Send Freesurfer mailing list submissions to
        freesurfer@nmr.mgh.harvard.edu

To subscribe or unsubscribe via the World Wide Web, visit
        https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
or, via email, send a message with subject or body 'help' to
        freesurfer-request@nmr.mgh.harvard.edu

You can reach the person managing the list at
        freesurfer-owner@nmr.mgh.harvard.edu

When replying, please edit your Subject line so it is more specific
than "Re: Contents of Freesurfer digest..."


Today's Topics:

   1. mri_parse_sdcmdir splitting a single series into two?
      (Oliver Hinds)
   2. Postdoc Positions for the Adolescent Brain Cognitive
      Development (ABCD) study (Don Hagler)
   3. Re: FreeSurfer pve correction tool (Mohamed Ali Bahri)
   4. Re: A mixed effect model approach in within subject dataset
      {Disarmed} (Martin Reuter)
   5. Re: FreeSurfer pve correction tool (Douglas N Greve)
   6. Understanding the brainstem AtlasMesh file structure      format
      (Jonathan Plasencia)
   7. Re: comparison of 4 groups: mri_glmfit or Qdec? (Sandy Schramm)
   8. Re: Talairach_afd error (Bruce Fischl) (Bruce Fischl)
   9. error finding Matlab (Jason Haberman)


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

Message: 1
Date: Tue, 27 Oct 2015 15:14:25 -0400 (EDT)
From: Oliver Hinds <ohinds@nmr.mgh.harvard.edu>
Subject: [Freesurfer] mri_parse_sdcmdir splitting a single series into
        two?
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
        <alpine.LRH.2.20.1510271455210.6558@gate.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=US-ASCII

Hi,

I'm running into an issue where the slices from one DICOM series are being
parsed by mri_parse_sdcmdir (and mri_info and mri_convert) as two separate
series.

A few example lines from a scan.out:

  6          AR_t.s40.c0  ok   64  64  41   1 <long file name>
  7          AR_t.s40.c0  ok   64  64  23   1 <different long file name>

The scan AR_t.s40.c0 was run as a single series on the scanner, with 64
slices. Inspection of the dicom header shows that the series UID is the
same for the DICOM files in each, except there is an extra string '.0.0.0'
at the end of series UID in the DICOMS that are parsed into the second
series.

Has anyone else experienced this behavior? If so, is there a workaround?

Thanks,
Oliver




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

Message: 2
Date: Tue, 27 Oct 2015 13:41:36 -0700
From: Don Hagler <dhaglerjr@hotmail.com>
Subject: [Freesurfer] Postdoc Positions for the Adolescent Brain
        Cognitive       Development (ABCD) study
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <BLU436-SMTP65024FB31221FBD3A8E848A6220@phx.gbl>
Content-Type: text/plain; charset="us-ascii"

Postdoc Positions for the Adolescent Brain Cognitive Development (ABCD) study



University of California, San Diego



Several funded postdoctoral positions are available in image analysis method development, including automated cortical- and subcortical segmentation, advanced diffusion tractography, and fMRI mapping and time series analysis. We are looking to build a team to help build the next generation of analysis pipelines and visualization tools for a newly funded study to follow 10,000 children with longitudinal structural and functional imaging across 19 sites across the US. The study will use a cross-platform Harmonized Human Connectome Protocol, optimized for quantitative accuracy and consistency of imaging biomarkers across scanners and time. To learn more about the ABCD study, please see http://www.drugabuse.gov/news-events/news-releases/2015/09/nih-launches-landmark-study-substance-use-adolescent-brain-development <http://www.drugabuse.gov/news-events/news-releases/2015/09/nih-launches-landmark-study-substance-use-adolescent-brain-development>.



Requirements: Applicants should have research experience in any of the above fields, with a Ph.D. or equivalent degree. They should be comfortable working in a distributed team environment, and should have a track record of quality scientific publications. Candidates are expected to be experienced in programming with Matlab, Python, and/or <> C/C++. Experience with FreeSurfer, FSL, and the Human Connectome analysis pipelines is strongly preferred.



