Grp1femaleVar2 Grp2maleVar1 Grp2femaleVar1 Grp2maleVar2
 Grp2femaleVar2

 And what I think is actually an F test looking for group x var 1
 interaction OR group x variable 2 interaction whilst accounting for gender.
 .5 .5 -.5 -.5 0 0 0 0 0 0
 0 0 0 0 0 0 .5 .5 -.5 -.5


 The Contrast for group*var1 would be: 0 0 0 0 .5 .5 0 0 -.5 -.5 0 0
 The Contrast for group*var2 would be: 0 0 0 0 0 0 .5 .5 0 0 -.5 -.5




 But what I actually WANT to test is a  multiple regression style model -
 i.e. if I put var 1 AND 2 into the model together do they explain more
 variance than either variable alone, AND does this vary by group (is this
 even a sensible contrast to make?). Which I *think* would look something
 like this...

 0 0 0 0 .125 .125 .125 .125 .125 .125 .125 .125


  People generally don't ask that question.  The answer is when you add
 more variables, you will explain more variance. Tests about overall model
 fits are generally assessed with the AIC, BIC, etc. metrics. I'm not sure
 if there is anyway in regression to say that the amount of variance
 explained is different by group unless you run 2 separate models. If you
 think this might be a valid question, I'd consult a statistician - which I
 am not.



 Laura.



 On Thu, Mar 21, 2013 at 5:51 PM, MCLAREN, Donald 
 mclaren.don...@gmail.com wrote:

 Please include the list of the column labels.

 Best Regards, Donald McLaren
 =
 D.G. McLaren, Ph.D.
 Research Fellow, Department of Neurology, Massachusetts General
 Hospital and
 Harvard Medical School
 Postdoctoral Research Fellow, GRECC, Bedford VA
 Website: http://www.martinos.org/~mclaren
 Office: (773) 406-2464
 =
 This e-mail contains CONFIDENTIAL INFORMATION which may contain
 PROTECTED
 HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
 intended only for the use of the individual or entity named above. If
 the
 reader of the e-mail is not the intended recipient or the employee or
 agent
 responsible for delivering it to the intended recipient, you are hereby
 notified that you are in possession of confidential and privileged
 information. Any unauthorized use, disclosure, copying or the taking of
 any
 action in reliance on the contents of this information is strictly
 prohibited and may be unlawful. If you have received this e-mail
 unintentionally, please immediately notify

Re: [Freesurfer] make a volume template from the surface-based template for non-human primates

[MCLAREN, Donald]

For many non-human primate species, volume templates already exist. I would
recommend using them and aligning your surface templates to them to aid in
the ability to compare studies across laboratories in the same space.

For rhesus, see the 112RM-SL atlas.



Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
=
This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
intended only for the use of the individual or entity named above. If the
reader of the e-mail is not the intended recipient or the employee or agent
responsible for delivering it to the intended recipient, you are hereby
notified that you are in possession of confidential and privileged
information. Any unauthorized use, disclosure, copying or the taking of any
action in reliance on the contents of this information is strictly
prohibited and may be unlawful. If you have received this e-mail
unintentionally, please immediately notify the sender via telephone at (773)
406-2464 or email.


On Fri, Mar 15, 2013 at 4:41 PM, Longchuan Li leonad...@yahoo.com wrote:

 Hi, FreeSurfer experts

 I have a question regarding making a volume template based on the surface
 template for non-human primates. I have made a surface template using a
 group of monkeys and now, we want to see the result, which is a mgh surface
 file, on the coronal slices of the template. So I am planning to generate a
 volume template corresponding to the surface template and then project the
 mgh file to the volume for viewing. Could someone tell me what is the best
 way to generate such a volume template?

 Many thanks in advance!

 Longchuan


 ___
 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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] preparing NHP data for whole brain analysis

[MCLAREN, Donald]

I would recommend using the volume space initially until you can get
more surfaces to create your group surface. The one issue with the
112RM_SL is that there is no EPI template.


Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
=
This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
intended only for the use of the individual or entity named above. If the
reader of the e-mail is not the intended recipient or the employee or agent
responsible for delivering it to the intended recipient, you are hereby
notified that you are in possession of confidential and privileged
information. Any unauthorized use, disclosure, copying or the taking of any
action in reliance on the contents of this information is strictly
prohibited and may be unlawful. If you have received this e-mail
unintentionally, please immediately notify the sender via telephone at (773)
406-2464 or email.


On Tue, Feb 12, 2013 at 4:16 PM, Caspar M. Schwiedrzik
cschwie...@mail.rockefeller.edu wrote:
 Hi Doug,
 the issue is that the 112RM atlas is only available as a volume; also, I do
 not have a surface for one of my subjects. I could either make a surface
 from the atlas volume and align to that surface for the group analysis, or
 align the data to the atlas in volume space (if possible) and perform the
 group analysis in volume space.
 What would you recommend?
 Thanks, Caspar



 2013/2/12 Douglas N Greve gr...@nmr.mgh.harvard.edu


 If you can create an average subject and register your individual surfaces
 to that subject, then it can be done. By default, recon-all will register to
 the human atlas to create ?h.sphere.reg
 doug



 On 02/12/2013 03:57 PM, Caspar M. Schwiedrzik wrote:

 Hi Doug,
 thank you very much.
 One more question: From the documentation, I wasn't really sure whether
 it would also be possible to do the analysis of the functional data in a
 common volume space (not MNI, as it is NHP data).
 Thanks again, Caspar


 2013/2/12 Douglas N Greve gr...@nmr.mgh.harvard.edu
 mailto:gr...@nmr.mgh.harvard.edu


 Hi Caspar, with 5.1 you would not use any of those programs (ie,
 func2sph, isxavg-re-sess, or isxavg-fe-sess). If you want to use
 FSFAST,
 then see the tutorial for getting started. You'll need to set up the
 directory structure properly, then run preproc-sess, mkanalysis-sess,
 and selxavg3-sess. For the group analysis you'll run isxconcat-sess
 followed by mri_glmfit and mri_glmfit-sim. If you don't have
 anatomicals
 for all subjects and you just want to use the average subject,
 then put
 the average subject into the subjectname file when you set up the
 directory structure.

 doug


 On 02/12/2013 07:55 AM, Caspar M. Schwiedrzik wrote:
  Dear Freesurfer experts,
  I am trying to prepare some NHP functional data for a whole brain
  group analysis, and I was wondering which sequence of steps you
 would
  recommend, given that the data cannot be processed with recon-all.
  I have surfaces from 4 subjects, but one subject for which I do not
  have an anatomy of sufficient quality and won't be able to
 obtain one.
  I would also like to align the data to the 112RM atlas by
 Mclaren et al.
  I was thinking that I could probably align the functional data per
  subject to the atlas, and then use this registration with
  func2sph-sess to align all subjects for the group analysis (again
 to
  the atlas). Does that make sense, given that I have only four out
 of
  five individual surfaces?
 
  A second question is when to smooth the data. I assume that it
 makes
  most sense to smooth it after it has been transformed into surface
  space. Would that be sphsmooth-sess?
 
  Finally, when doing the analysis, I would use isxavg-re-sess or
  isxavg-fe-sess, correct?
 
  I am using Freesurfer v5.1.
  Thank you very much for your advice,
  Caspar
 
 
 
 
  ___
  Freesurfer mailing list
  Freesurfer@nmr.mgh.harvard.edu
 mailto:Freesurfer@nmr.mgh.harvard.edu

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

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

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 

Re: [Freesurfer] preparing NHP data for whole brain analysis

[MCLAREN, Donald]

If you can get good alignment between the EPI and the T1 images for
the 4 subjects with good T1 images, you might try the following:
(1) coregister each T1 to the corresponding EPI;
(2) normalize the coregistered T1 to the 112RM-SL atlas (see McLaren
et al. 2010 in Methods for your options)
(3) apply the normalization to EPI data
(4) create a mean image from the 4 monkeys (call this the 112RM-SL_EPI
and make it public after you publish your paper).
(5) use the new EPI atlas to normalize the EPI images. This way all 5
monkeys are aligned to the same template space. If you can create the
EPI template in a separate set of animals not in the current
experiment, it would be better. You might want to contact Justin
Vincent to see if he know any good EPI and T1 datasets in monkeys that
could be used to make an EPI template or surfaces for a 112RM-SL
surface atlas.

Hope this helps.

Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
=
This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
intended only for the use of the individual or entity named above. If the
reader of the e-mail is not the intended recipient or the employee or agent
responsible for delivering it to the intended recipient, you are hereby
notified that you are in possession of confidential and privileged
information. Any unauthorized use, disclosure, copying or the taking of any
action in reliance on the contents of this information is strictly
prohibited and may be unlawful. If you have received this e-mail
unintentionally, please immediately notify the sender via telephone at (773)
406-2464 or email.


On Tue, Feb 12, 2013 at 6:44 PM, Caspar M. Schwiedrzik
cschwie...@mail.rockefeller.edu wrote:
 Thanks for your input, Donald. Unfortunately, I won't be able to acquire the
 missing high quality anatomy.
 Doug, I did not get from the documentation how to use preproc-sess to align
 data to an NHP atlas in volume space (that is not in human MNI space).
 Please advise.
 Thanks!
 Caspar



 2013/2/12 MCLAREN, Donald mclaren.don...@gmail.com

 I would recommend using the volume space initially until you can get
 more surfaces to create your group surface. The one issue with the
 112RM_SL is that there is no EPI template.


