Hi Bruce,

Thanks for the reply. The talairach.xfm file generated by the palarellizing machine is empty; it looks as follows:

Talairach.xfm file:

MNI Transform File

% avi2talxfm

Transform_Type = Linear;

Linear_Transform =

However, the talaraich.xfm file generated by the non-paralellizing machine is the following:

MNI Transform File

% avi2talxfm

Transform_Type = Linear;

Linear_Transform =

1.088816 -0.036409 -0.059575 1.880753

0.047590 1.030018 0.245325 -4.493217

0.029937 -0.211744 1.231518 94.663368;

Anna

On Thu, Oct 22, 2015 at 6:00 PM, <freesurfer-request@nmr.mgh.harvard.edu> wrote:

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When replying, please edit your Subject line so it is more specific
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Today's Topics:

1. normalization of hippocampal volume (geschwind2013)
2. Postdoctoral Opportunity: Multimodal MRI registration and
analysis (Frederic Andersson)
3. Re: A mixed effect model approach in within subject dataset
{Disarmed} {Disarmed} (jorge luis)
4. Re: Sulcal depth units (Bruce Fischl)
5. Re: mris_expand - problem reading thickness file? (Bruce Fischl)
6. Re: How to compute the measures on the average brain?
(Bruce Fischl)
7. Re: Talairach_afd error (Bruce Fischl)
8. Re: How to compute the measures on the average brain?
(Douglas N Greve)
9. Re: normalization of hippocampal volume (Douglas N Greve)
10. Re: per analysis with covariates (Douglas N Greve)

----------------------------------------------------------------------

Message: 1
Date: Thu, 22 Oct 2015 17:18:21 +0900
From: geschwind2013 <neurofree@gmail.com>
Subject: [Freesurfer] normalization of hippocampal volume
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <27AF7ECA-E1B4-4337-BB2C-4CBE4109F342@gmail.com>
Content-Type: text/plain; charset=euc-kr

Hi, FS Experts,

I?m using version 5.3 and have performed hippo-subfields analysis.

To perform the statistics, shall I get the normalized volumes of each hippo-subfields?
or just to do correction for ICV is enough ?

thanks..

Hyon

------------------------------

Message: 2
Date: Thu, 22 Oct 2015 15:30:14 +0200
From: Frederic Andersson <andersson@univ-tours.fr>
Subject: [Freesurfer] Postdoctoral Opportunity: Multimodal MRI
registration and analysis
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <6E3A85F5-C942-49D0-BBE0-4C51C4E8EC27@univ-tours.fr>
Content-Type: text/plain; charset="utf-8"

Postdoctoral Opportunity: Multimodal MRI registration and analysis

Context and methodology
This postdoctoral position will focus on the registration of ex-vivo onto in-vivo MR data. Based on some recent advances extending the combined volume and surface registration, efficient approaches can be provided for dealing with this issue. However, these methods need to be validated and several open theoretical questions are related to this problem and will be investigated during this postdoctoral work. The theoretical results obtained will be tested and used on real human data in a larger framework aiming at tractography validation (French National Research Agency Grant ANR 2014, collaborative study Inserm U930, Universit? de Tours, Neurospin and Martinos Center).

Applicant profile
Candidates should have a strong background in image registration and MR imaging, a good publication record, and strong experience in c++ and matlab coding. Proficiency in English is required, as well as scientific writing skills.
Applicants should send a CV, including list of publications and a description of previous research experience, as well as the names and emails of two academic referees to: Clovis Tauber (clovis.tauber@univ-tours.fr <mailto:clovis.tauber@univ-tours.fr>) and Christophe Destrieux (christophe.destrieux@univtours.fr <mailto:christophe.destrieux@univtours.fr> )

Conditions
Starting date: January 2016 (adjustable)
Contract: 2 years
Location: Imaging and Brain unit, INSERM U930, Tours.
Salary: related to experience

References
G.M. Postelnicu, L. Z?llei, B. Fischl: Combined Volumetric and Surface Registration, IEEE Transactions on Medical Imaging 28 (4), April 2009, p. 508--522
Zemmoura I, Serres B, Andersson F, Barrantin L, Tauber C, Filipiak I, Cottier JP, Venturini G and Destrieux C 2014 FIBRASCAN: a novel method for 3D white matter tract reconstruction in MR space from cadaveric dissection Neuroimage 103 106?118
Serres B, Zemmoura I, Andersson F, Tauber C, Destrieux C and Venturini G 2013 Brain Virtual Dissection and White Matter 3D Visualization Stud. Health Technol. Inform. 184 392--396
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Message: 3
Date: Thu, 22 Oct 2015 13:45:28 +0000 (UTC)
From: jorge luis <jbernal0019@yahoo.es>
Subject: Re: [Freesurfer] A mixed effect model approach in within
subject dataset {Disarmed} {Disarmed}
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Cc: "pablonajt@hotmail.com" <pablonajt@hotmail.com>
Message-ID:
<1841220171.2266406.1445521528699.JavaMail.yahoo@mail.yahoo.com>
Content-Type: text/plain; charset="utf-8"