To formally apply, submit a current CV, a personal statement describing your research experience and interests, and contact information for 2-3 references to abcd@ucsd.edu <mailto:abcd@ucsd.edu>. Or feel free to email Dr. Donald Hagler (dhagler@ucsd.edu <mailto:dhagler@ucsd.edu>) or Anders M. Dale (amdale@ucsd.edu <mailto:amdale@ucsd.edu>) for more information.



The University of California, San Diego is an Equal Opportunity/Affirmative Action Employer advancing inclusive excellence. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, age, protected veteran status, or other protected categories covered by the UC nondiscrimination policy.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20151027/034123ad/attachment-0001.html

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

Message: 3
Date: Tue, 27 Oct 2015 21:47:36 +0100
From: Mohamed Ali Bahri <m.bahri@ulg.ac.be>
Subject: Re: [Freesurfer] FreeSurfer pve correction tool
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <562FE2E8.9050605@ulg.ac.be>
Content-Type: text/plain; charset=windows-1252; format=flowed

Dear Bruce,

Am I missed the answer of Dr. Greve about the following questions?

Is it possible to tell what are the implemented methods for the PET pve correction? and how we can
obtain the corrected 4D (dynamic) PET images (for a voxel-by-voxel modeling)?


Many thanks,

Mohamed



On 26/10/15 14:52, Bruce Fischl wrote:
> oh, then I'll leave it for Doug
> Bruce
> On Mon, 26 Oct 2015, Mohamed Ali Bahri
> wrote:
>
>> Hi Bruce,
>>
>> Yes, for PET analysis.
>>
>> Best,
>>
>> Mohamed
>>
>> On 26/10/15 14:45, Bruce Fischl wrote:
>>> Hi Mohamed
>>>
>>> do you mean for PET analysis or for the recent paper that Rebecca Shafee
>>> wrote on e.g. tissue intensity properties?
>>>
>>> cheers
>>> Bruce
>>>
>>>
>>>
>>> On Mon, 26 Oct 2015, Mohamed Ali Bahri wrote:
>>>
>>>> Is it possible to tell what are the implemented methods? and how we can
>>>> obtain the corrected 4D (dynamic) images (for a voxel-by-voxel modeling)?
>>>>
>>>> Best,
>>>>
>>>> Mohamed
>>>>
>>>> On 26/10/15 13:27, Bruce Fischl wrote:
>>>>> no, sorry, we haven't had time to document it
>>>>> On Mon, 26 Oct 2015,
>>>>> m.bahri@ulg.ac.be wrote:
>>>>>
>>>>>> Dear FreeSurfer Experts,
>>>>>>
>>>>>> Are there any documentation comes out for the pve correction tool implemented in the FreeSurfer V6?
>>>>>>
>>>>>> Many thanks in advance,
>>>>>>
>>>>>> Best,
>>>>>>
>>>>>> Mohamed
>>>>>> _______________________________________________
>>>>>> 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

--
Dr. Mohamed Ali Bahri,
1er Logisticien de Recherche,
Cyclotron Research Centre,
University of Li?ge, Belgium
m.bahri@ulg.ac.be



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

Message: 4
Date: Tue, 27 Oct 2015 17:13:51 -0400
From: Martin Reuter <mreuter@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] A mixed effect model approach in within
        subject dataset {Disarmed}
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <562FE90F.3000909@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"

Hi Pablo,

the sortData function sorts the rows so that entries from the same
subject (in your case same family) are blocked and that within each
block the time variable (2nd parameter specifies which column that is in
your M matrix, in your case the first =1) is increasing.
It is important, when creating your design matrix X, that ordering
agrees with Y. That is guaranteed if you generate X from M (which is
ordered like Y after the sort command).

