On Jul 09, 2016, at 09:00 AM, freesurfer-requ...@nmr.mgh.harvard.edu wrote:
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Today's Topics:
1. Longitudinal LME contrast vectors (K)
2. Re: Longitudinal LME contrast vectors (Martin Reuter)
3. Question about NULL event with Optseq2 (Feng Zhou)
4. Cerebral volume without ventricles (Kaiming Yin)
5. Re: FSFAST error: ERROR: fast_selxavg3() failed\n (Douglas Greve)
----------------------------------------------------------------------
Message: 1
Date: Fri, 8 Jul 2016 15:02:58 -0700
From: K <kam.n...@gmail.com>
Subject: [Freesurfer] Longitudinal LME contrast vectors
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<CAH54DzgqKWSCwm0gu_ecbB3jrQmLc=y6nun5j4dujkwaxn7...@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Hello! We are trying to run a longitudinal morphometry analysis with a
control group and clinical group scanned twice. We'd like to look at group
x time interactions and would like help figuring out the best way to do so.
As the time variable we use centered age -- the deviation from the mean age
across all subjects and timepoints. To do so, we use the following
lme model:
intercept + centeredage.controls + centeredage.clinical + group(0,1)
+ sex(0,1)
Contrast vector: [0 1 -1 0 0]
where the centeredage column contains only the centered age for that group
and zeros for the opposite group. The thinking behind this is to
investigate which cortical regions show opposite effects of time
between the groups.
However, the FreeSurfer lme software requests a specified "time
column". Obviously, we cannot add a centered age for all subjects, nor does
it seem to make sense to use one of the two group-specific
centeredage columns as the time column.
Our alternative model for investigating interatction is:
intercept + centeredage + group(0,1) + sex(0,1) + groupxcenteredage
where centeredage is the time columns and is a common regressor for both
groups and thus, groupxcenteredage becomes 0 for control subjects.
Contrast vector: [0 0 0 0 1]
This would test whether there is an added effect of centered age in the
clinical group.
Is there a better way to do an group x time interaction analysis here, or
is there a solution for the time column? Thanks!
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Message: 2
Date: Sat, 9 Jul 2016 00:39:59 +0200
From: Martin Reuter <mreu...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Longitudinal LME contrast vectors
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <a8a075cb-740e-4032-8a0e-6bc432663...@nmr.mgh.harvard.edu>
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Hi K,
the models are equivalent (they are linear combinations of each other). The preferred way (at least for the Matlab LME stuff) is the second one.
Note that usually people want to control for age (or test for an age effect).
To do so they would have
intercept + time_from_baseline + age_at_baseline + group + sex +
groupXtime_from_baseline
Best, Martin
On Jul 9, 2016, at 12:02 AM, K <kam.n...@gmail.com> wrote:
Hello! We are trying to run a longitudinal morphometry analysis with a control
group and clinical group scanned twice. We'd like to look at group x time
interactions and would like help figuring out the best way to do so. As the
time variable we use centered age -- the deviation from the mean age across all
subjects and timepoints. To do so, we use the following lme model:
intercept + centeredage.controls + centeredage.clinical + group(0,1) + sex(0,1)
Contrast vector: [0 1 -1 0 0]
where the centeredage column contains only the centered age for that group and
zeros for the opposite group. The thinking behind this is to investigate which
cortical regions show opposite effects of time between the groups.
However, the FreeSurfer lme software requests a specified "time column".
Obviously, we cannot add a centered age for all subjects, nor does it seem to make sense
to use one of the two group-specific centeredage columns as the time column.
Our alternative model for investigating interatction is:
intercept + centeredage + group(0,1) + sex(0,1) + groupxcenteredage
where centeredage is the time columns and is a common regressor for both groups
and thus, groupxcenteredage becomes 0 for control subjects.
Contrast vector: [0 0 0 0 1]
This would test whether there is an added effect of centered age in the
clinical group.
Is there a better way to do an group x time interaction analysis here, or is
there a solution for the time column? Thanks!