Hi Pablo

If you havethoroughly checked that everything is properly setup so that theordering of the design matrix's rows is in proper correspondence withthe ordering of the image data matrix's rows and it is also in propercorrespondence with the ordering of the entries in vector ni (eachentry of this vector has the number of subjects belonging to the samefamily) and the design matrix has enough covariates to describe yourdata then the analysis should be correct.

Bear in mind thatyou are not analyzing longitudinal data for which a proper imageregistration pipeline exists in Freesurfer and there is a clearwithin-subject correlation between cortical thickness values acrosstime points at the same surface vertex. Instead you are analyzingfamily data in which you are trying to model vertex-wise correlationsacross different subjects. Although in principle there should bewithin-family correlation the image registration procedure (and imageprocessing pipeline in general) as well as individual variation couldhave introduced a lot of noise in your data making the vertex-wisewithin-family correlations rather weak. This makes it hard for theLME estimation procedure to converge and give precise parameterestimates.

Best-Jorge

De: pablo najt <pablonajt@hotmail.com>
Para: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Enviado: Jueves 22 de octubre de 2015 1:15
Asunto: Re: [Freesurfer] A mixed effect model approach in within subject dataset {Disarmed} {Disarmed}

Hello again,I have now also run the model with 2 random effects and it is definitively worst. The final line says:Algorithm did not converge at 79.5859 percent of the total number of locations.
Any suggestion if I should trust in the model with 1 random effect? I know you Martin had doubts, so I am wondering what Jorge thinks of it.ThanksPablo

To: freesurfer@nmr.mgh.harvard.edu
From: mreuter@nmr.mgh.harvard.edu
Date: Wed, 21 Oct 2015 08:55:04 -0400
Subject: Re: [Freesurfer] A mixed effect model approach in within subject dataset {Disarmed} {Disarmed}

Hi Pablo,

23% still seems a lot, but may be OK (maybe Jorge can comment on that)?

If you want to do a model comparison (2 random vs 1) take a look at the wiki. It describes how to do that.

Best, Martin

On 10/21/2015 01:19 AM, pablo najt wrote:

 Martin, Doing the changes in the matrix allowed me to run the command. The command with just one random effect for the intercept term give me the following output:
Aproximate percentage of fitted locations: 100% Summary: Algorithm did not converge at 23.407 percent of the total number of locations. Total elapsed time is 116.2184 minutes.

Is this ok? Is there anything I should check? Should I also try two random effects as well? Thank you Pablo
To: freesurfer@nmr.mgh.harvard.edu
From: mreuter@nmr.mgh.harvard.edu
Date: Tue, 20 Oct 2015 09:06:53 -0400
Subject: Re: [Freesurfer] A mixed effect model approach in within subject dataset {Disarmed} {Disarmed}

Hi Pablo,

the zero columns could be outside the cortex and then this would be fine. Do
min(sum(lhY(:,lhcortex)))
if you get 0 you have at least one location where the column is all zero (as we should not have any negative values, you can test that with min(lhY(:))
Now even if you still have a column of 0 , then that vertex is problematic, but who cares about a single vertex. If you do a region approach, it will be part of a region anyway. so you should check how often you get 0 columns (inside cortex).

About your M: I would subtract 1 from gender (to have 0 and 1)
Also you only need 2 columns for the groups: keep only column 3 and 4. A HC is someone who has 0 in both.

Best, Martin

On 10/20/2015 04:37 AM, pablo najt wrote:

 Dear ?FS experts, I am following up on an issue I am having when trying to run linear mixed effects model. I keep getting 'Algorithm did not converge'. So far I have changed the preprocessing steps following literally from the wiki as in message below. Also I tried to use only one random effect for the intercept. Also I have checked that?sum of vectors of (ni) is equal to the number of rows in (X).
As none of the above worked I started to have concerns about the dimensions of my lh.thickness_sm10.mgh. ?When I load in matlab in working space says 'too many variables'. Is this ok? ? ?

Also, when I open 'lhY' variable it shows a column of Zeros every nine columns as below. Is this alright?
? ?