Best, Martin

On 10/27/2015 01:32 PM, pablo najt wrote:
> Thank you for your input.
> I noticed that if I follow literally all the steps in the wiki, my
> data which is ordered by variable 'family' (instead of subjects, in my
> case is number of members belonging to e.g. family_1) is shuffled.
> This happens after I run the command sortData below. Especially I
> noticed that ni and X do not match sID.
> It would be really helpful to know what is this command doing. I am
> wondering whether my data differs in number of columns or else and
> because of this I end with a shuffled data. Any suggestion or tips to
> figure what could be happening?
> Thanks
> Pablo
>
> [M, Y, ni] = sortData(M,1,Y,sID)
>
> ------------------------------------------------------------------------
> 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
>     <mailto:jbernal0019@yahoo.es> To: freesurfer@nmr.mgh.harvard.edu
>     <mailto: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>
>         <mailto:pablonajt@hotmail.com> *Para:*
>         "freesurfer@nmr.mgh.harvard.edu"
>         <mailto:freesurfer@nmr.mgh.harvard.edu>
>         <freesurfer@nmr.mgh.harvard.edu>
>         <mailto: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
>         <mailto:michaelnotter@hotmail.com> To:
>         freesurfer@nmr.mgh.harvard.edu
>         <mailto: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 GroupB; Class 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)
>         <http://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels%29>
>         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 specifying 'ni' as a vector of'1's even
>         legitimate? Thanks, Michael
>         _______________________________________________ Freesurfer
>         mailing list Freesurfer@nmr.mgh.harvard.edu
>         <mailto: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
>         <mailto: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
>         <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
>     <mailto: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 <mailto: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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20151027/469b7437/attachment-0001.html
-------------- next part --------------
A non-text attachment was scrubbed...
Name: not available
Type: application/octet-stream
Size: 27 bytes
Desc: not available
Url : http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20151027/469b7437/attachment-0001.obj

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

Message: 5
Date: Tue, 27 Oct 2015 18:33:09 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] FreeSurfer pve correction tool
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <562FFBA5.5090800@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed

Hi Mohamed, sorry, I have not fully documented the procedure yet. I've
put some notes below
doug


1. To start, run

gtmseg --s subject

This will take a couple of hours and produces some files needed for GTM
PVC (which is used for GTM, MG, RBV).

2. You'd then register the PET to the anatomical with bbregister (with
--t2 weighting). Make sure to save the output as an LTA (--lta). I
usually use the mean TAC as the input. You can do this in parallel with #1.

3. You'd then run mri_gtmpvc, something like

mri_gtmpvc --i tac.nii.gz --psf PSF  --auto-mask PSF+2 .01 --seg
gtmseg.mgz --reg reg.lta --default-seg-merge --mgx .01 --o gtmpvc.output
--km-hb 11 12 13 50 51 52 --km-ref 8 47 --no-rescale

PSF is the point-spread FWHM of the scanner; reg.lta is the registration
from #2.  --km-hb specifies the highbinding region for MRTM2. --km-ref
specifies the reference region.  --mgx specifies to output a
muller-gartner map (not necessary for GTM ROI analysis).

4. For the GTM (ROI) MRTM1 KM analysis, you would then run

  mri_glmfit --y km.hb.tac.nii.gz --mrtm1 km.ref.tac.dat time.dat --o
mrtm1 --no-est-fwhm --nii.gz

where time.dat is a text file withe acquisition time of each time point
in the tac.

5. For the MRTM2 analysis

set k2p = `cat mrtm1/k2prime.dat`
mri_glmfit --y km.hb.tac.nii.gz --mrtm2 km.ref.tac.dat time.dat $k2p --o
mrtm1 --no-est-fwhm --nii.gz

If you want to run a voxel-wise analysis, then you can use the mgx
volume as input (--y). Probably you'll want to sample this to the
surface using mri_vol2surf and the registration file aux/anat2pet.lta,
then smooth on the surface