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Message: 3
Date: Sat, 9 Jul 2016 07:39:43 +0800
From: Feng Zhou <fengzhou...@gmail.com>
Subject: [Freesurfer] Question about NULL event with Optseq2
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<cakkeuhmfndthq-zlioryvrqy7emi4tvwxdjhscfcv+img_2...@mail.gmail.com>
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Dear experts,
I'd like to use optseq2 to optimize the order of events as well as inter
stimulus intervals. My experiment contains 3 runs and each run contains 3
events, say Cp, Cn and Pobe events
Each stimulu will be presented 4, 4 and 1 sec and the numbers of times that
each event type will be presented during the course of the run are 12 12
and 4 respectively, and interstimulus interval ranges from 8?12 sec. So
each run would last around 380 sec. I used the following code:
optseq2 --ntp 380 --tr 1 --psdwin 0 20 1 --ev Cp 4 12 --ev Cn 4 12 --ev
Prob 1 3 --evc 1 -1 0 --tnullmin 8 --tnullmax 12 --nkeep 3 --o IAPS
--nsearch 10000
However, the durations of some NULL events were more than 12 sec and the
last NULL events were more than 30 sec.
Did I use optseq2 in the right way? How could I fix it?
Thanks in advance & Best regards,
Feng Zhou
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Message: 4
Date: Sat, 9 Jul 2016 12:32:42 +0100
From: Kaiming Yin <yinkaiming6...@gmail.com>
Subject: [Freesurfer] Cerebral volume without ventricles
To: FreeSurfer Mailing List <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<caeooxg0uyz9qt3wzib7++zkyqoryzfy_uxk-5lztph5myuo...@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Dear FS experts,
Could I ask which value in the aseg.stats file represent the whole cerebral
volume without ventricles?
Thanks,
Kaiming
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Message: 5
Thanks, you gave me the clue I needed to better understand my problem.
I figured it out. When running "which matlab” it did not give me an error. It
just went to the next line. I did find out that matlab was not in my path, I guess
this means that the terminal window did not have access to the scripts in the matlab
program (bin)? To remedy this, I added matlab to my path by going to my applications
(where the matlab application was) I opened the application folder by right clicking
on it and then selecting “Show Package Contents” Form here I found the address for
the “bin” file (by dragging it into my terminal window). I then entered this line of
code into my .profile file so it would add this path each time I opened terminal:
PATH=$PATH\:/Applications/MATLAB_R2015a.app/bin
When I examined the PATH by entering $PATH this showed it was now in my PATH.
/Applications/freesurfer/mni/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Applications/MATLAB_R2015a.app/bin
Now when i run the “which matlab” command i get the address for the folder.
/Applications/MATLAB_R2015a.app/bin/matlab
However, I then had a second problem with my license. I had been running
everything as sudo (super user) so when I tried to run the command again, it
said my matlab license did not match my username. I realized I needed to move
the project folder outside my application folder so it could write to the file
using my username and not under sudo.
Happily it now all works. I don’t know if this is the right way to do things,
but it works now. Let me know if I should have done something different.
Hopefully, this can be of some help to others.
Erik
Date: Sat, 9 Jul 2016 11:27:32 -0400
From: Douglas Greve <gr...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] FSFAST error: ERROR: fast_selxavg3()
failed\n
To: Erik Jahner <erik.jah...@icloud.com>, free surfer
<freesurfer@nmr.mgh.harvard.edu>
Message-ID: <db1bb81e-4481-03db-b261-af94a8648...@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"
what do you mean nothing happens? After you hit the return key, it
should either give you the path to the command or it should say Command
not found.
doug
ps. Please remember to post to the list and not to us individually
On 7/8/16 7:16 PM, Erik Jahner wrote:
When I type "which matlab? in the command window, nothing happens. My
$PATH structure is a s follows:
echo $PATH
/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/usr/local/fsl/bin:/Applications/freesurfer/mni/bin:/opt/local/bin:/opt/local/sbin:/opt/local/bin:/opt/local/sbin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin
Sorry if my response seems na?ve, I?am new to running command
lines although I?m trying learn.