Perhaps this is fine but I would like to check on anything that is creating this problem. For matrix 'M' I created a matlab script that loads a matrix with intercept (all ones), HC (ones to HC otherwise zero), U_PT (relatives of patients ones otherwise zero), PT (patients one otherwise zero), gender, age (see below). The three columns for groups do not match?the qdec.table.dat which have only one column for groups (HC, U_PT, PT). However the?order of the rows is identical in M and qdec.table.dat ? ?

?Please let me know if this should be set differently. Thank you Pablo

To: freesurfer@nmr.mgh.harvard.edu
From: mreuter@nmr.mgh.harvard.edu
Date: Mon, 19 Oct 2015 09:00:57 -0400
Subject: Re: [Freesurfer] A mixed effect model approach in within subject dataset {Disarmed}

Hi Pablo,

since you did not run this through the longitudinal stream, you won't have a base ( or subject-template), also you won't have <tpid>.long.<base> directories, so the first command should fail. For that you simply replace the --qdec-long with --qdec and use the same table. Should work. The second command is fine (it just smoothes the thickness stack).

Best, Martin

On 10/19/2015 06:51 AM, pablo najt wrote:

 Hi Jorge and FS experts, I have run again the analysis and still get the convergence problem. I am assuming the issue has to do with the preprocessing steps, as I had doubts on how to follow from the instructions if I am not using qdec and have a cross sectional design.
Instructions on lme in the wiki for preprocessing specify the following:
mris_preproc --qdec-long qdec.table.dat --target study_average --hemi lh --meas thickness --out lh.thickness.mgh mri_surf2surf --hemi lh --s study_average --sval lh.thickness.mgh --tval lh.thickness_sm10.mgh --fwhm-trg 10 --cortex --noreshape My data -as I explained below- is cross section but I want to treat it as longitudinal as I want to analyse subjects belonging to the same family.? Here is my 2 main questions:? 1) for preprocessing should I follow instructions as it would be longitudinal data? 2) Although my design does not allow using qdec (3 groups) do I still create a qdec table and follow literally the two instructions above ? Thank you Pablo
____________________________________________________________________________________________________________________________________

Date: Fri, 16 Oct 2015 16:24:36 +0000
From: jbernal0019@yahoo.es
To: freesurfer@nmr.mgh.harvard.edu
CC: pablonajt@hotmail.com
Subject: Re: [Freesurfer] A mixed effect model approach in within subject dataset {Disarmed}

Hi Pablo
Yes, too many locations at which the estimation algorithm didn't converge is problematic. That might mean that having two random effects is not appropriate for your data. You should try to run the command with just a single random effect for the intercept term:
lhstats = lme_mass_fit_vw(X, [1], lhY, ni, lhcortex, [], 4);
If the result still have too many non-convergence locations then something might be wrong with the ordering of the design matrix and its correspondence with the ordering of the ni vector or the ordering of the image data etc... You will need to check it thoroughly.
Cheers -Jorge

De: pablo najt <pablonajt@hotmail.com>
Para: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Enviado: Viernes 16 de octubre de 2015 1:43
Asunto: Re: [Freesurfer] A mixed effect model approach in within subject dataset {Disarmed}

 Thanks you for the replies. Jorge and FS experts, I have run the analysis and first double checked that the sum of vectors of (ni) is equal to the number of rows in (X). Both are 140 which is the number of my subjects. The analysis gave the following 'error'(?) below: I looked up a previous thread coming across this. At that case you recommended Would you recommend this afain>

Aproximate percentage of fitted locations: 100% Warning: matlabpool will be removed in a future release. To query the size of an already started parallel pool, query the 'NumWorkers' property of the pool. To check if a pool is already started use 'isempty(gcp('nocreate'))'.? Warning: matlabpool will be removed in a future release. To shutdown a parallel pool use 'delete(gcp('nocreate'))' instead.? Parallel pool using the 'local' profile is shutting down. ?? Summary: Algorithm did not converge at 90.0637 percent of the total number of locations. Total elapsed time is 550.1023 minutes.