On 10/27/2015 04:47 PM, Mohamed Ali Bahri wrote:
> Dear Bruce,
>
> Am I missed the answer of Dr. Greve about the following questions?
>
> Is it possible to tell what are the implemented methods for the PET pve correction? and how we can
> obtain the corrected 4D (dynamic) PET images (for a voxel-by-voxel modeling)?
>
>
> Many thanks,
>
> Mohamed
>
>
>
> On 26/10/15 14:52, Bruce Fischl wrote:
>> oh, then I'll leave it for Doug
>> Bruce
>> On Mon, 26 Oct 2015, Mohamed Ali Bahri
>> wrote:
>>
>>> Hi Bruce,
>>>
>>> Yes, for PET analysis.
>>>
>>> Best,
>>>
>>> Mohamed
>>>
>>> On 26/10/15 14:45, Bruce Fischl wrote:
>>>> Hi Mohamed
>>>>
>>>> do you mean for PET analysis or for the recent paper that Rebecca Shafee
>>>> wrote on e.g. tissue intensity properties?
>>>>
>>>> cheers
>>>> Bruce
>>>>
>>>>
>>>>
>>>> On Mon, 26 Oct 2015, Mohamed Ali Bahri wrote:
>>>>
>>>>> Is it possible to tell what are the implemented methods? and how we can
>>>>> obtain the corrected 4D (dynamic) images (for a voxel-by-voxel modeling)?
>>>>>
>>>>> Best,
>>>>>
>>>>> Mohamed
>>>>>
>>>>> On 26/10/15 13:27, Bruce Fischl wrote:
>>>>>> no, sorry, we haven't had time to document it
>>>>>> On Mon, 26 Oct 2015,
>>>>>> m.bahri@ulg.ac.be wrote:
>>>>>>
>>>>>>> Dear FreeSurfer Experts,
>>>>>>>
>>>>>>> Are there any documentation comes out for the pve correction tool implemented in the FreeSurfer V6?
>>>>>>>
>>>>>>> Many thanks in advance,
>>>>>>>
>>>>>>> Best,
>>>>>>>
>>>>>>> Mohamed
>>>>>>> _______________________________________________
>>>>>>> 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: 6
Date: Tue, 27 Oct 2015 23:55:35 -0700
From: Jonathan Plasencia <jplasenc@asu.edu>
Subject: [Freesurfer] Understanding the brainstem AtlasMesh file
        structure       format
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <CA+_OnouN9KrrfRwU34Zid4M+N2vTOD4=wAFME8ekTPtdkTj=Eg@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Hello,

Is the AtlasMesh under the following pathway a standard mesh structure? If
so, what is it? Better yet, is there a way for those meshes in the
AtlasMesh to be converted to a standard stl file or some other standard
mesh file format? To be clear, I know the .gz is a compressed file;  I'm
referring to the data within the text.

freesurfer -> average -> BrainstemSS -> atlas -> AtlasMesh.gz

I ask because I would like to use this this template as a target mesh for
vertex analysis with the brainstem data I processed using freesurfer.

Best,

Jon
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20151027/9d7af516/attachment-0001.html

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

Message: 7
Date: Wed, 28 Oct 2015 09:23:34 +0100
From: "Sandy Schramm" <sandy_schramm@web.de>
Subject: Re: [Freesurfer] comparison of 4 groups: mri_glmfit or Qdec?
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
        <trinity-9ae3f0fc-82f9-4982-99bf-7bdc43b9595b-1446020614161@3capp-webde-bap28>

Content-Type: text/plain; charset="us-ascii"

An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20151028/78f67c75/attachment-0001.html

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

Message: 8
Date: Wed, 28 Oct 2015 08:38:55 -0400 (EDT)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Talairach_afd error (Bruce Fischl)
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <alpine.LRH.2.20.1510280838280.22695@gate.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

wow, we haven't seen that happen. Does the recon-all.log from the
parallel machine have any clues as to why it is empy?
On Mon, 26 Oct
2015, Anna I. Garcia Diaz wrote:

> 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:
>       Send Freesurfer mailing list submissions to
>       ? ? ? ? freesurfer@nmr.mgh.harvard.edu
>
>       To subscribe or unsubscribe via the World Wide Web, visit
>       ? ? ? ?
>       https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>       or, via email, send a message with subject or body 'help' to
>       ? ? ? ? freesurfer-request@nmr.mgh.harvard.edu
>
>       You can reach the person managing the list at
>       ? ? ? ? freesurfer-owner@nmr.mgh.harvard.edu
>
>       When replying, please edit your Subject line so it is more
>       specific
>       than "Re: Contents of Freesurfer digest..."
>
>
>       Today's Topics:
>
>       ? ?1.? 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
>       -------------- next part --------------
>       An HTML attachment was scrubbed...
>       URL:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20151022/e
>       d70621d/attachment-0001.html
>
>       ------------------------------
>
>       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}
>
>       <!--#yiv0632092676 .yiv0632092676hmmessage
>       P{margin:0px;padding:0px;}#yiv0632092676
>       body.yiv0632092676hmmessage{font-size:12pt;font-family:Calibri;}-->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:
>
>       ?<!--#yiv0632092676 .yiv0632092676ExternalClass
>       .yiv0632092676ecxhmmessage P {padding:0px;}#yiv0632092676
>       .yiv0632092676ExternalClass body.yiv0632092676ecxhmmessage
>       {font-size:12pt;font-family:Calibri;}--> 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:
>
>       ?<!--#yiv0632092676 .yiv0632092676ExternalClass
>       .yiv0632092676ecxhmmessage P {padding:0px;}#yiv0632092676
>       .yiv0632092676ExternalClass body.yiv0632092676ecxhmmessage
>       {font-size:12pt;font-family:Calibri;}--> 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:
>
>       ?<!--#yiv0632092676 .yiv0632092676ExternalClass
>       .yiv0632092676ecxhmmessage P {padding:0px;}#yiv0632092676
>       .yiv0632092676ExternalClass body.yiv0632092676ecxhmmessage
>       {font-size:12pt;font-family:Calibri;}--> 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}
>
>       ? <!--#yiv0632092676 .yiv0632092676ExternalClass
>       #yiv0632092676ecxyiv7275178360
>       body.yiv0632092676ecxyiv7275178360hmmessage
>       {font-size:12pt;font-family:Calibri;}-->? 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 andmris_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 thefollowing------------------------------------------------------------------
>       ------------------------------%
>
>
>
>       ?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
>       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
>
>
>       ?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
>       mailinglistFreesurfer@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.
>       _______________________________________________
>       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.
>
>
>
>       -------------- next part --------------
>       An HTML attachment was scrubbed...
>       URL:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20151022/a
>       be3af53/attachment-0001.html
>       -------------- next part --------------
>       A non-text attachment was scrubbed...
>       Name: ATT00002
>       Type: image/jpeg
>       Size: 64802 bytes
>       Desc: not available
>       Url :http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20151022/a
>       be3af53/attachment-0004.jpe
>       -------------- next part --------------
>       A non-text attachment was scrubbed...
>       Name: ATT00003
>       Type: image/jpeg
>       Size: 8031 bytes
>       Desc: not available
>       Url :http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20151022/a
>       be3af53/attachment-0005.jpe
>       -------------- next part --------------
>       A non-text attachment was scrubbed...
>       Name: ATT00004
>       Type: image/jpeg
>       Size: 9926 bytes
>       Desc: not available
>       Url :http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20151022/a
>       be3af53/attachment-0006.jpe
>       -------------- next part --------------
>       A non-text attachment was scrubbed...
>       Name: ATT00001
>       Type: image/jpeg
>       Size: 13124 bytes
>       Desc: not available
>       Url :http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20151022/a
>       be3af53/attachment-0007.jpe
>
>       ------------------------------
>
>       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
>       *******************************************
>
>
>
>

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

Message: 9
Date: Wed, 28 Oct 2015 08:36:04 -0500
From: Jason Haberman <habermanj@rhodes.edu>
Subject: [Freesurfer] error finding Matlab
To: <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <CAOPeGYP5rTaSAQ9cGoVowdA+SzegPd=NfVALezheQ9qDxSRG1Q@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Dear Freesurfer Community,

I am very new to Freesurfer and am trying to work my way through the
tutorial. I am currently stuck at the
mkcontrast-sess -analysis my-workmem.sm05.lh -contrast encode-v-base
-a 1 section,
having received the error:
ERROR: cannot find matlab. Is it in your path?

I have searched the forums and found one instance of this being reported,
but the suggested solutions did not resolve the problem. Is there anyway
further recommendations you might make?

I have attached a screenshot of my .bash_profile and of my attempts to run
mkcontrast. I would be most grateful for any assistance you might offer.

Warm Regards,
Jason

[image: Inline image 1]

--

Jason Haberman
Assistant Professor of Psychology
Rhodes College
Clough Hall 119
901-843-3231
http://jasonmarchaberman.wordpress.com/
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20151028/54542bc1/attachment.html
-------------- next part --------------
A non-text attachment was scrubbed...
Name: bash_profile.jpg
Type: image/jpeg
Size: 275074 bytes
Desc: not available
Url : http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20151028/54542bc1/attachment.jpg

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

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

End of Freesurfer Digest, Vol 140, Issue 44
*******************************************