Erik
Message: 6
Date: Fri, 8 Jul 2016 14:30:43 -0400
From: Douglas N Greve <gr...@nmr.mgh.harvard.edu
<mailto:gr...@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] FSFAST error: ERROR: fast_selxavg3()
failed\n
To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>
Message-ID: <577ff153.1080...@nmr.mgh.harvard.edu
<mailto:577ff153.1080...@nmr.mgh.harvard.edu>>
Content-Type: text/plain; charset=windows-1252; format=flowed
Is matlab in your path? What happens if you type
which matlab
at the command line?
On 07/08/2016 12:34 AM, ERIK JAHNER wrote:
Hello FreeSurfer Developers,
This is Erik Jahner, I?m attempting to complete the final step in the
tutorial concerning FSFast Functional connectivity walkthrough
(http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough
),
but for I get the following error when I run the following command:
selxavg3-sess -s subj439rest -a fc.lpccseed.surf.lh
Mon Jul 4 11:01:41 PDT 2016
rawfunc2surf-sess completed
----------------------------------------
Started at Mon Jul 4 11:01:40 PDT 2016
Ended at Mon Jul 4 11:01:41 PDT 2016
preproc-sess done
-------------------------------------------
/Applications/freesurfer/LagStructure/subj439rest
Mon Jul 4 11:01:41 PDT 2016
anadir =
/Applications/freesurfer/LagStructure/subj439rest/rest/fc.lpccseed.surf.lh
DoGLMFit = 1
DoContrasts = 1
UpdateNeeded = 1
------------------------------------------
------- matlab output --------------------
matlab: Command not found.
------------------------------------------
*ERROR: fast_selxavg3() failed\n*
I've searched the list and no similar errors have been reported. I
have tried to reinstall MATLAB; I have tried following the
instructions to install the runtime environment; I have tried redoing
all analysis from scratch. I have noticed that STEP 5 does not work
unless I change the -cfg from ?L_Posteriorcingulate.config?
to ?mean.L_Posteriorcingulate.config?. I don?t think this is the
problem, but I thought I would point it out.
My session directory is ?subj439rest?
Instead of titling the sub directory ?bold?, I titled it ?rest?
1) FreeSurfer version: freesurfer-Darwin-lion-stable-pub-v5.3.0
2) Platform: OSX Yousemite
3) uname -a: Darwin ERIKs-iMac.local 15.5.0 Darwin Kernel Version
15.5.0: Tue Apr 19 18:36:36 PDT 2016;
root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64
4) selxavg3-sess-rest-fc.lpccseed.surf.lh-160704110140.log: see attached
___________________________________________________
Here are the command lines I put in for steps 4-8, incase this is of
some use:
STEP 4
fcseed-config-segid 1010 -fcname L_Posteriorcingulate.dat -fsd rest
-mean-cfg mean.L_Posteriorcingulate.config
STEP 5
fcseed-sess-s subj439rest -cfg mean.L_Posteriorcingulate.config
STEP 6
* fcseed-config -wm -fcname wm.dat -fsd rest -pca -cfg wm.config
* fcseed-sess -s subj439rest -cfg wm.config
* fcseed-config -vcsf -fcname vcsf.dat -fsd rest -pca -cfg vcsf.config
* fcseed-sess -s subj439rest -cfg vcsf.config
STEP7
mkanalysis-sess-analysis fc.lpccseed.surf.lh -surface fsaverage lh
-fwhm 5 -notask-taskreg L_Posteriorcingulate.dat 1 -nuisreg vcsf.dat 5
-nuisreg wm.dat 5 -mcextreg-polyfit 5 -nskip 4 -fsd rest -TR 2 -per-run
STEP 8
selxavg3-sess-s subj439rest -a fc.lpccseed.surf.lh
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