Also almost all the time the screen showed the following message:
144114: Algorithm did not converge. Initial and final likelihoods: -38.3408-1.5708i,-241.4153-1.570796i. Location 144113: Algorithm did not converge. Initial and final likelihoods: -5.5424-1.5708i, -133.8004-1.570796i. Location 144112: Algorithm did not converge. Initial and final likelihoods: -7.7571-1.5708i, -319.1378-1.570796i. Location 144111: Algorithm did not converge. Initial and final likelihoods: -16.8597-1.5708i, 0.74448. Aproximate percentage of fitted locations: 100%

So my two questions are: 1. Is this problematic? 2. Are there any fixes to this issue? Thank you, Pablo
Date: Thu, 15 Oct 2015 13:38:22 +0000
From: jbernal0019@yahoo.es
To: freesurfer@nmr.mgh.harvard.edu
CC: pablonajt@hotmail.com
Subject: Re: [Freesurfer] A mixed effect model approach in within subject dataset {Disarmed}

Hi Pablo
The error you are getting is because in your Matlab setup you can only request a maximum of 4 matlab parallel workers and by default lme requests 8. So you just need to modify your command like this:
lhstats = lme_mass_fit_vw(X, [1 2], lhY, ni, lhcortex, [], 4);
Please make sure that sum(ni) and length(X) give the same value before running the above command.
Cheers -Jorge

De: pablo najt <pablonajt@hotmail.com>
Para: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Enviado: Jueves 15 de octubre de 2015 7:18
Asunto: Re: [Freesurfer] A mixed effect model approach in within subject dataset {Disarmed}

 Thank you Martin. I am trying to run the following command line and get the error below. Would you have a suggestion to overcome this issue? Just in case I am also including a snapshot of my loaded variables at the bottom. Many thanks, Pablo >> lhstats = lme_mass_fit_vw(X, [1 2], lhY, ni, lhcortex);

Warning: matlabpool will be removed in a future release.

To query the size of an already started parallel pool, query the 'NumWorkers'

property of the pool.

To check if a pool is already started use 'isempty(gcp('nocreate'))'.?

Warning: matlabpool will be removed in a future release.

To query the size of an already started parallel pool, query the 'NumWorkers'

property of the pool.

To check if a pool is already started use 'isempty(gcp('nocreate'))'.?

Warning: matlabpool will be removed in a future release.

Use parpool instead.?

Starting matlabpool using the 'local' profile ...?

Error using matlabpool (line 148)

Failed to start a parallel pool. (For information in addition to the causing error,

validate the profile 'local' in the Cluster Profile Manager.)

Error in lme_mass_fit (line 128)

? ? ? ? matlabpool(prs);

Error in lme_mass_fit_vw (line 73)

[stats1,st1] = lme_mass_fit(X,[],Xrows,Zcols,Y,ni,prs,e);

Caused by:

? ? Error using parallel.internal.pool.InteractiveClient/start (line 330)

? ? Failed to start pool.

? ? ? ? Error using parallel.Job/submit (line 304)

? ? ? ? You requested a minimum of 8 workers, but the cluster "local" has the

? ? ? ? NumWorkers property set to allow a maximum of 4 workers. To run a

? ? ? ? communicating job on more workers than this (up to a maximum of 512 for the

? ? ? ? Local cluster), increase the value of the NumWorkers property for the

? ? ? ? cluster. The default value of NumWorkers for a Local cluster is the number of

? ? ? ? cores on the local machine.

? ???

To: freesurfer@nmr.mgh.harvard.edu
From: mreuter@nmr.mgh.harvard.edu
Date: Wed, 14 Oct 2015 10:54:41 -0400
Subject: Re: [Freesurfer] A mixed effect model approach in within subject dataset {Disarmed}

Hi Pablo,

you should run something like this to get the ni:

[M,Y,ni] = sortData(M,1,Y,sID); # (sorts the data) see
https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels

hope that helps, Martin

On 10/14/2015 10:43 AM, pablo najt wrote:

 Dear FS experts. I have query about a relating to a previous email (below).?I am aiming to run a LME analysis on cross-sectional data from different families and have variable 'family' (number of families) as my NI vector.? My design has three groups and therefore I am not able to use qdec. I am running the matlab commands below and finding some difficulty would really appreciate if you could help out. Thanks Pablo
Start analysis as follows:
1-Read your label eg.:
lhcortex = fs_read_label('freesurfer/subjects/fsaverage/label/lh.cortex.label');
2-Read the data file eg.:
[lhY, lhmri] = fs_read_Y('lh.thickness.mgh');?

%---------------------I input the concatenated .mgh image from preproc and mris_surf2surf-----------------------------------------------------------------------%

3-Fit a vertex-wise lme model with random effects.:
lhstats = lme_mass_fit_vw(X, [1 2], lhY, ni, lhcortex);

Here I am getting the following problems: %-------------------- If I use number of families as my ni get the following------------------------------------------------------------------------------------------------%

lhstats = lme_mass_fit_vw(X, [1 2], lhY, 82, lhcortex);

Error using lme_mass_fit (line 108)

The total number of measurements, indicated by sum(ni), mustbe the same as the number of rows of the design

matrix X

Error in lme_mass_fit_vw (line 73)

[stats1,st1] = lme_mass_fit(X,[],Xrows,Zcols,Y,ni,prs,e);

My matrix is organised in "family", "group", Sex" and "age" columns".
? ?
4-Perform vertex-wise inference eg.: CM.C = [your contrast matrix]; F_lhstats = lme_mass_F(lhstats, CM); 5-Save results eg.:? fs_write_fstats(F_lhstats, lhmri,' sig.mgh', 'sig');??