 Best Regards, Donald McLaren
 =
 D.G. McLaren, Ph.D.
 Research Fellow, Department of Neurology, Massachusetts General Hospital
 and
 Harvard Medical School
 Postdoctoral Research Fellow, GRECC, Bedford VA
 Website: http://www.martinos.org/~mclaren
 Office: (773) 406-2464
 =
 This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
 HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
 intended only for the use of the individual or entity named above. If the
 reader of the e-mail is not the intended recipient or the employee or
 agent
 responsible for delivering it to the intended recipient, you are hereby
 notified that you are in possession of confidential and privileged
 information. Any unauthorized use, disclosure, copying or the taking of
 any
 action in reliance on the contents of this information is strictly
 prohibited and may be unlawful. If you have received this e-mail
 unintentionally, please immediately notify the sender via telephone at
 (773)
 406-2464 or email.


 On Tue, Feb 12, 2013 at 4:16 PM, Caspar M. Schwiedrzik
 cschwie...@mail.rockefeller.edu wrote:
  Hi Doug,
  the issue is that the 112RM atlas is only available as a volume; also, I
  do
  not have a surface for one of my subjects. I could either make a surface
  from the atlas volume and align to that surface for the group analysis,
  or
  align the data to the atlas in volume space (if possible) and perform
  the
  group analysis in volume space.
  What would you recommend?
  Thanks, Caspar
 
 
 
  2013/2/12 Douglas N Greve gr...@nmr.mgh.harvard.edu
 
 
  If you can create an average subject and register your individual
  surfaces
  to that subject, then it can be done. By default, recon-all will
  register to
  the human atlas to create ?h.sphere.reg
  doug
 
 
 
  On 02/12/2013 03:57 PM, Caspar M. Schwiedrzik wrote:
 
  Hi Doug,
  thank you very much.
  One more question: From the documentation, I wasn't really sure
  whether
  it would also be possible to do the analysis of the functional data in
  a
  common volume space (not MNI, as it is NHP data).
  Thanks again, Caspar
 
 
  2013/2/12 Douglas N Greve gr...@nmr.mgh.harvard.edu
  mailto:gr...@nmr.mgh.harvard.edu
 
 
  Hi Caspar, with 5.1 you would not use any of those programs (ie,
  func2sph, isxavg-re-sess, or isxavg-fe-sess). If you want to use
  FSFAST,
  then see the tutorial

Re: [Freesurfer] L-R Volume Flipping

[MCLAREN, Donald]

When we added the --spm-nii option, the problem disappears. The
following thread is also relevant:
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-April/017981.html


On Tue, Dec 18, 2012 at 8:26 PM, MCLAREN, Donald
mclaren.don...@gmail.com wrote:
 Thanks, that's what I thought might be happening. I'll check a few
 different programs to see if I can recover the correct orientation. If
 we need to reverse the images, would you recommend doing it before or
 after the bbregister step? Would it be sufficient just to change the
 header of the image or do we need to physically change the data?

 Best Regards, Donald McLaren
 =
 D.G. McLaren, Ph.D.
 Research Fellow, Department of Neurology, Massachusetts General Hospital and
 Harvard Medical School
 Postdoctoral Research Fellow, GRECC, Bedford VA
 Website: http://www.martinos.org/~mclaren
 Office: (773) 406-2464
 =
 This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
 HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
 intended only for the use of the individual or entity named above. If the
 reader of the e-mail is not the intended recipient or the employee or agent
 responsible for delivering it to the intended recipient, you are hereby
 notified that you are in possession of confidential and privileged
 information. Any unauthorized use, disclosure, copying or the taking of any
 action in reliance on the contents of this information is strictly
 prohibited and may be unlawful. If you have received this e-mail
 unintentionally, please immediately notify the sender via telephone at (773)
 406-2464 or email.


 On Tue, Dec 18, 2012 at 11:20 PM, Douglas Greve
 gr...@nmr.mgh.harvard.edu wrote:
 Hi Donald, it might be the case. If the fmri has an ordering such that the
 columns increase as you go from left to right, then they will have to be
 reversed when you map them to the orig.mgz. This is generally not a problem
 because we always keep track of which side is left and right. If you are
 using a visualization tool that does not read in and act on the geometry,
 then things can appear to flip around.

 doug



 On 12/18/12 8:47 PM, MCLAREN, Donald wrote:

 Dear All,

 I've noticed something strange with some data I'm helping to process:

 When looking at the L/R asymmetry in the brains (attached), the images
 seem to flip after bbregister/mri_vol2vol. The exact commands:
 bbregister --s FS_D011 --mov meanfMRI.nii --reg register.dat --init-spm --t2
 mri_vol2vol --s FS_D011 --targ orig.mgz --mov fMRI.nii --reg
 register.dat --no-resample --o transformed_fMRI.nii

 I've attached a document that shows the flipping. You'll notice the
 highest point of the ventricle flips sides after
 bbregister/mri_vol2vol. Any thoughts on what is going on would be
 appreciated.

 The contents of register.dat are as follows:
 FS_D011
 3.00
 3.54
 0.15
 -9.972292184829712e-01 -6.125224381685257e-02 4.221317172050476e-02
 1.619825601577759e+00
 6.049362570047379e-02 -3.374822735786438e-01 9.393859505653381e-01
 -1.230294322967529e+01
 4.329330846667290e-02 -9.393369555473328e-01 -3.402525186538696e-01
 -1.072110843658447e+01
 0 0 0 1
 round


 Best Regards, Donald McLaren
 =
 D.G. McLaren, Ph.D.
 Research Fellow, Department of Neurology, Massachusetts General Hospital and
 Harvard Medical School
 Postdoctoral Research Fellow, GRECC, Bedford VA
 Website: http://www.martinos.org/~mclaren
 Office: (773) 406-2464
 =
 This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
 HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
 intended only for the use of the individual or entity named above. If the
 reader of the e-mail is not the intended recipient or the employee or agent
 responsible for delivering it to the intended recipient, you are hereby
 notified that you are in possession of confidential and privileged
 information. Any unauthorized use, disclosure, copying or the taking of any
 action in reliance on the contents of this information is strictly
 prohibited and may be unlawful. If you have received this e-mail
 unintentionally, please immediately notify the sender via telephone at (773)
 406-2464 or email.



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



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


 The information in this e-mail is intended only for the person to whom it is
 addressed. If you believe this e-mail was sent to you in error and the
 e-mail
 contains patient information, please contact the Partners Compliance
 HelpLine at
 http://www.partners.org/complianceline . If the e-mail was sent to you in
 error
 but does not contain patient information, please

Re: [Freesurfer] L-R Volume Flipping

[MCLAREN, Donald]

Thanks, that's what I thought might be happening. I'll check a few
different programs to see if I can recover the correct orientation. If
we need to reverse the images, would you recommend doing it before or
after the bbregister step? Would it be sufficient just to change the
header of the image or do we need to physically change the data?

Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
=
This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
intended only for the use of the individual or entity named above. If the
reader of the e-mail is not the intended recipient or the employee or agent
responsible for delivering it to the intended recipient, you are hereby
notified that you are in possession of confidential and privileged
information. Any unauthorized use, disclosure, copying or the taking of any
action in reliance on the contents of this information is strictly
prohibited and may be unlawful. If you have received this e-mail
unintentionally, please immediately notify the sender via telephone at (773)
406-2464 or email.


On Tue, Dec 18, 2012 at 11:20 PM, Douglas Greve
gr...@nmr.mgh.harvard.edu wrote:
 Hi Donald, it might be the case. If the fmri has an ordering such that the
 columns increase as you go from left to right, then they will have to be
 reversed when you map them to the orig.mgz. This is generally not a problem
 because we always keep track of which side is left and right. If you are
 using a visualization tool that does not read in and act on the geometry,
 then things can appear to flip around.

 doug



 On 12/18/12 8:47 PM, MCLAREN, Donald wrote:

 Dear All,

 I've noticed something strange with some data I'm helping to process:

 When looking at the L/R asymmetry in the brains (attached), the images
 seem to flip after bbregister/mri_vol2vol. The exact commands:
 bbregister --s FS_D011 --mov meanfMRI.nii --reg register.dat --init-spm --t2
 mri_vol2vol --s FS_D011 --targ orig.mgz --mov fMRI.nii --reg
 register.dat --no-resample --o transformed_fMRI.nii

 I've attached a document that shows the flipping. You'll notice the
 highest point of the ventricle flips sides after
 bbregister/mri_vol2vol. Any thoughts on what is going on would be
 appreciated.

 The contents of register.dat are as follows:
 FS_D011
 3.00
 3.54
 0.15
 -9.972292184829712e-01 -6.125224381685257e-02 4.221317172050476e-02
 1.619825601577759e+00
 6.049362570047379e-02 -3.374822735786438e-01 9.393859505653381e-01
 -1.230294322967529e+01
 4.329330846667290e-02 -9.393369555473328e-01 -3.402525186538696e-01
 -1.072110843658447e+01
 0 0 0 1
 round


 Best Regards, Donald McLaren
 =
 D.G. McLaren, Ph.D.
 Research Fellow, Department of Neurology, Massachusetts General Hospital and
 Harvard Medical School
 Postdoctoral Research Fellow, GRECC, Bedford VA
 Website: http://www.martinos.org/~mclaren
 Office: (773) 406-2464
 =
 This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
 HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
 intended only for the use of the individual or entity named above. If the
 reader of the e-mail is not the intended recipient or the employee or agent
 responsible for delivering it to the intended recipient, you are hereby
 notified that you are in possession of confidential and privileged
 information. Any unauthorized use, disclosure, copying or the taking of any
 action in reliance on the contents of this information is strictly
 prohibited and may be unlawful. If you have received this e-mail
 unintentionally, please immediately notify the sender via telephone at (773)
 406-2464 or email.



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



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


 The information in this e-mail is intended only for the person to whom it is
 addressed. If you believe this e-mail was sent to you in error and the
 e-mail
 contains patient information, please contact the Partners Compliance
 HelpLine at
 http://www.partners.org/complianceline . If the e-mail was sent to you in
 error
 but does not contain patient information, please contact the sender and
 properly
 dispose of the e-mail.

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

Re: [Freesurfer] Reference for clusterwise correction for multiple comparisons

[MCLAREN, Donald]

For volumes, I usually cite:
Forman, S.D., Cohen, J.D., Fitzgerald, M., Eddy, W.F., Mintun, M.A.,
Noll, D.C., 1995. Improved assessment of significant activation in
functional magnetic resonance imaging (fMRI): use of a cluster-size
threshold. Magn. Reson. Med. 33, 636–647.

It's also referenced several time in Hagler.

Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
=
This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
intended only for the use of the individual or entity named above. If the
reader of the e-mail is not the intended recipient or the employee or agent
responsible for delivering it to the intended recipient, you are hereby
notified that you are in possession of confidential and privileged
information. Any unauthorized use, disclosure, copying or the taking of any
action in reliance on the contents of this information is strictly
prohibited and may be unlawful. If you have received this e-mail
unintentionally, please immediately notify the sender via telephone at (773)
406-2464 or email.


On Thu, Nov 29, 2012 at 4:52 AM, Ed Gronenschild
ed.gronensch...@np.unimaas.nl wrote:
 Hi,

 Can you give me a reference to the method used for the
 clusterwise correction for multiple comparisons (CSD)?
 Is it Hagler et al, NeuroImage 2006, vol 33, 1093-1103?

 Cheers,
 Ed

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


 The information in this e-mail is intended only for the person to whom it is
 addressed. If you believe this e-mail was sent to you in error and the e-mail
 contains patient information, please contact the Partners Compliance HelpLine 
 at
 http://www.partners.org/complianceline . If the e-mail was sent to you in 
 error
 but does not contain patient information, please contact the sender and 
 properly
 dispose of the e-mail.


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

Re: [Freesurfer] Subgroup analysis

[MCLAREN, Donald]

On Tue, Nov 27, 2012 at 1:28 PM, Mahinda Yogarajah y.mahi...@gmail.com wrote:

 Hi,

 Thanks for the reference and explanation of the subtle statistical 
 inferences. It was very useful.

 You are right in what i am trying to show (c- controls, p1 to p4 patients 
 with varying levels of endogenous factor) which is that when patients are 
 subdivided into levels of endogenous factor there is correlation with the 
 changes seen in dependent variables compared to controls. So far,

 C v whole P gp - differences seen in plausible areas.
 C v P1 (greatest endo factor) subgp  - no differences
 C v P4 subgp (lowest endo factor) - differences seen in plausible areas.

 Given that it is not valid to compare c v p1 and c v p4 (and p1 v p4 shows 
 nothing) is the following valid - perhaps it is similar to what you proposed:

 compare c v p1 and c v p4 (and p1 v p4 shows nothing) These are all 
 valid tests on their own. The issue waas that you were making qualitative 
 interpretations of the results.


 Consider c and p1 to p4 as one group of subjects (theoretically the only 
 difference between subjects being level of endogenous factor) but assign each 
 subject a variable which represents level of endoenous factor (c - 1 p1 - 2 
 p3 - 4 p4 - 5) - then run glm looking for correlation between endogenous 
 factor and dependent variable.

 Is this very different to what you suggested and any less valid ?

 If you have you have entered 5 groups and want to test the linear change 
 over the groups. You can use [2 1 0 -1 2] as the contrast. If you want the 
 linear change over the patients, then you can use [0 1.5 .5 -.5 -1.5]. If 
 you want to detect any difference in the patients, you could try an F-test 
 of [0 1 -1 0 0; 0 0 1 -1 0; 0 0 0 1 -1].


 Thanks.

 M

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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] How to design the contrast matrix with 12 regressors?

[MCLAREN, Donald]

I assume that your 12 columns are: your 6 groups followed by 6 columns
representing your covariate.

You must first test that the slopes are not different with an F-test:
0 0 0 0 0 0 1 -1 0 0 0 0
0 0 0 0 0 0 0 1 -1 0 0 0
0 0 0 0 0 0 0 0 1 -1 0 0
0 0 0 0 0 0 0 0 0 1 -1 0

If you don't find any differences, then you can use the DOSS model. If
you find differences, then you have an interaction between your
covariate and groups. When this happens, you should consult a
statistician if you want to interpret the effects of group as the
general rule of thumb is not to interpret the main effects in the
presence of an interaction. Using the DOSS model will leave you with 7
regressors. The test for group differences will be:
1 -1 0 0 0 0 0
or
0 1 -1 0 0 0 0
etc.
depending on what you are wanting to test. Simply having the covariate
in the model corrects for age.

A couple of points on covariates - for more details see
(http://mumford.fmripower.org/mean_centering/):
(A) If you don't mean center, then you will be looking at the group intercepts;
(B) If you mean center, then you will be looking at the
covariate-adjusted group means;
(C) If you mean center by group, then you will be looking at the group
means and reducing the variance due to age. For example, if you want
to compare old and young subjects, but control for age within each
group.

A and B will give you the same answer in the DOSS since the slopes of
each group are parallel. C will give you a different result. Depending
on how you want to interpret your results will effect which method you
want to use for mean-centering or not-mean centering the data. In all
cases, mean-centering will not effect the slope
estimates/significance.

Hope this clears up the confusion.

Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
=
This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
intended only for the use of the individual or entity named above. If the
reader of the e-mail is not the intended recipient or the employee or agent
responsible for delivering it to the intended recipient, you are hereby
notified that you are in possession of confidential and privileged
information. Any unauthorized use, disclosure, copying or the taking of any
action in reliance on the contents of this information is strictly
prohibited and may be unlawful. If you have received this e-mail
unintentionally, please immediately notify the sender via telephone at (773)
406-2464 or email.


On Fri, Nov 23, 2012 at 2:01 AM, 李仕广 imaging_shiguan...@163.com wrote:
 Dear FreeSurfers:
 I hope you can help me out with a problem in disgning my .mtx file.
 I want to examine the difference among three groups (HC group, EX group and
 PT group). Considing gender, I have six groups as similar as the example
 described in http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf6G0V. But I want
 to correct for age.
 Then, I have 6 classes (two factors/three l! evels) a nd one covariate
 (age).
 How can I compare the difference among three groups (HC group, EX group, and
 PT group)?
 Could you please tall me how to design the contrast matrix with 12
 regressors?

 Thanks a zillion times!

 Best wishes

 shiguangli





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


 The information in this e-mail is intended only for the person to whom it is
 addressed. If you believe this e-mail was sent to you in error and the
 e-mail
 contains patient information, please contact the Partners Compliance
 HelpLine at
 http://www.partners.org/complianceline . If the e-mail was sent to you in
 error
 but does not contain patient information, please contact the sender and
 properly
 dispose of the e-mail.


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

Re: [Freesurfer] How to design the contrast matrix with 12 regressors?

[MCLAREN, Donald]

Michael,

I'm also not aware of any program that will automatically demean by
group when you request an interaction or when you add a covariate.

I still think its important to stress that if you demean the entire
group, you are looking at the covariate-adjusted group means rather
than the actual group means. There are clearly times when you might
want to compare group means and control for variance associated with a
variable. One example that comes to mind is AD versus normal controls
and MMSE scores. For this hypothetical, lets say the mean MMSE across
the entire group was 27. You wouldn't want to compare AD subjects with
a mean of 27 to controls with a mean of 27 as AD subjects very rarely
have an MMSE score of 27 as well as controls rarely having and MMSE
score of 27. Nevertheless, you might want to account for the variance
associated with MMSE scores within each group.

Neither solution is right or wrong, it just needs to be stated that
the comparison is of covariate-adjusted means/intercepts/means in
papers.

Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
=
This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
intended only for the use of the individual or entity named above. If the
reader of the e-mail is not the intended recipient or the employee or agent
responsible for delivering it to the intended recipient, you are hereby
notified that you are in possession of confidential and privileged
information. Any unauthorized use, disclosure, copying or the taking of any
action in reliance on the contents of this information is strictly
prohibited and may be unlawful. If you have received this e-mail
unintentionally, please immediately notify the sender via telephone at (773)
406-2464 or email.


On Mon, Nov 26, 2012 at 5:53 PM, Michael Harms mha...@conte.wustl.edu wrote:

 Just wanted to mention that, to my knowledge no commercial stat package
 will mean center by group (Donald's case (C)) if you request an
 interaction model.  Mean centering by group is a very unusual operation.

 cheers,
 -MH

 --
 Michael Harms, Ph.D.