Date: Thu, 10 Sep 2015 13:44:36 +0000 From: jbernal0019@yahoo.es To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] A mixed effect model approach in within subject dataset Hi Pablo I think you can use LME to analyze your data by ordering the rows of your design matrix appropriately. You can consider all subjects belonging to the same family as if they were a single subject in a longitudinal analysis. You can put in your design matrix all subjects belonging to family1 first, then all subjects belonging to family 2 and so on. Then the 'ni' required by lme_mass_fit_vw is a vector with the number of subjects in each family as its entries (ordered according to your design matrix). So the length of the 'ni' vector is equal to the number of different families in your data. Now you can go further and additionally order the rows of your design matrix within each family by age. This will allow you to test the effect of age within family. When choosing the random effects for your statistical model remember that a random effect can only be the intercept term or any covariate that varies within family. For example you can compare a model with a single random effect for the intercept term against the same model but considering both the intercept term and age as random effects. Hope that helps Cheers -Jorge
De: pablo najt <pablonajt@hotmail.com> Para: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> Enviado: Jueves 10 de septiembre de 2015 8:07 Asunto: [Freesurfer] A mixed effect model approach in within subject dataset  Dear Freesurfer users, I wanted to enquire if anyone had successfully been able to implement Bernal's Linear Mixed Effects (LME) Models in cross-section dataset *not longitudinal* (please see previous thread below). ?I am willing to perform a LME (3 groups (HC, PT and Unaffected_relatives) and 3 covariates (sex, age, and family) with "family" variable been a within-subject factor. LME?will allow?to control for the non-independence of data contributed by patients and relatives from the same families. Thanks in advance! Pablo From: michaelnotter@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Date: Wed, 19 Feb 2014 13:10:09 +0100 Subject: [Freesurfer] Analysis of structural data acquired from multiple sites by using a mixed effect model approach  Hi everybody, I want to compare the surface data of 3 groups (GroupA, GroupB and Controlls) but have the problem that they were acquired from 4 different scanner sites. As I can see it, there are three ways how I could tackle this problem: 1. I could use mri_glmfit and create a qdec table / fsgd-file with 12 classes: Class GroupA_site1; Class GroupA_site2,... And then use the contrasts [0.25 0.25 0.25 0.25 0 0 0 0 -0.25 -0.25 -0.25 -0.25] to compare GroupA to the Controlls. My Problem with this approach is, that the sites don't contribute the same amount of subjects to the analysis. I'm not sure if this could be handled by simply using a weighted contrast. Meaning, if Site1 and Site2 had twice as many subjects than Site3 and Site4, I could modify the contrast to [0.33 0.33 0.17 0.17 0 0 0 0 -0.33 -0.33 -0.17 -0.17]. 2. I could create dummy variables to account for the variability between sites. In this case, I only need to specify 3 classes (Class GroupA; Class Gro!
upB; Cla
ss Controlls) in my fsgd-file. And I use a design matrix that has 4 dummy variables at the end, which specify to which site a subject belongs. This approach might work, but I'm not confident that it is the right one. 3. I could use a mixed effect model approach and specify site as a random effect. If I understand it correctly, the mixed effect model approach would be the best one, as it accounts for the variability within sites. Is that correct or are there other issues/better approaches? I tried to implement a mixed effect model by using Bernal's Linear Mixed Effects (LME) Models (http://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels) but run into some problems. I'm not sure if LME can only be applied on longitudinal data or if my implementation is wrong. I have a design matrix X that specifies the characteristics of each subject per row as follows: Intercept?? GroupA?? GroupB?? Controll?? Age?? IQ?? Site1?? Site2?? Site3?? Site4 1? 1? 0? 0? 11.1? 99?? 0 0 1 0 1? 0? 1? 0? 11.1? 101? 0 0 1 0 1? 1? 0? 0? 11.4? 95?? 1 0 0 0 1? 0? 0? 1? 12.4? 100? 1 0 0 0 ... As I have no repeated measures, 'ni' is just a vector with length X containing '1's. If I do now the vertex-wise linear mixed-effects estimation, I get the following output: >> stats = lme_mass_fit_vw(X,[7 8 9 10],Y,ni,lhcortex); Starting matlabpool using the 'local' profile ... connected to 8 workers. ? Starting model fitting at each location ... ? Location 24994: Index exceeds matrix dimensions. Location 24994: Algorithm did not converge. Initial and final likelihoods: -10000000000, -10000000000. Location 62484: Index exceeds matrix dimensions. Location 62484: Algorithm did not converge. Initial and final likelihoods: -10000000000, -10000000000. ... I've checked the matrix dimensions of X, Y, ni and lhcortex and compared them to the LME mass_univariate example stored in ADNI_Long_50sMCI_vs_50cMCI.mat but couldn't find any divergence. Has anybody encountered similar problems? Is my approach of s!
pecifyin
g 'ni' as a vector of'1's even legitimate? Thanks, Michael _______________________________________________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. _______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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--
Martin Reuter, PhD
Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
Web : 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.
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in 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.