 ---
 Conte Center for the Neuroscience of Mental Disorders
 Washington University School of Medicine
 Department of Psychiatry, Box 8134
 660 South Euclid Ave.   Tel: 314-747-6173
 St. Louis, MO  63110Email: mha...@wustl.edu




 On 11/26/12 4:32 PM, MCLAREN, Donald mclaren.don...@gmail.com wrote:

I assume that your 12 columns are: your 6 groups followed by 6 columns
representing your covariate.

You must first test that the slopes are not different with an F-test:
0 0 0 0 0 0 1 -1 0 0 0 0
0 0 0 0 0 0 0 1 -1 0 0 0
0 0 0 0 0 0 0 0 1 -1 0 0
0 0 0 0 0 0 0 0 0 1 -1 0

If you don't find any differences, then you can use the DOSS model. If
you find differences, then you have an interaction between your
covariate and groups. When this happens, you should consult a
statistician if you want to interpret the effects of group as the
general rule of thumb is not to interpret the main effects in the
presence of an interaction. Using the DOSS model will leave you with 7
regressors. The test for group differences will be:
1 -1 0 0 0 0 0
or
0 1 -1 0 0 0 0
etc.
depending on what you are wanting to test. Simply having the covariate
in the model corrects for age.

A couple of points on covariates - for more details see
(http://mumford.fmripower.org/mean_centering/):
(A) If you don't mean center, then you will be looking at the group
intercepts;
(B) If you mean center, then you will be looking at the
covariate-adjusted group means;
(C) If you mean center by group, then you will be looking at the group
means and reducing the variance due to age. For example, if you want
to compare old and young subjects, but control for age within each
group.

A and B will give you the same answer in the DOSS since the slopes of
each group are parallel. C will give you a different result. Depending
on how you want to interpret your results will effect which method you
want to use for mean-centering or not-mean centering the data. In all
cases, mean-centering will not effect the slope
estimates/significance.

Hope this clears up the confusion.

Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital
and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
=
This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
intended only

Re: [Freesurfer] contrast matrix

[MCLAREN, Donald]

Please explain what are the columns represent.

Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
=
This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
intended only for the use of the individual or entity named above. If the
reader of the e-mail is not the intended recipient or the employee or agent
responsible for delivering it to the intended recipient, you are hereby
notified that you are in possession of confidential and privileged
information. Any unauthorized use, disclosure, copying or the taking of any
action in reliance on the contents of this information is strictly
prohibited and may be unlawful. If you have received this e-mail
unintentionally, please immediately notify the sender via telephone at (773)
406-2464 or email.


On Wed, Nov 21, 2012 at 2:50 PM,  xiangbo_2...@126.com wrote:
 No, I want to compute the interaction between factor 1 and factor 2 ,
 gender and age as covariates. thanks

 Bo Xiang

 在 2012-11-22 04:22:06，Douglas N Greve gr...@nmr.mgh.harvard.edu 写道：
Hi Bo, I don't understand the contrast you are trying to make. Are you
really trying to compute the interaction between four variables (factor
1, factor 2, gender, and age)?
doug

On 11/21/2012 10:49 AM, xiangbo_2010 wrote:
 Dear Donald McLaren
 Thank you for your reply! I make the contrast according to your method
 is following，but I want to make interaction between factor 1 (A,B)and
 factor 2(C,D,E), gender (M,F) and one continuous variable (age) as
 covariates, the following contrast:
 2 -2 0 -2 2 0 2 -2 0 -2 2 0 0 0 0 0 0 0 0 0 0 0 0 0
 0 2 -2 0 -2 2 0 2 -2 0 -2 2 0 0 0 0 0 0 0 0 0 0 0 0

 is correct? Thanks!
 Bo Xiang





 At 2012-11-21 04:07:37,MCLAREN, Donaldmclaren.don...@gmail.com  
 mailto:mclaren.don...@gmail.com  wrote:
 On Tue, Nov 20, 2012 at 12:56 PM, Douglas N Greve
 gr...@nmr.mgh.harvard.edu  mailto:gr...@nmr.mgh.harvard.edu  wrote:
   Thanks Donald. Is this the standard way to do this? I had used 8 rows
   instead of 4 with the difference being that 8 rows gives you an 
  opportunity
   to look for an effect in males OR females.
 
 Yes. Having 8 rows would tell you if you have an interaction between
 factor 1 and 2 in either males or females. My 4 rows only tell you if
 the interaction exists. Technically speaking, one would run the
 three-way interaction first. If nothing existed then you do the
 two-way interaction as I suggested. If there is a three-way
 interaction, then you would use Doug's approach of the interaction in
 either males or females.
 
 If there is an effect in both
   males and females but the effects go in opposite directions, then the 4 
  row
   implementation will resolve to 0 (no effect). Or am I misunderstanding
   something (again:)?
 
 Nope. You are right. If the male and female effects are different,
 then they could cancel each other out. If you suspect this to be the
 case, then you should be able to demonstrate a three-way interaction.
 
   thanks!
   doug
 
 
   On 11/20/2012 01:50 PM, MCLAREN, Donald wrote:
 
   Bo,
 
   Doug asked me to chime in on your issue. Here are some points that you
   (and others) will hopefully find useful.
 
   (1) Inferences are two-step process. First, you create and estimate
   the design matrix. Every column in the design matrix accounts can
   account for some of the variance in the data. Second, you have
   contrasts that allow you to infer specific effects. Because the model
   contains your covariates, you are always controlling for the
   covariates and by extension any factor/covariate not in the contrast.
 
   (2) Forming contrasts is often the most difficult thing to do. I
   assume that your three factors (1, 2, and gender) are all
   between-subject factors. If one of them is a within-subject factor
   please let me know and disregard the rest of the email. The final
   F-contrast will have 4 rows (factor 1 levels-1)*(factor 2 levels
   -1)=(3-1)*(3-1)=2*2=4
 
   The following is an outline for creating contrasts:
   (a) Start simple - difference between levels of 1 factor
   (b) Define your null hypothesis: AO=AP=AQ
   (c) Make it equal to 0: AO-AP=0 AND AP-AQ=0
   (d) Repeat for the other levels of the factor...
   BO-BP=0 AND BP-BQ=0
   CO-CP=0 AND CP-CQ=0
 
   (e) Now combine them AO-AP=BO-BP=CO-CP AND AP-AQ=BP-BQ=CP-CQ
 
   (f) Make them equal to 0:
   AO-AP-BO+BP=0
   BO-BP-CO+CP=0
   AP-AQ-BP+BQ=0
   BP-BQ-CP+CQ=0
 
   (g) Expand them to include gender, for example:
   AO-AP-BO+BP=0 becomes FAO-FAP-FBO+FBP+MAO-MAP-MBO+MBP=0
 
   Since the contrast now has 2 columns per level, you should divide all
   values by 2. This will produce the correct amplitude and statistics.
   If you leave

Re: [Freesurfer] contrast matrix

[MCLAREN, Donald]

Bo,

Doug asked me to chime in on your issue. Here are some points that you
(and others) will hopefully find useful.

(1) Inferences are two-step process. First, you create and estimate
the design matrix. Every column in the design matrix accounts can
account for some of the variance in the data. Second, you have
contrasts that allow you to infer specific effects. Because the model
contains your covariates, you are always controlling for the
covariates and by extension any factor/covariate not in the contrast.

(2) Forming contrasts is often the most difficult thing to do. I
assume that your three factors (1, 2, and gender) are all
between-subject factors. If one of them is a within-subject factor
please let me know and disregard the rest of the email. The final
F-contrast will have 4 rows (factor 1 levels-1)*(factor 2 levels
-1)=(3-1)*(3-1)=2*2=4

The following is an outline for creating contrasts:
(a) Start simple - difference between levels of 1 factor
(b) Define your null hypothesis: AO=AP=AQ
(c) Make it equal to 0: AO-AP=0 AND AP-AQ=0
(d) Repeat for the other levels of the factor...
BO-BP=0 AND BP-BQ=0
CO-CP=0 AND CP-CQ=0

(e) Now combine them AO-AP=BO-BP=CO-CP AND AP-AQ=BP-BQ=CP-CQ

(f) Make them equal to 0:
AO-AP-BO+BP=0
BO-BP-CO+CP=0
AP-AQ-BP+BQ=0
BP-BQ-CP+CQ=0

(g) Expand them to include gender, for example:
AO-AP-BO+BP=0 becomes FAO-FAP-FBO+FBP+MAO-MAP-MBO+MBP=0

Since the contrast now has 2 columns per level, you should divide all
values by 2. This will produce the correct amplitude and statistics.
If you leave the values as 1 and -1, then you will have an incorrect
amplitude, but the statistics will still be correct.

(h) Fill in the respective columns of your design matrix.

(3) The degrees of freedom are defined based on the rows of the
F-matrix and the number of rows in the design matrix. The F-test has a
numerator and denominator degrees of freedom. F(n,d).

Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
=
This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
intended only for the use of the individual or entity named above. If the
reader of the e-mail is not the intended recipient or the employee or agent
responsible for delivering it to the intended recipient, you are hereby
notified that you are in possession of confidential and privileged
information. Any unauthorized use, disclosure, copying or the taking of any
action in reliance on the contents of this information is strictly
prohibited and may be unlawful. If you have received this e-mail
unintentionally, please immediately notify the sender via telephone at (773)
406-2464 or email.


On Tue, Nov 20, 2012 at 8:17 AM, xiangbo_2010 xiangbo_2...@126.com wrote:
 Dear doug
Thank you for your reply!
 +AOM -BOM -APM -BPM00000
  +AOM -BOM00 -AQM +BQM000
  +AOM0 -APM000 -COM +CPM0
  +AOM000 -AQM  -COM0 +CQM
 there should be use 1 -1 or 0.5 -0.5? whether the -BPM should be change BPM?
 Thanks

 Bo Xiang






 At 2012-11-19 07:23:31,Douglas Greve gr...@nmr.mgh.harvard.edu wrote:


 Hi Bo, you can think of  the Ftest as a logical 'OR' between the t-test
 contrasts indicated in each row. Each row is a difference of differences, so

 1. (A-B)om - (A-B)pm -- Does the difference between A and B differ between
 groups O and P for Males?
 2. (A-B)om - (A-B)qm
 3. (A-C)om - (A-C)pm
 4. (A-C)om - (A-C)qm
 5. (A-B)of - (A-B)pf -- Does the difference between A and B differ between
 groups O and P for Females?
 6. (A-B)of - (A-B)qf
 7. (A-C)of - (A-C)pf
 8. (A-C)of - (A-C)pf

 I've put together the first 9 columns of the first 4 rows. The last 9
 columns are all 0s. For the last for rows, the 0s and below matrix are
 swapped to give you the same for the females

 doug

  AOM  BOM  APM  BPM  AQM  BQM  COM  CPM  CQM
 --
  +AOM -BOM -APM -BPM00000
  +AOM -BOM00 -AQM +BQM000
  +AOM0 -APM000 -COM +CPM0  ! nbsp;nb sp;
  +AOM000 -AQM  -COM0 +CQM



 On 11/17/12 9:21 PM, xiangbo_2010 wrote:

 Hi Freesurfer experts,

 I'm very sorry to bother you, but I am very confused with the following
 questions:

 My experimental design includes three discrete factors:  factor 1 with three
 levels (A,B,C ); factor 2 with three levels (O,P,Q); gender (F, M), and one
 covariate.

 So I can get 18 classes: FAO, FAP,FAQ,FBO,FBP,FBQ,FCO,FCP,FCQ,MAO,
 MAP,MAQ,MBO,MBP,MBQ,MCO,MCP,MCQ.  I want to perform the interaction between
 factor 1 and factor 2 regressing out the effect of gender and one covariate,
 but 

Re: [Freesurfer] Subgroup analysis

[MCLAREN, Donald]

On Mon, Nov 19, 2012 at 12:36 PM, Mahinda Yogarajah y.mahi...@gmail.com wrote:
 Hi Donald and Doug,

 Thanks for advice. Can I be a little bit clearer as I suspect I need a little 
 more guidance.

 When comparing controls (gp c) and whole patient group (gp p) I see 
 interesting differences in area (DOSS model after checking for no interaction 
 and with age and ICV  as correction factors). I also see an interesting 
 interaction between age and group (DODS model with ICV as nuisance factor) 
 such that that thickness correlates stronger with age in one group compared 
 to another group.

 This suggests that you need the DODS model for your analysis.

 The patient group can be split into 4 subgroups (gp p1 to gp p4) depending on 
 level of an endogenous substance. I want to see whether when running gp c 
 against gp p1, if the interaction between group and age (for thickness) is 
 stronger/weaker than the interaction when running gp p4 against gp c. I also 
 want to see whether differences in area between a subgroup and controls are 
 bigger/smaller compared to differences between other subgps and controls.


 The difference between C and gp1 AND C and gp4 is the same as the 
 difference between pg1 and pg4. If you are only wanting to make 
 comparisons between patients, which it sounds like, then only enter the 4 
 patient groups. If you want to know where pg1 and pg4 differ from 
 controls, you'll need a conjunction as suggested by Doug.


 To do this can I use the original method (granted power will b smaller) or if 
 I follow the method suggested by Donald should I demean individually within 
 subgroups. Also is this kind of model qdec friendly, and if not could you 
 offer any guidance on design matrix and contrasts.

 Demeaning does not change the slope estimation. Demeaning only changes the 
 group means. (1) If you do not demean, you get the group intercepts as if 
 your covariate is 0; (2) if you demean across everyone, you get the 
 covariate-adjusted group means; and (3) if you demean by group, then you 
 get the group means. One additional point, if you have an interaction 
 between group and a covariate, then you generally can't interpret the group 
 means.

Hope this helps.



 Hope i make some sense !

 Thanks.

 Mahinda



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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] contrast matrix

[MCLAREN, Donald]

On Tue, Nov 20, 2012 at 12:56 PM, Douglas N Greve
gr...@nmr.mgh.harvard.edu wrote:
 Thanks Donald. Is this the standard way to do this? I had used 8 rows
 instead of 4 with the difference being that 8 rows gives you an opportunity
 to look for an effect in males OR females.

Yes. Having 8 rows would tell you if you have an interaction between
factor 1 and 2 in either males or females. My 4 rows only tell you if
the interaction exists. Technically speaking, one would run the
three-way interaction first. If nothing existed then you do the
two-way interaction as I suggested. If there is a three-way
interaction, then you would use Doug's approach of the interaction in
either males or females.

If there is an effect in both
 males and females but the effects go in opposite directions, then the 4 row
 implementation will resolve to 0 (no effect). Or am I misunderstanding
 something (again:)?

Nope. You are right. If the male and female effects are different,
then they could cancel each other out. If you suspect this to be the
case, then you should be able to demonstrate a three-way interaction.

 thanks!
 doug


 On 11/20/2012 01:50 PM, MCLAREN, Donald wrote:

 Bo,

 Doug asked me to chime in on your issue. Here are some points that you
 (and others) will hopefully find useful.

 (1) Inferences are two-step process. First, you create and estimate
 the design matrix. Every column in the design matrix accounts can
 account for some of the variance in the data. Second, you have
 contrasts that allow you to infer specific effects. Because the model
 contains your covariates, you are always controlling for the
 covariates and by extension any factor/covariate not in the contrast.

 (2) Forming contrasts is often the most difficult thing to do. I
 assume that your three factors (1, 2, and gender) are all
 between-subject factors. If one of them is a within-subject factor
 please let me know and disregard the rest of the email. The final
 F-contrast will have 4 rows (factor 1 levels-1)*(factor 2 levels
 -1)=(3-1)*(3-1)=2*2=4

 The following is an outline for creating contrasts:
 (a) Start simple - difference between levels of 1 factor
 (b) Define your null hypothesis: AO=AP=AQ
 (c) Make it equal to 0: AO-AP=0 AND AP-AQ=0
 (d) Repeat for the other levels of the factor...
 BO-BP=0 AND BP-BQ=0
 CO-CP=0 AND CP-CQ=0

 (e) Now combine them AO-AP=BO-BP=CO-CP AND AP-AQ=BP-BQ=CP-CQ

 (f) Make them equal to 0:
 AO-AP-BO+BP=0
 BO-BP-CO+CP=0
 AP-AQ-BP+BQ=0
 BP-BQ-CP+CQ=0

 (g) Expand them to include gender, for example:
 AO-AP-BO+BP=0 becomes FAO-FAP-FBO+FBP+MAO-MAP-MBO+MBP=0

 Since the contrast now has 2 columns per level, you should divide all
 values by 2. This will produce the correct amplitude and statistics.
 If you leave the values as 1 and -1, then you will have an incorrect
 amplitude, but the statistics will still be correct.

 (h) Fill in the respective columns of your design matrix.

 (3) The degrees of freedom are defined based on the rows of the
 F-matrix and the number of rows in the design matrix. The F-test has a
 numerator and denominator degrees of freedom. F(n,d).

 Best Regards, Donald McLaren
 =
 D.G. McLaren, Ph.D.
 Research Fellow, Department of Neurology, Massachusetts General Hospital
 and
 Harvard Medical School
 Postdoctoral Research Fellow, GRECC, Bedford VA
 Website: http://www.martinos.org/~mclaren
 Office: (773) 406-2464
 =
 This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
 HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
 intended only for the use of the individual or entity named above. If the
 reader of the e-mail is not the intended recipient or the employee or
 agent
 responsible for delivering it to the intended recipient, you are hereby
 notified that you are in possession of confidential and privileged
 information. Any unauthorized use, disclosure, copying or the taking of
 any
 action in reliance on the contents of this information is strictly
 prohibited and may be unlawful. If you have received this e-mail
 unintentionally, please immediately notify the sender via telephone at
 (773)
 406-2464 or email.


 On Tue, Nov 20, 2012 at 8:17 AM, xiangbo_2010xiangbo_2...@126.com
 wrote:

 Dear doug
 Thank you for your reply!
 +AOM -BOM -APM -BPM00000
   +AOM -BOM00 -AQM +BQM000
   +AOM0 -APM000 -COM +CPM0
   +AOM000 -AQM  -COM0 +CQM
 there should be use 1 -1 or 0.5 -0.5? whether the -BPM should be change
 BPM?
 Thanks

 Bo Xiang






 At 2012-11-19 07:23:31,Douglas Grevegr...@nmr.mgh.harvard.edu  wrote:


 Hi Bo, you can think of  the Ftest as a logical 'OR' between the t-test
 contrasts indicated in each row. Each row is a difference of differences,
 so

 1. (A-B)om - (A-B)pm --  Does the difference between A and B differ
 between
 groups O and P for Males?
 2. (A-B)om - (A-B)qm
 3. (A-C)om - (A-C)pm
 4. (A-C)om - (A-C)qm
 5

[Freesurfer] bbregister

[MCLAREN, Donald]

Doug,

I received this question from a colleague, Exactly which segmentation
file from recon -all is being used in the bbregister command?