_______________________________________________ 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

--
Martin Reuter, PhD
Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
Web : 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

--
Martin Reuter, PhD
Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
Web : 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

--
Martin Reuter, PhD
Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
Web : http://reuter.mit.edu
_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferThe information in this e-mail is intended only for the person to whom it isaddressed. If you believe this e-mail was sent to you in error and the e-mailcontains patient information, please contact the Partners Compliance HelpLine athttp://www.partners.org/complianceline . If the e-mail was sent to you in errorbut does not contain patient information, please contact the sender and properlydispose of the e-mail.
_______________________________________________
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
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------------------------------

Message: 4
Date: Thu, 22 Oct 2015 10:58:55 -0400 (EDT)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Sulcal depth units
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<alpine.LRH.2.20.1510221058360.3848@gate.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=US-ASCII; format=flowed

Hi Simon

they are originally mm, but I believe we z-score normalize them so that
the sulc file is 0 mean and unit variance.

cheers
Bruce
On Wed, 21 Oct 2015, Simon
Vandekar wrote:

> Dear Freesurfer experts,
>
> I am reading the manuscript "Cortical Surface-Based Analysis II: Inflation, Flattening, and a Surface-Based Coordinate System" by Fischl, Sereno, and Dale (1999) where the estimation of sulcal depth is described on page 199, however from the description I am still unsure of the exact units of sulcal depth.
> Are the units for sulcal depth in mm or are they in arbitrary units?
>
> Thanks in advance,
> Simon
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>

------------------------------

Message: 5
Date: Thu, 22 Oct 2015 11:05:06 -0400 (EDT)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mris_expand - problem reading thickness
file?
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<alpine.LRH.2.20.1510221104450.3848@gate.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

Hi Alex

if you upload the subject that is causing this problem I'll take a look.
What version are you running and what OS?

cheers
Bruce
On Thu, 22 Oct 2015, Alex Puckett
wrote:

>
> Hello!
>
>
> I'm having trouble with mris_expand using the -thickness flag.??If I expand
> by a fixed distance instead of % thickness?then mris_expand works no problem
> -??the program seems to be hanging up when?reading the thickness file. Has
> anyone else?experienced?this?
>
>
> The command I'm running (from the surf folder)?is:
>
> mris_expand -thickness lh.white 0.5 lh.expandWhiteThick0p5
>
> The output from this is:
> "?using distance as a % of thickness
> expanding surface lh.white by 50.0% of thickness and writing it to
> lh.expandWhiteThick0p5
> reading thickness..."
>
> And then...nothing! Watching the CPU usage it appears that resources are
> used for about 10 -12 minutes and then drops to 0 and just sits there for as
> long as I'll let it (>4 days)?- no error.
>
> Also, the thickness files do not appear to be corrupt. I can overlay the
> thickness data onto a surface no problem.?
>
> Any help would be appreciated.
>
> Cheers,
>
> Alex
>
> ---------------------------------------------------------------------
>
> FREESURFER_HOME: /usr/local/freesurfer
>
> Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
>
> RedHat release: CentOS Linux release 7.1.1503 (Core)?
>
> Kernel info: Linux 3.10.0-229.1.2.el7.x86_64 x86_64
>
> ---------------------------------------------------------------------
>
>
>
>
>
>
>
>
>
> ?

------------------------------

Message: 6
Date: Thu, 22 Oct 2015 11:08:04 -0400 (EDT)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] How to compute the measures on the average
brain?
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<alpine.LRH.2.20.1510221107490.3848@gate.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"

Hi Mathieu

I don't see any reason we wouldn't continue to support it
Bruce
On Thu, 22 Oct
2015, Mathieu Dubois wrote:

> Hi again,
>
> Another advantage of using qcache in my case is that the file names are
> automatically generated and therefore standard.
>
> Is there any risk (particularly for future compatibility) in using
> qcache? Did anyone had some problem with it?
>
> Thanks in advance,
> Mathieu
>
> Le 21/10/2015 18:07, Mathieu Dubois a ?crit :
>> Hi Doug,
>>
>> Thanks for your answer.
>>
>> If I understand correctly, the tutorial describes the use of
>> mris_preproc with a group description file. If the data has not been
>> cached, it will compute them and stack all the results in a big file
>> (will it write individual files?) . Of course if the data has been
>> cached, it will only stack them (this probably result in more disk usage
>> but that's OK).
>>
>> I don't plan to use FreeSurfer's linear model for group analysis (my
>> goal is to use those data in machine learning algorithms) but other
>> people at the institute I work for may be interested in that. I think
>> it's more convenient to have one file per subject (so I can group them
>> in a more flexible way).
>>
>> So I guess I can always run recon-all for each subject with -qcache (I
>> have read that is safe to do so) in order to generate the data for each
>> subject (this can easily be distributed across a cluster and compute
>> several measures). I can then load the data for each subject and people
>> interested into running FreeSurfer group analysis can also use them. Is
>> it correct?
>>
>> My only concern is: will -qcache be supported in future versions of
>> FreeSurfer? Couldn't some part of it (like the resampling on the average
>> subject but no the smoothing) be integrated into -all?
>>
>> Mathieu
>>
>> Le 21/10/2015 16:37, Douglas Greve a ?crit :
>>> Hi Mathieu, look at the group analysis tutorial on our wiki. Basically,
>>> you will run mris_preproc, mri_surf2surf to smooth, then mri_glmfit to
>>> do the group analysis, then mri_glmfit-sim to do the correction for
>>> multiple comparisons.
>>> doug
>>>
>>> On 10/21/15 10:15 AM, Mathieu Dubois wrote:
>>>> Hi,
>>>>
>>>> I'm a beginner with freesurfer so I apologize if it's a trivial question.
>>>>
>>>> I recently run recon-all with the -all on many subjects. As far as I can
>>>> say, all the steps worked. However, the measures on the average brain
>>>> (output of mris_preproc and friends) were not computed.
>>>>
>>>> A colleague told me that he usually re-run recon-all with the -qcache
>>>> flag to compute those. This seems to work but I don't understand if it
>>>> is the recommended way to run mris_preproc and why it is not included
>>>> with -all. Is it possible to get those measures in one call to recon-all?
>>>>
>>>> I don't think that the issue comes from the data (e.g. that the failing
>>>> of a step stops some branch of the pipeline) because it seems to run
>>>> correctly with -qcache.
>>>>
>>>> I haven't found any help on -qcache and the help of recon-all doesn't
>>>> mention mris_preproc or mri_surf2surf.
>>>>
>>>> Thanks in advance,
>>>> Mathieu
>>>> _______________________________________________
>>>> 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
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>

------------------------------

Message: 7
Date: Thu, 22 Oct 2015 11:39:22 -0400 (EDT)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Talairach_afd error
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<alpine.LRH.2.20.1510221138530.19286@gate.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

Hi Anna

are the talairach.xfm files generated by the two machines similar?

Bruce
On Wed,
21 Oct 2015, Anna I. Garcia Diaz wrote:

> Dear all,
> I am having problems running the recon-all process. The error log is attached to this e-mail.?
>
> This error appears only when I run recon-all in a machine able to parallelize preprocesses, however, if I use the same
> reconstructed oriented image in a machine sent as a normal job directly to the terminal, the preprocess runs without
> any errors and the output looks correct. I have tried to use the -notal-check flag as the error log suggests, but it
> fails anyway.?
>
> Since our team is working in a longitudinal study, and the images from the other time points have been preprocessed
> with the parallelizing machine, we are concerned that using the non-parallelizing machine could add significant
> methodological variabilities to our studies, and we would rather be consistent with the previous procedures.?
>
> Do you have any comments or further suggestions on how we might be able to fix this error?
>
> Thanks in advance for your time and help
> Anna Garcia
>
>

------------------------------

Message: 8
Date: Thu, 22 Oct 2015 11:42:07 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] How to compute the measures on the average
brain?
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <562903CF.6030403@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed

No, we will continue to support it

On 10/21/2015 11:13 PM, Mathieu Dubois wrote:
> Hi again,
>
> Another advantage of using qcache in my case is that the file names are
> automatically generated and therefore standard.
>
> Is there any risk (particularly for future compatibility) in using
> qcache? Did anyone had some problem with it?
>
> Thanks in advance,
> Mathieu
>
> Le 21/10/2015 18:07, Mathieu Dubois a ?crit :
>> Hi Doug,
>>
>> Thanks for your answer.
>>
>> If I understand correctly, the tutorial describes the use of
>> mris_preproc with a group description file. If the data has not been
>> cached, it will compute them and stack all the results in a big file
>> (will it write individual files?) . Of course if the data has been
>> cached, it will only stack them (this probably result in more disk usage
>> but that's OK).
>>
>> I don't plan to use FreeSurfer's linear model for group analysis (my
>> goal is to use those data in machine learning algorithms) but other
>> people at the institute I work for may be interested in that. I think
>> it's more convenient to have one file per subject (so I can group them
>> in a more flexible way).
>>
>> So I guess I can always run recon-all for each subject with -qcache (I
>> have read that is safe to do so) in order to generate the data for each
>> subject (this can easily be distributed across a cluster and compute
>> several measures). I can then load the data for each subject and people
>> interested into running FreeSurfer group analysis can also use them. Is
>> it correct?
>>
>> My only concern is: will -qcache be supported in future versions of
>> FreeSurfer? Couldn't some part of it (like the resampling on the average
>> subject but no the smoothing) be integrated into -all?
>>
>> Mathieu
>>
>> Le 21/10/2015 16:37, Douglas Greve a ?crit :
>>> Hi Mathieu, look at the group analysis tutorial on our wiki. Basically,
>>> you will run mris_preproc, mri_surf2surf to smooth, then mri_glmfit to
>>> do the group analysis, then mri_glmfit-sim to do the correction for
>>> multiple comparisons.
>>> doug
>>>
>>> On 10/21/15 10:15 AM, Mathieu Dubois wrote:
>>>> Hi,
>>>>
>>>> I'm a beginner with freesurfer so I apologize if it's a trivial question.
>>>>
>>>> I recently run recon-all with the -all on many subjects. As far as I can
>>>> say, all the steps worked. However, the measures on the average brain
>>>> (output of mris_preproc and friends) were not computed.
>>>>
>>>> A colleague told me that he usually re-run recon-all with the -qcache
>>>> flag to compute those. This seems to work but I don't understand if it
>>>> is the recommended way to run mris_preproc and why it is not included
>>>> with -all. Is it possible to get those measures in one call to recon-all?
>>>>
>>>> I don't think that the issue comes from the data (e.g. that the failing
>>>> of a step stops some branch of the pipeline) because it seems to run
>>>> correctly with -qcache.
>>>>
>>>> I haven't found any help on -qcache and the help of recon-all doesn't
>>>> mention mris_preproc or mri_surf2surf.
>>>>
>>>> Thanks in advance,
>>>> Mathieu
>>>> _______________________________________________
>>>> 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
> _______________________________________________
> 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
greve@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/

------------------------------

Message: 9
Date: Thu, 22 Oct 2015 11:48:26 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] normalization of hippocampal volume
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <5629054A.8090200@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=euc-kr

I'm not sure what you mean by either of those options. can you explain?

On 10/22/2015 04:18 AM, geschwind2013 wrote:
> Hi, FS Experts,
>
> I?m using version 5.3 and have performed hippo-subfields analysis.
>
> To perform the statistics, shall I get the normalized volumes of each hippo-subfields?
> or just to do correction for ICV is enough ?
>
> thanks..
>
> Hyon
> _______________________________________________
> 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
greve@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/

------------------------------

Message: 10
Date: Thu, 22 Oct 2015 11:50:10 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] per analysis with covariates
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <562905B2.6070607@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed

what do you mean to control age and gender on both lGI and thickness? If
you have thickness = f(gender,age,lGI), then you control for gender,
age, and lGI on thickness.

On 10/20/2015 06:20 AM, marica.padula@libero.it wrote:
>
> Hi,
>
> I am running a vertex-wise correlation analysis between local gyrification (--
> y) and thickness (--pvr) using as covariates age and gender.
> I want to control for the effect of age and gender both the lGI and the
> thickness values. Does the command does this? Or the effect of the covariates
> is only taken into account for the lGI?
>
> Here my command line:
>
> mri_glmfit --glmdir left --y lh.lGI.mgh --fsgd fsgd_control.txt --pvr lh.
> thickness.mgh --C contrast_control.txt --surface fsaverage lh
>
> And my contrast:
>
> 0 0 0 1 (first 0 for the class, second and third for the 2 covariates).
>
> Thanks,
> Marica
> _______________________________________________
> 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
greve@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

End of Freesurfer Digest, Vol 140, Issue 37
*******************************************