Thanks,

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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] bbregister

[MCLAREN, Donald]

Which surfaces does it use?

On Tue, Nov 20, 2012 at 2:21 PM, Douglas N Greve
gr...@nmr.mgh.harvard.edu wrote:
 Hi Donald,
 It does not use any of the segmentations. In fact, it does not use any
 of the anatomical volumes. It only uses the surfaces.
 doug


 On 11/20/2012 03:19 PM, MCLAREN, Donald wrote:
 Doug,

 I received this question from a colleague, Exactly which segmentation
 file from recon -all is being used in the bbregister command?

 Thanks,

 Donald
 ___
 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: 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

Re: [Freesurfer] Subgroup analysis

[MCLAREN, Donald]

Doug and Mahinda,

Since the assumption is that the slope is the same across all
subjects, I would demean once. I would use one model with 1 control
group and N patient group. The model will then test whether or not the
covariate-adjusted group means are the same or different. By doing it
in a single test, you will have more power since you will be using the
pooled variance across all groups. You will also have the same slope
estimate for all comparisons.

Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
=
This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
intended only for the use of the individual or entity named above. If the
reader of the e-mail is not the intended recipient or the employee or agent
responsible for delivering it to the intended recipient, you are hereby
notified that you are in possession of confidential and privileged
information. Any unauthorized use, disclosure, copying or the taking of any
action in reliance on the contents of this information is strictly
prohibited and may be unlawful. If you have received this e-mail
unintentionally, please immediately notify the sender via telephone at (773)
406-2464 or email.


On Mon, Nov 19, 2012 at 9:46 AM, Douglas N Greve
gr...@nmr.mgh.harvard.edu wrote:


 On 11/19/2012 03:04 AM, Mahinda Yogarajah wrote:
 Dear Experts,

 I have a two groups - a control group and patient group. The patient group 
 can also be divided into 4 subgroups (but not control gp). Both groups are 
 evenly split between male and female. So far I have compared the patient and 
 control groups as a whole (age and icv as continuous/nuisance variables) but 
 now i want to compare each of the subgroups to controls. I have tried doing 
 this in qdec very crudely by running 4 analyses in qdec where I exclude all 
 the subgroup cases execpt for those belonging to the subgroup I am looking 
 at. My questions are

 1) Is this valid (I would correct for the multiple tests) ? How does qdec 
 cope with exclusions given that variables (age) have been demeaned across a 
 whole group.
 whether it is valid or not depends on what you are trying to conclude.
 If you want to compare across the tests, I would do the demeaning once
 across all subjects and not individually for each test.

 2) Is there a better way of comparing my subgroups to controls ?
 Not that I can think of

 Thanks.

 Mahinda


 ___
 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: 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

[Freesurfer] AAL labels

[MCLAREN, Donald]

Has anyone created an AAL label file for Freesurfer? I've done some
ROI analysis using AAL regions and want to display regional values on
the freesurfer surface.

Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
=
This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
intended only for the use of the individual or entity named above. If the
reader of the e-mail is not the intended recipient or the employee or agent
responsible for delivering it to the intended recipient, you are hereby
notified that you are in possession of confidential and privileged
information. Any unauthorized use, disclosure, copying or the taking of any
action in reliance on the contents of this information is strictly
prohibited and may be unlawful. If you have received this e-mail
unintentionally, please immediately notify the sender via telephone at (773)
406-2464 or email.
___
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] Brainhack 2012

[MCLAREN, Donald]

Dear colleagues,

I wanted to draw your attention on the upcoming 2012 Brainhack, 1st
edition, to be held from September 1-4 at the Max Plank Institute for Human
Cognitive and Brain Sciences, Leipzig, Germany. Brainhack is not a
conference or a workshop. It should be closer to one of those exciting
conversations you may have had at HBM during cocktail or poster sessions.
Except that we will have over three days to build up those conversations
into full-fledge collaborations. One should come to brainhack ready to
engage into collaborative projects, and with some material (slides, ideas,
data, tools) ready to start a project or a discussion panel. Brainhack will
build on the successful techniques used in other
unconferenceshttp://en.wikipedia.org/wiki/Unconference to
keep the meeting focussed and productive. It is possible to start a project
and build a team as early as today. Please have a look at the website for
informations on the conference and a sample of projects (more will be added
over the summer):
http://brainhack.org/2012/04/06/brainhack-2012-unconference/

The list of confirmed attendees includes F. Xavier Castellanos, Michael
Hanke, Michael P. Milham, Tal Yarkoni, Arno Villringer, and many members of
the neurobureau http://www.neurobureau.org/NeuroBureau/Welcome.html.
Brainhack
is a satellite of the resting-state connectivity
conferencehttp://www.restingstate.com/.
Although many participants will have an interest in connectivity analysis,
there will also be attendees coming from a variety of backgrounds within
neuroscience. Registration is now opened:
http://www.cbs.mpg.de/events/workshops/brainhack

Please do not hesitate to share this invitation with your circles.

Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital
and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
=
This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
intended only for the use of the individual or entity named above. If the
reader of the e-mail is not the intended recipient or the employee or agent
responsible for delivering it to the intended recipient, you are hereby
notified that you are in possession of confidential and privileged
information. Any unauthorized use, disclosure, copying or the taking of any
action in reliance on the contents of this information is strictly
prohibited and may be unlawful. If you have received this e-mail
unintentionally, please immediately notify the sender via telephone at
(773)
406-2464 or email.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] FA (DTI) statistical analysis: 3 covariates

[MCLAREN, Donald]

I don't believe that Freesurfer has the tools to use non-imaging data as
the dependent variable. The GLM in freesurfer is setup to use the imaging
data at the dependent variable.

For your question, I'd recommend SAS, STATA, SPSS, or another standard
statistical package.

Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Postdoctoral Research Fellow, GRECC, Bedford VA
Research Fellow, Department of Neurology, Massachusetts General Hospital
and
Harvard Medical School
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
=
This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
intended only for the use of the individual or entity named above. If the
reader of the e-mail is not the intended recipient or the employee or agent
responsible for delivering it to the intended recipient, you are hereby
notified that you are in possession of confidential and privileged
information. Any unauthorized use, disclosure, copying or the taking of any
action in reliance on the contents of this information is strictly
prohibited and may be unlawful. If you have received this e-mail
unintentionally, please immediately notify the sender via telephone at
(773)
406-2464 or email.



On Sun, Jul 1, 2012 at 8:27 PM, Jay Morozov morozov...@gmail.com wrote:



 Dear Freesurfer experts,
 We are trying to run a statistical analysis for FA in 5 ROIs.
 We have one group of subjects and our goal is to run regression analysis
 to find a relation between one behavioral test (episodic memory test) and
 FA.
  We are planning to set
 - the accuracy on episodic memory test as the dependent variable.
 - age, sex and MMSE (range 21-30) as covariates
 - FA in each ROI is the predictor
  We couldn't find an example of 3 covariates on the tutorial website,
 could you kindly let us know how to run glm analysis for 3 covariates?
 Thank you
 Jay Morozov


 ___
 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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] DODS, DOSS, and interactions

[MCLAREN, Donald]

If the covariates are collinear, then you can't properly estimate the
model. They are collinear if they explain the variance of each other.

I would first test for the relationship of your covariates before putting
them into the model as you don't want the covariates to be collinear.

Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Postdoctoral Research Fellow, GRECC, Bedford VA
Research Fellow, Department of Neurology, Massachusetts General Hospital
and
Harvard Medical School
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
=
This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
intended only for the use of the individual or entity named above. If the
reader of the e-mail is not the intended recipient or the employee or agent
responsible for delivering it to the intended recipient, you are hereby
notified that you are in possession of confidential and privileged
information. Any unauthorized use, disclosure, copying or the taking of any
action in reliance on the contents of this information is strictly
prohibited and may be unlawful. If you have received this e-mail
unintentionally, please immediately notify the sender via telephone at
(773)
406-2464 or email.



On Wed, Jun 27, 2012 at 3:42 PM, mdkrue...@uwalumni.com 
mdkrue...@uwalumni.com wrote:

 Freesurfers-

 Question, when looking for interactions to justify using DOSS say i am
 looking at cortical thickness and i have two discrete variables (G1 and G2)
 and 4 continious variables (V1, V2, V3, V4). My thinking is that i should
 look to see if there are interactions with the groups and each individual
 variable. However what if it is likely that an interaction of G1, G2, and
 V1 can be explained by V2?

 Michael

 --
 Michael D. Kruepke
 PhD - University of Illinois at Urbana-Champaign
 BA - Psych - University of Wisconsin-Madison
 mdkrue...@gmail.com
 (262)-483-7449


 ___
 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


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] Allen Brain Institute to Freesurfer Labels

[MCLAREN, Donald]

Does anyone have a mapping of the Allen Brain Institute labels to the
freesurfer parcellations? Just the labels would be sufficient for these
purposes.

Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Postdoctoral Research Fellow, GRECC, Bedford VA
Research Fellow, Department of Neurology, Massachusetts General Hospital
and
Harvard Medical School
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
=
This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
intended only for the use of the individual or entity named above. If the
reader of the e-mail is not the intended recipient or the employee or agent
responsible for delivering it to the intended recipient, you are hereby
notified that you are in possession of confidential and privileged
information. Any unauthorized use, disclosure, copying or the taking of any
action in reliance on the contents of this information is strictly
prohibited and may be unlawful. If you have received this e-mail
unintentionally, please immediately notify the sender via telephone at
(773)
406-2464 or email.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] treatment of missing values in mri_glmfit

[MCLAREN, Donald]

Kristine/Doug,

Are you missing Dependent Variable values or Independent Variable Values?

If you are missing some IV values, there are two potential solutions:
(1) Drop the subject;
(2) Impute the value of that subject given other variables and
relationships of those variables and the variable with the missing value.

If you are missing some DV values, the easiest solution would be to use
GLM_Flex (
http://nmr.mgh.harvard.edu/harvardagingbrain/People/AaronSchultz/GLM_Flex.html
).

The one caveat of GLM_Flex is that we don't have a computation for surface
smoothness yet, we should probably talk to Doug about the best way to deal
with this issue. Another caveat is that it won't be useable in some of the
freesurfer viewing tools (such as qdec as the file structure of the model
is different), but contrasts can be viewed with tksurfer.

One other caveat, the output of GLM_Flex is T/F-statistics, not
log-transformed p-values as is traditionally done in Freesurfer. I think
that this will be updated at some point in the future.

Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Postdoctoral Research Fellow, GRECC, Bedford VA
Research Fellow, Department of Neurology, Massachusetts General Hospital
and
Harvard Medical School
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
=
This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
intended only for the use of the individual or entity named above. If the
reader of the e-mail is not the intended recipient or the employee or agent
responsible for delivering it to the intended recipient, you are hereby
notified that you are in possession of confidential and privileged
information. Any unauthorized use, disclosure, copying or the taking of any
action in reliance on the contents of this information is strictly
prohibited and may be unlawful. If you have received this e-mail
unintentionally, please immediately notify the sender via telephone at
(773)
406-2464 or email.



On Fri, Feb 24, 2012 at 3:27 PM, Kristine Beate Walhovd 
k.b.walh...@psykologi.uio.no wrote:

  Hi,

  we´re running FS 5.1 and have a data set with a lot of missing values.
  There are different subsets of persons missing different values of
  interest, and we´re running analyses on concat files. mri_glmfit not
  qdec). Is there anyway we can run analyses w/ missings in the fsgd file?

  Best,

  Kristine


 ___
 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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Problem with covariates in design for surface based analysis

[MCLAREN, Donald]

Charlotte,

There is no difference, from a statistical perspective, of nuisance
factors and covariates.

The key questions are:
(1) Do any of these covariates have a differential effect on thickness
between groups?
(2) Do you want to compare the actual group means or the
covariate-adjusted group means (e.g. test the means for subjects as if
the subjects all had the same covariate values)?
(3) Do you have enough subjects to add 5 covariates?
(4) Do you have a valid reason for why all the covariates would have
an effect on thickness? One can always add more covariates to reduce
the error, but its not always a good thing to add covariates just to
reduce the error of the model.

On 2/23/12, Charlotte Bernard chak...@live.fr wrote:

 Dear Freesurfur users,

 I have a question about the design for a surface based analysis! I want to
 compare controls and patients. I have 5 covariates. One is a continous
 variable. The others are categorial variables (4 with 2 levels and 1 with 5
 levels). I want to ajust my result with all of thoses variables. I am
 interested in the difference in thickness between patients and controls.
 Is it possible to construct such design?
 Can I put some of my variables in the nuisance factors ? I don't really
 understand the difference between nuisance factor and covariabes.
 I really hope somebody can help me.
 Thanks for all!
 All the best,
 Charlotte
   


-- 
Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Postdoctoral Research Fellow, GRECC, Bedford VA
Research Fellow, Department of Neurology, Massachusetts General Hospital
and
Harvard Medical School
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
=
This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
intended only for the use of the individual or entity named above. If the
reader of the e-mail is not the intended recipient or the employee or agent
responsible for delivering it to the intended recipient, you are hereby
notified that you are in possession of confidential and privileged
information. Any unauthorized use, disclosure, copying or the taking of any
action in reliance on the contents of this information is strictly
prohibited and may be unlawful. If you have received this e-mail
unintentionally, please immediately notify the sender via telephone at
(773)
406-2464 or email.
___
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] Reliability and accuracy of Freesurfer

[MCLAREN, Donald]

I've looked through a number of freesurfer papers, but haven't been able to
find the answer to what I am looking for and was hoping someone had the
references easily available.

(1) What is the reliability of regional volumes generated from freesurfer
over time?

(2) What is the accuracy of labels for these volumes from subject to
subject (e.g. how close are the freesurfer labels to cytoarchitecture or
manually drawing the labels)?


Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Postdoctoral Research Fellow, GRECC, Bedford VA
Research Fellow, Department of Neurology, Massachusetts General Hospital
and
Harvard Medical School
Office: (773) 406-2464
=
This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
intended only for the use of the individual or entity named above. If the
reader of the e-mail is not the intended recipient or the employee or agent
responsible for delivering it to the intended recipient, you are hereby
notified that you are in possession of confidential and privileged
information. Any unauthorized use, disclosure, copying or the taking of any
action in reliance on the contents of this information is strictly
prohibited and may be unlawful. If you have received this e-mail
unintentionally, please immediately notify the sender via telephone at
(773)
406-2464 or email.
___
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] Surface Area from mri_surfcluster versus mri_segstats

[MCLAREN, Donald]

I've noticed that if I run mri_surfcluster to produce a label file, then
merge the labels into a single label using mri_mergelabels, then
mri_segstats with the slabel option with the fsaverage subject; I get
different surface areas from mri_surfcluster (summed all the cluster areas)
and mri_segstats (1 area). Is there something wrong with my implementation
of these three commands or is it expected that the two methods would
produce different values?



Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Postdoctoral Research Fellow, GRECC, Bedford VA
Research Fellow, Department of Neurology, Massachusetts General Hospital
and
Harvard Medical School
Office: (773) 406-2464
=
This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
intended only for the use of the individual or entity named above. If the
reader of the e-mail is not the intended recipient or the employee or agent
responsible for delivering it to the intended recipient, you are hereby
notified that you are in possession of confidential and privileged
information. Any unauthorized use, disclosure, copying or the taking of any
action in reliance on the contents of this information is strictly
prohibited and may be unlawful. If you have received this e-mail
unintentionally, please immediately notify the sender via telephone at
(773)
406-2464 or email.
___
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] Image Filtering

[MCLAREN, Donald]

Bruce and others,

Are there any spatial filters applied during the segmentation process
other than a bias field correction? For example, a spatially adaptive
non-linear means filter (e.g VBM8)?

If not, do you think denoising filters will improve the accuracy
and/or reduce manual editting?

Thanks.

Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Postdoctoral Research Fellow, GRECC, Bedford VA
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Office: (773) 406-2464
=
This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
intended only for the use of the individual or entity named above. If the
reader of the e-mail is not the intended recipient or the employee or agent
responsible for delivering it to the intended recipient, you are hereby
notified that you are in possession of confidential and privileged
information. Any unauthorized use, disclosure, copying or the taking of any
action in reliance on the contents of this information is strictly
prohibited and may be unlawful. If you have received this e-mail
unintentionally, please immediately notify the sender via telephone at (773)
406-2464 or email.
___
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] Concatenate surfaces

[MCLAREN, Donald]

Is there a way to concatenate surfaces for use with mri_segstats? The
surfaces are already in fsaverage space.

Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Postdoctoral Research Fellow, GRECC, Bedford VA
Research Fellow, Department of Neurology, Massachusetts General Hospital and

Harvard Medical School
Office: (773) 406-2464
=
This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
intended only for the use of the individual or entity named above. If the
reader of the e-mail is not the intended recipient or the employee or agent
responsible for delivering it to the intended recipient, you are hereby
notified that you are in possession of confidential and privileged
information. Any unauthorized use, disclosure, copying or the taking of any
action in reliance on the contents of this information is strictly
prohibited and may be unlawful. If you have received this e-mail
unintentionally, please immediately notify the sender via telephone at (773)

406-2464 or email.
___
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] mri_mcsim and mri_glmfit-sim

[MCLAREN, Donald]

I am trying to figure out how to cluster some data on the cortical
surface; however, I've run into a few issues:

(1) I can't seem to find a description or examples for running
mri_mcsim and mri_glmfit-sim won't work because I'm not using FSFAST
to create my statistical maps.

(2) A previous email suggested that there are stored values that I
could lookup, but I can't seem to locate the files anywhere.

(3) With respect to the fwhm values used in the simulations, it was
suggested that this be matched to the fwhm.dat file output from
mri_glmfit; however, since I didn't use mri_glmfit, I don't have
fwhm.data file. Should I just use the smoothing used on the surfaces?

Any thoughts would be appreciated.

Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Postdoctoral Research Fellow, GRECC, Bedford VA
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Office: (773) 406-2464
=
This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
intended only for the use of the individual or entity named above. If the
reader of the e-mail is not the intended recipient or the employee or agent
responsible for delivering it to the intended recipient, you are hereby
notified that you are in possession of confidential and privileged
information. Any unauthorized use, disclosure, copying or the taking of any
action in reliance on the contents of this information is strictly
prohibited and may be unlawful. If you have received this e-mail
unintentionally, please immediately notify the sender via telephone at (773)
406-2464 or email.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] two questions regarding qdec and conjunction analysis is FS

[MCLAREN, Donald]

See inline responses.On Wed, Aug 24, 2011 at 7:35 AM, Tetiana Dadakova 
tetian...@gmail.com wrote:

 Dear FS experts,

 I have two questions:

 1. In qdec.table.dat file I am specifying several continuous factors,
 e.g factor1 and factor2. For some subjects factor2 is missing,
 therefore I leave empty space in those cells. When I load a
 qdec.table.dat into qdec, the whole line of the subject with missing
 factor2 is omitted.
 I was wondering if I can make some input into the empty cell, so that
 qdec recognizes that for this subject the value is missing only for
 factor2, and the value for factor1 is present.


I'm not sure about Freesurfer, but in all my work with neuroimaging data
across platforms, missing data in X requires that the subject to be
excluded. The reason is the Y=X1*B+X2*B. Since you don't know X2, you can't
find predicted Y and thus you can't find the error associated with that
subject. Programs that all allow you to keep the subject often impute the
value of the missing data to get the full X matrix or do not use the General
Linear Model to find the solution. The GLM approach inverts the X matrix and
you can't invert a matrix with an empty cell, as far as I know.



 2. Is it possible to do conjunction analysis in FreeSurfer, I mean
 looking at common differences in two groups as compared to the third
 group?


When I do conjunctions, I use a logical AND. There are other ways, but there
are statistical issues. The logical AND will show where group A  group C
and where group B  group C.
To do this, I load the thresholded surfaces into matlab, make them both
binary, multiply one of them by 2, then add the two datasets together. Then
write the data back out to the surface. The new values will be 0 for no
difference in either group, 1 or 2 for a difference in one of the group
comparison, 3 where both groups are different from the third.




 Thank you for your time and help,
 Tanja.
 ___
 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.


Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Postdoctoral Research Fellow, GRECC, Bedford VA
Research Fellow, Department of Neurology, Massachusetts General Hospital and

Harvard Medical School
Office: (773) 406-2464
=
This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
intended only for the use of the individual or entity named above. If the
reader of the e-mail is not the intended recipient or the employee or agent
responsible for delivering it to the intended recipient, you are hereby
notified that you are in possession of confidential and privileged
information. Any unauthorized use, disclosure, copying or the taking of any
action in reliance on the contents of this information is strictly
prohibited and may be unlawful. If you have received this e-mail
unintentionally, please immediately notify the sender via telephone at (773)

406-2464 or email.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] DOSS or DODS

[MCLAREN, Donald]

For question #3; #4.

#3
Any good stastistical textbook will be useful. The two that come to mind
are:
(a) Meyers and Wells. Research Design and Statistical A nalysis
(b) Keppel and Wickens. Design and Analysis: A Researcher's Handbook (4th
Edition)

#4

SPM uses the General Linear Model for all of its second level models. The
DODS and DOSS are terms used in the freesurfer package and not in other
packages; however, the designs can easily be generated in SPM.

DODS -- Design matrix with different slopes per group
Select two-sample t-test (or flexible factorial)
Specify your two groups of scans
Specify the covariate values, names, and select interaction with factor 1

You can ask if the slopes are different

DOSS -- Design matrix with same slopes across all groups
Select two-sample t-test (or flexible factorial)
Specify your two groups of scans
Specify the covariate values, names, and select interaction none.

The slopes are modelled as a single regressor, so you can't ask about the
difference in slopes between groups.

Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Postdoctoral Research Fellow, GRECC, Bedford VA
Research Fellow, Department of Neurology, Massachusetts General Hospital and

Harvard Medical School
Office: (773) 406-2464
=
This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
intended only for the use of the individual or entity named above. If the
reader of the e-mail is not the intended recipient or the employee or agent
responsible for delivering it to the intended recipient, you are hereby
notified that you are in possession of confidential and privileged
information. Any unauthorized use, disclosure, copying or the taking of any
action in reliance on the contents of this information is strictly
prohibited and may be unlawful. If you have received this e-mail
unintentionally, please immediately notify the sender via telephone at (773)

406-2464 or email.



On Mon, Aug 22, 2011 at 8:46 AM, Tetiana Dadakova tetian...@gmail.comwrote:

 Hello Douglas,

 I did as you suggested and I got the results, but I still have
 difficulty understanding how exactly the choice of Design Matrix Type
 influences the analysis, so I have several questions:

 1. When I look at thickness difference between two groups and choose
 age as nuisance parameter, doesn't it mean that calculation take into
 account the difference in slopes already (as I correct for age)? So
 therefore, when I also choose DODS or DOSS I do kind of double
 correction (matrix type + nuisance), don't I?
 2. When I choose e.g. DODS and do the analysis, can I see the slopes
 (or the values of slopes) for two groups somehow? In which file this
 output is?
 3. Can you recommend me anything to read regarding mathematics of how
 the analysis is done with either matrix type?
 4. Just in case you know: how is this step implemented in SPM? It also
 uses glm, but it doesn't ask for the DODS vs DOSS choice.

 Thank you, I appreciate you time and help,
 Tanja.



 On Wed, Aug 17, 2011 at 6:19 PM, Tetiana Dadakova tetian...@gmail.com
 wrote:
  Thank you, Douglas.
 
  On Wed, Aug 17, 2011 at 5:48 PM, Douglas N Greve
  gr...@nmr.mgh.harvard.edu wrote:
 
  Hi Tanja, you should use DODS and test for a difference between the age
  slopes of the groups (ie, an interaction between group and age). If
 there
  are no significant interactions, you should then use DOSS to test for
 the
  difference between thicknesses.
  doug
 
  Tetiana Dadakova wrote:
 
  Dear all,
 
  I have two groups of subjects, and I want to see a difference in
  thickness between them controlling for age.
  I couldn't find any information in the literature on how the subject's
  brains in my groups develop with age. Therefore I can't tell whether
  thickness as a function of age for both groups has the same slope or
  different.
 
  My question is if in this case I should use DODS?
 
  Thank you,
  Tanja.
  ___
  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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 
 
 
  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
 

Re: [Freesurfer] statistical question

[MCLAREN, Donald]

Just a couple of thoughts.

It depends on what you want to control for AND how you want to control
for it. For example, if the relationship of ICV to X differs between
boys and girls, you might want to control ICV separately for each
group.

The results after controlling for ICV are those brain
regions/volumes/thickness that are not explained by ICV. If ICV and
region X are highly correlated and region X is related to your
independent variable, then you would conclude that that region is
related, whereas it could be due to ICV. Additionally, there are
probably a number of regions highly correlated with ICV, which make
them potentially less interesting.

Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Postdoctoral Research Fellow, GRECC, Bedford VA
Research Fellow, Department of Neurology, Massachusetts General
Hospital and Harvard Medical School
Office: (773) 406-2464
=
This e-mail contains CONFIDENTIAL INFORMATION which may contain
PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED
and which is intended only for the use of the individual or entity
named above. If the reader of the e-mail is not the intended recipient
or the employee or agent responsible for delivering it to the intended
recipient, you are hereby notified that you are in possession of
confidential and privileged information. Any unauthorized use,
disclosure, copying or the taking of any action in reliance on the
contents of this information is strictly prohibited and may be
unlawful. If you have received this e-mail unintentionally, please
immediately notify the sender via telephone at (773) 406-2464 or
email.



On Mon, Jan 24, 2011 at 11:59 AM, Ilana Hairston hairstons...@gmail.com wrote:
 Hi there,
 This is a bit outside the pure technical questions.
 My subject pool has both boys and girls, with the boys having larger
 intracranial volume.
 My results when controlling for gender and intracranial volume however are
 not the same (obviously, one is a dichotomous variable, the other
 continuous).
 Looking at the results, i prefer the latter over the former, more consistent
 with the literature, and more internally consistent (i.e., brain regions
 associated with intenalizing sub-scales and the internalizing total scale).
 But it could be argued that I am removing important variance - maybe
 stressed out kids have smaller heads?

 Any recommendation?

 thanks




 --
 ***
 peligro! flaca pero mala!
 **


 ___
 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

[Freesurfer] Non-human primate surface template

[MCLAREN, Donald]

Dear all,
Does anyone have or  is perhaps working on a surface template for the rhesus
macaque brain?

-- 
Best Regards, Donald McLaren
=
Support the Alzheimer's Association Memory Walk 2009 ~~~
Join the Wisconsin Alzheimer's Disease Research Center team or make a
donation.
http://madison.kintera.org/2009/donaldmclaren


=
D.G. McLaren
University of Wisconsin - Madison
Neuroscience Training Program
Office: (608) 265-9672
Lab: (608) 256-1901 ext 12914
=
This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED
HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is
intended only for the use of the individual or entity named above. If the
reader of the e-mail is not the intended recipient or the employee or agent
responsible for delivering it to the intended recipient, you are hereby
notified that you are in possession of confidential and privileged
information. Any unauthorized use, disclosure, copying or the taking of any
action in reliance on the contents of this information is strictly
prohibited and may be unlawful. If you have received this e-mail
unintentionally, please immediately notify the sender via telephone at (608)
265-9672 or email.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer