The contents of the runlist file are:

014

016

018

026

028

030

040

042

044

052

054

056

As a reminder, the error involved is: "ERROR: cannot find [subject_path]/bold/014/fmc.sm0".

On Thu, Apr 20, 2017 at 12:00 PM, <freesurfer-request@nmr.mgh.harvard.edu> wrote:

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Today's Topics:

1. Re: Worse determination of ?h.white with v6.0 in comparison
to v5.3 - worse GM/WM contrast (Bruce Fischl)
2. Re: White matter atrophy (Douglas N Greve)
3. Re: Worse determination of ?h.white with v6.0 in comparison
to v5.3 - worse GM/WM contrast (Bruce Fischl)
4. Re: mri_glmfit error with aparc table flag (Douglas N Greve)
5. Re: plot-twf-sess display error (Douglas N Greve)
6. Re: 5. Re: Selxavg3-sess Looking for (and can't find)
"fmc.sm0" (Douglas N Greve)
7. Re: Using registration.dat to register a dataset (Jacobson, Aaron)
8. Re: Using registration.dat to register a dataset (Douglas N Greve)

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

Message: 1
Date: Thu, 20 Apr 2017 11:09:58 -0400 (EDT)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Worse determination of ?h.white with v6.0 in
comparison to v5.3 - worse GM/WM contrast
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Cc: David Semanek <SemanekD@nyspi.columbia.edu>
Message-ID:
<alpine.LRH.2.20.1704201108490.32551@door.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

Hi Antonin

yes, the -mprage flag is likely to be at least one source of the
differences. It makes the normalization more aggressive (since mprage
trades higher CNR for lower SNR). I'm surprised removing it didn't help. I
think that changing things like wlo could also help depending on how wrong
the normalization is. Upload a subject and I'll take a look

cheers
Bruce

On Thu, 20 Apr 2017,
Antonin Skoch wrote:

> Dear David,
>
> thank you for the feedback; I saw your posts concerning edits and responded
> to them, see
>
> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg52549.html
>
> Just my case is not concerning poor response to the edits (which I believe
> is not systematically different between 5.3 and 6.0), my concern is that the
> data processed by v6.0 need much more wm.mgz edits than data processed by
> v5.3.
>
> I think that my issue lies in -normalization2 step of recon-all. One of the
> difference between v5.3 and v6.0 is that by default the -mprage flag is
> passed to mri_normalize. This affects several parameters inside
> mri_normalize. I tried to reprocess my subjects using v6.0 with -no-mprage,
> but unfortunately this did not help.
>
> See the example screenshots processed by v5.3 and v6.0 with -no-mprage:
>
> The brain.mgz is still more aggressively filtered in v6.0 and there is much
> more prominent leak of ?h.white outside brain, which is probably caused by
> extended filtration which affects GM/WM contrast.
>
> Looking at the source code of mri_normalize.c I did not comprehend where the
> basis of the issue lies, but in any case there are big differences in
> mri_normalize.c code between versions.
>
> Antonin
>
> From: David Semanek <SemanekD@nyspi.columbia.edu>
> To: Antonin Skoch <ansk@ikem.cz>, "freesurfer@nmr.mgh.harvard.edu"
> <freesurfer@nmr.mgh.harvard.edu>
> Sent: 4/20/2017 3:41 PM
> Subject: Re: [Freesurfer] Worse determination of ?h.white with v6.0 in
> comparison to v5.3 - worse GM/WM contrast
>
> Agreed. A validated protocol run on a very large group of
> subjects in 5.3 was attempted with similar data in 6.0 and not
> only was the longitudinal edit stream nearly non-functional for
> white matter edits, cross edit performance was disappointing.
>
> ?
>
> I am currently waiting on a response to these potential issues
> before pursuing further work with 6.0.
>
> ?
>
> Best,
>
> ?
>
> David P. Semanek, HCISPP
>
> Research Technician, Posner Lab
>
> Division of Child and Adolescent Psychiatry
>
> Columbia University Medical Center
>
> New York State Psychiatric Institute
>
> 1051 Riverside Drive, Pardes Bldg. Rm. 2424
>
> New York, NY 10032
>
> PH: (646) 774-5885
>
> ?
>
> IMPORTANT NOTICE:? This e-mail is meant only for the use of the
> intended recipient.? It may contain confidential information which is
> legally privileged or otherwise protected by law.? If you received
> this e-mail in error or from someone who was not authorized to send it
> to you, you are strictly prohibited from reviewing, using,
> disseminating, distributing or copying the e-mail.? PLEASE NOTIFY US
> IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM
> YOUR SYSTEM.? Thank you for your cooperation.
>
> ?
>
> From: Antonin Skoch <ansk@ikem.cz>
> Date: Wednesday, April 19, 2017 at 5:23 PM
> To: <freesurfer@nmr.mgh.harvard.edu>
> Subject: [Freesurfer] Worse determination of ?h.white with v6.0 in
> comparison to v5.3 - worse GM/WM contrast
>
> ?
>
> Dear experts,
>
> I am sending just one more example to illustrate issue with white
> surface estimation in v6.0. See the attached screenshots: In v6.0
> there seems to be insufficient contrast in brain.finalsurfs.mgz, so
> the white surface is leaking at three spots dramatically outwards
> towards pial surface. The white surface in v5.3 looks much more
> anatomically relevant in the same spot.
>
> Could you please comment on how to avoid such issues in v.6.0?
>
> Regards,
>
> Antonin Skoch
>
>
>
>

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

Message: 2
Date: Thu, 20 Apr 2017 11:14:20 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] White matter atrophy
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <f1cefc9e-424e-4cdb-0721-d19a83caf4da@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed

Not other than just comparing the total WM volume. I guess you could do
some type of VBM analysis, but I would recommend using a package that
specializes in that type of analysis

On 04/20/2017 07:42 AM, John Anderson wrote:
> Dear Freesurfer experts,
> I know how to do cortical thickness group analysis using Freesurfer,
> also I know how to use Qdec to compare groups regarding gray matter
> volume differences, cortical thickness, curvatures, area,... etc.
> I am wondering if there is any way in Freesurfer to study the
> difference in white matter volume between two groups?
>
> I highly appreciate any suggestion!
> John
>
>
>
>
> _______________________________________________
> 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: 3
Date: Thu, 20 Apr 2017 11:14:45 -0400 (EDT)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Worse determination of ?h.white with v6.0 in
comparison to v5.3 - worse GM/WM contrast
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Cc: Antonin Skoch <ansk@ikem.cz>
Message-ID:
<alpine.LRH.2.20.1704201113370.32551@door.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

Hi David

I can take a look at a subject of yours as well if you upload it (both 5.3
and 6.0 processed versions if you have them) and point me at voxel coords.
The white surface is by design insensitive to local variations which is
what makes it robust, but also makes it more difficult to modify. I'll take
a look and think about how to make it easier

cheers
Bruce

On Thu, 20 Apr 2017, David Semanek
wrote:

>
> Thank you for looking into the deeper mechanics of this issue. In my case I
> am dealing with motion contaminated 1.5T data which require extensive and
> somewhat intricate edits to the white matter bleed into the pial surface, as
> well as into dura. In working with a past dataset of similar characteristics
> I was consistently impressed with fs 5.3?s ability to properly segment white
> matter in most cases and the robustness of the editing response. I was left
> with the overall impression that freesurfer handled noisy data quite well
> with a little bit of help. Our results from the analysis of corrected vs
> uncorrected data were very strong in favor of the editing protocol.
>
> ?
>
> My experience with 6.0, aside from any issues of information not propagating
> through the longitudinal stream, is that there are many more cases in which
> the white matter surface will not conform to the edits suggested in the
> white matter volume. A number of tricks to ?convince? the software in cases
> of non-response used in 5.3, such as making sure to complete edits on
> adjacent slices, are simply not effective. I am left with the overall
> impression that I have very little control over the white matter surfaces
> really, beyond making suggestions which may only slightly change the degree
> of error, but does not fundamentally change the structure of the white
> matter surface enough to remove the misclassification entirely in many
> cases.
>
> ?
>
> Best,
>
> ?
>
> David P. Semanek, HCISPP
>
> Research Technician, Posner Lab
>
> Division of Child and Adolescent Psychiatry
>
> Columbia University Medical Center
>
> New York State Psychiatric Institute
>
> 1051 Riverside Drive, Pardes Bldg. Rm. 2424
>
> New York, NY 10032
>
> PH: (646) 774-5885
>
> ?
>
> IMPORTANT NOTICE:? This e-mail is meant only for the use of the intended
> recipient.? It may contain confidential information which is legally
> privileged or otherwise protected by law.? If you received this e-mail in
> error or from someone who was not authorized to send it to you, you are
> strictly prohibited from reviewing, using, disseminating, distributing or
> copying the e-mail.? PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN
> E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM.? Thank you for your
> cooperation.
>
> ?
>
> From: Antonin Skoch <ansk@ikem.cz>
> Date: Thursday, April 20, 2017 at 10:25 AM
> To: David Semanek <SemanekD@nyspi.columbia.edu>,
> "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] Worse determination of ?h.white with v6.0 in
> comparison to v5.3 - worse GM/WM contrast
>
> ?
>
> Dear David,
>
> thank you for the feedback; I saw your posts concerning edits and responded
> to them, see
>
> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg52549.html
>
> Just my case is not concerning poor response to the edits (which I believe
> is not systematically different between 5.3 and 6.0), my concern is that the
> data processed by v6.0 need much more wm.mgz edits than data processed by
> v5.3.
>
> I think that my issue lies in -normalization2 step of recon-all. One of the
> difference between v5.3 and v6.0 is that by default the -mprage flag is
> passed to mri_normalize. This affects several parameters inside
> mri_normalize. I tried to reprocess my subjects using v6.0 with -no-mprage,
> but unfortunately this did not help.
>
> See the example screenshots processed by v5.3 and v6.0 with -no-mprage:
>
> The brain.mgz is still more aggressively filtered in v6.0 and there is much
> more prominent leak of ?h.white outside brain, which is probably caused by
> extended filtration which affects GM/WM contrast.
>
> Looking at the source code of mri_normalize.c I did not comprehend where the
> basis of the issue lies, but in any case there are big differences in
> mri_normalize.c code between versions.
>
> Antonin
>
> From: David Semanek <SemanekD@nyspi.columbia.edu>
> To: Antonin Skoch <ansk@ikem.cz>, "freesurfer@nmr.mgh.harvard.edu"
> <freesurfer@nmr.mgh.harvard.edu>
> Sent: 4/20/2017 3:41 PM
> Subject: Re: [Freesurfer] Worse determination of ?h.white with v6.0 in
> comparison to v5.3 - worse GM/WM contrast
>
> Agreed. A validated protocol run on a very large group of
> subjects in 5.3 was attempted with similar data in 6.0 and not
> only was the longitudinal edit stream nearly non-functional for
> white matter edits, cross edit performance was disappointing.
>
> ?
>
> I am currently waiting on a response to these potential issues
> before pursuing further work with 6.0.
>
> ?
>
> Best,
>
> ?
>
> David P. Semanek, HCISPP
>
> Research Technician, Posner Lab
>
> Division of Child and Adolescent Psychiatry
>
> Columbia University Medical Center
>
> New York State Psychiatric Institute
>
> 1051 Riverside Drive, Pardes Bldg. Rm. 2424
>
> New York, NY 10032
>
> PH: (646) 774-5885
>
> ?
>
> IMPORTANT NOTICE:? This e-mail is meant only for the use of the
> intended recipient.? It may contain confidential information which is
> legally privileged or otherwise protected by law.? If you received
> this e-mail in error or from someone who was not authorized to send it
> to you, you are strictly prohibited from reviewing, using,
> disseminating, distributing or copying the e-mail.? PLEASE NOTIFY US
> IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM
> YOUR SYSTEM.? Thank you for your cooperation.
>
> ?
>
> From: Antonin Skoch <ansk@ikem.cz>
> Date: Wednesday, April 19, 2017 at 5:23 PM
> To: <freesurfer@nmr.mgh.harvard.edu>
> Subject: [Freesurfer] Worse determination of ?h.white with v6.0 in
> comparison to v5.3 - worse GM/WM contrast
>
> ?
>
> Dear experts,
>
> I am sending just one more example to illustrate issue with white
> surface estimation in v6.0. See the attached screenshots: In v6.0
> there seems to be insufficient contrast in brain.finalsurfs.mgz, so
> the white surface is leaking at three spots dramatically outwards
> towards pial surface. The white surface in v5.3 looks much more
> anatomically relevant in the same spot.
>
> Could you please comment on how to avoid such issues in v.6.0?
>
> Regards,
>
> Antonin Skoch
>
>
>

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

Message: 4
Date: Thu, 20 Apr 2017 11:16:16 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mri_glmfit error with aparc table flag
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <9a07f2b3-c9b9-cfba-8450-036c83a8b6ba@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=UTF-8; format=flowed

On 04/20/2017 11:08 AM, miracle ozzoude wrote:
> Thank very much Doug. Also, I was looking into the
> annotval2surfoverlay file and I have couple of questions.
> % Run these commands in matlab
> % annotnames = strvcat('superiortemporal','insula','postcentral');
> % annotvals = [1.1 2.2 3.7];
> % annotfile = '~/paul_analysis/fsaverage/label/lh.aparc.annot';
> % surfoverlay = annotval2surfoverlay(annotvals,annotnames,annotfile);
> % clear mri
> % mri.vol = surfoverlay;
> % MRIwrite(mri,'vals.mgh');
> %
> 1) Correct me if I am wrong, the annotation values (annotvals) are
> from results after correcting for multiple comparisons using mri_fdr?
They can be anything that you have one value per annotation.
> 2) Is this correct way to add octave path to freesurfer's path?
Sorry, I have no idea
> setenv FS_USE_OCTAVE 4.0.3
>
> setenv FS_OCTAVE_LIB /Applications/octave/lib
> setenv FS_OCTAVE_BIN /Application/octave/binary
> Thanks,
> Best,
> Paul
>
> On Thu, Apr 20, 2017 at 10:55 AM, Douglas N Greve
> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:
>
> you can get it here
>
> https://gate.nmr.mgh.harvard.edu/safelinks/greve/annotval2surfoverlay.m
> <https://gate.nmr.mgh.harvard.edu/safelinks/greve/annotval2surfoverlay.m>
>
> On 04/20/2017 10:10 AM, miracle ozzoude wrote:
> > Hello Doug,
> > I downloaded and installed octave. However, I can't find the
> > annotval2surfoverlay.m file in the matlab directory of freesurfer.
> > Does it come with FS v6 or do i need to download the file? Also,
> I was
> > looking into the annotval2surfoverlay file and I have couple of
> > questions.
> > % Run these commands in matlab
> > % annotnames = strvcat('superiortemporal','insula','postcentral');
> > % annotvals = [1.1 2.2 3.7];
> > % annotfile = '~/subjects/fsaverage/label/lh.aparc.annot';
> > % surfoverlay =
> annotval2surfoverlay(annotvals,annotnames,annotfile);
> > % clear mri
> > % mri.vol = surfoverlay;
> > % MRIwrite(mri,'vals.mgh');
> > %
> > 1) Are the annotation values (annotvals) from results after
> correcting
> > for multiple comparisons using mri_fdr?
> > 2) Do I need to add octave path to freesurfer PATH like the example
> > below?
> > setenv FS_USE_OCTAVE 4.0.3
> >
> > setenv FS_OCTAVE_LIB /Applications/octave/lib
> > setenv FS_OCTAVE_BIN /Application/octave/binary
> >
> > On Wed, Apr 19, 2017 at 3:39 PM, Douglas N Greve
> > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>> wrote:
> >
> > I think that will work
> >
> >
> > On 04/19/2017 03:33 PM, miracle ozzoude wrote:
> > > Hello Doug,
> > > Do you think writing the script with octave can substitute for
> > matlab?
> > > I am using FS v6.0 and I have the annotval2surfoverlay.m.
> Thanks
> > > Best,
> > > Paul
> > >
> > > On Wed, Apr 19, 2017 at 1:47 PM, Douglas N Greve
> > > <greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>
> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> > <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>>> wrote:
> > >
> > > Sorry, I don't have another solution for you.
> > >
> > >
> > > On 04/19/2017 01:42 PM, miracle ozzoude wrote:
> > > > Thanks Doug. However, I am running freesurfer
> analysis on my
> > > personal
> > > > computer and I don't have matlab. Also, I don't know how
> > this matlab
> > > > script works/ matlab works. Any instructions on how
> to use
> > it or
> > > > alternate? Please and thank you.
> > > > Best,
> > > > Paul.
> > > >
> > > > On Wed, Apr 19, 2017 at 1:33 PM, Douglas N Greve
> > > > <greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>
> > <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>
> > <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>
> > > <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>
> > <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>
> > > <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>
> > <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>>>> wrote:
> > > >
> > > > It is a table of data, so you can't visualize it
> > directly on
> > > anything.
> > > > You can try using annotval2surfoverlay.m to create a
> > surface
> > > > overlay of
> > > > the data.
> > > >
> > > >
> > > > On 04/19/2017 10:05 AM, miracle ozzoude wrote:
> > > > > Hello Doug,
> > > > > It worked. The issue was due to formatting error
> > with the
> > > aparc
> > > > file.
> > > > > Also, I was trying to visualize the result on the
> > surface
> > > using
> > > > > freeview -f fsaverage/lh.pial -viewport 3d
> (clicking
> > > overlay on
> > > > > freeview and loading the sig.mgh). However, i
> got an
> > error "
> > > > failed to
> > > > > display overlay". How can I visualize the
> result? Thanks
> > > > > Best,
> > > > > Paul
> > > > >
> > > > > On Tue, Apr 18, 2017 at 10:03 PM, Douglas Greve
> > > > > <greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>
> > <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>
> > > <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>
> > <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>>
> > > <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>
> > <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>
> > <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>>>
> > > > <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>
> > <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>
> > > <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>
> > <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>>
> > > > <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>
> > <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>
> > <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>
> > <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>>>>> wrote:
> > > > >
> > > > > You have a table of data, so no template is
> > needed. If you
> > > > put the
> > > > > --surf before the --table, it probably
> runs, but it
> > > will ignore
> > > > > the surface
> > > > >
> > > > >
> > > > > On 4/18/17 9:58 PM, miracooloz@gmail.com
> <mailto:miracooloz@gmail.com>
> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>
> > > <mailto:miracooloz@gmail.com
> <mailto:miracooloz@gmail.com> <mailto:miracooloz@gmail.com
> <mailto:miracooloz@gmail.com>>>
> > > > <mailto:miracooloz@gmail.com
> <mailto:miracooloz@gmail.com>
> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>
> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>
> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>>>
> > > > > <mailto:miracooloz@gmail.com
> <mailto:miracooloz@gmail.com>
> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>
> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>
> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>>
> > > <mailto:miracooloz@gmail.com
> <mailto:miracooloz@gmail.com> <mailto:miracooloz@gmail.com
> <mailto:miracooloz@gmail.com>>
> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>
> <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>>>>> wrote:
> > > > >> Thanks doug. Does it mean when using the
> --table
> > > flag, you
> > > > can't
> > > > >> use the fsaverage template? I came across
> several
> > > post in the
> > > > >> forum that used "--surf fsaverage lh "?
> and it
> > worked.
> > > > >> Best,
> > > > >> Paul
> > > > >>
> > > > >> Sent from my BlackBerry 10 smartphone.
> > > > >> *From: *Douglas Greve
> > > > >> *Sent: *Tuesday, April 18, 2017 9:52 PM
> > > > >> *To: *freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>
> > > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>>
> > > > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>
> > > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>>>
> > > > >> <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>
> > > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>>
> > > > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>
> > > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>>>>
> > > > >> *Reply To: *Freesurfer support list
> > > > >> *Subject: *Re: [Freesurfer] mri_glmfit error
> > with aparc
> > > > table flag
> > > > >>
> > > > >>
> > > > >> Don't include --surf fsaverage lh. It
> thinks the
> > > input is a
> > > > >> surface, not a table
> > > > >>
> > > > >>
> > > > >>
> > > > >> On 4/18/17 9:21 PM, miracle ozzoude wrote:
> > > > >>> Hello freesurfer,
> > > > >>> I am trying to run mri_glmfit with the
> --table
> > flag. My
> > > > >>> aparc_lh_thick_stats.txt contain entorhinal and
> > > > parahippocampal
> > > > >>> thickness values for 32 subjects. I ran
> the glm
> > > command and
> > > > >>> received an error. Please, how can i
> solve this
> > > issue? I have
> > > > >>> included my command, fsgd file, contrast
> > matrix and
> > > error
> > > > below.
> > > > >>> Thanks
> > > > >>> Best,
> > > > >>> Paul
> > > > >>>
> > > > >>> GLM command: mri_glmfit --table
> > aparc_lh_thick_stats.txt
> > > > --fsgd
> > > > >>> age.fsgd --C age1.mtx --C age2.mtx --surf
> > fsaverage lh
> > > > --cortex
> > > > >>> --glmdir lh.thickness.glmdir
> > > > >>>
> > > > >>>
> > > > >>> ERROR= "gdfRead(): reading age.fsgd
> > > > >>>
> > > > >>> INFO: DeMeanFlag keyword not found,
> DeMeaning will
> > > NOT be
> > > > done.
> > > > >>>
> > > > >>> Continuous Variable Means (all subjects)
> > > > >>>
> > > > >>> 0 Age 39.9375 17.3312
> > > > >>>
> > > > >>> Class Means of each Continuous Variable
> > > > >>>
> > > > >>> 1 Group1 35.6316
> > > > >>>
> > > > >>> 2 Group2 46.2308
> > > > >>>
> > > > >>> INFO: gd2mtx_method is dods
> > > > >>>
> > > > >>> Reading source surface
> > > > >>>
> > > >
> > >
> >
> /Users/MiracleOz/Documents/improvervsdeclinermri/fsaverage/surf/lh.white
> > > > >>>
> > > > >>> Number of vertices 163842
> > > > >>>
> > > > >>> Number of faces 327680
> > > > >>>
> > > > >>> Total area 65416.984375
> > > > >>>
> > > > >>> AvgVtxArea 0.399269
> > > > >>>
> > > > >>> AvgVtxDist 0.721953
> > > > >>>
> > > > >>> StdVtxDist 0.195470
> > > > >>>
> > > > >>>
> > > > >>> $Id: mri_glmfit.c,v 1.241.2.4 2016/12/08
> 22:02:40
> > > zkaufman
> > > > Exp $
> > > > >>>
> > > > >>> cwd
> > /Users/MiracleOz/Documents/improvervsdeclinermri
> > > > >>>
> > > > >>> cmdline mri_glmfit.bin --table
> > > aparc_lh_thick_stats.txt --fsgd
> > > > >>> age.fsgd --C age1.mtx --C age2.mtx --surf
> > fsaverage lh
> > > > --cortex
> > > > >>> --glmdir lh.thickness.glmdir
> > > > >>>
> > > > >>> sysname Darwin
> > > > >>>
> > > > >>> hostname MacBook-Pro.local
> > > > >>>
> > > > >>> machine x86_64
> > > > >>>
> > > > >>> user MiracleOz
> > > > >>>
> > > > >>> FixVertexAreaFlag = 1
> > > > >>>
> > > > >>> UseMaskWithSmoothing 1
> > > > >>>
> > > > >>> OneSampleGroupMean 0
> > > > >>>
> > > > >>> y
> > > > >>>
> > > >
> > >
> >
> /Users/MiracleOz/Documents/improvervsdeclinermri/aparc_lh_thick_stats.txt
> > > > >>>
> > > > >>> logyflag 0
> > > > >>>
> > > > >>> usedti 0
> > > > >>>
> > > > >>> FSGD age.fsgd
> > > > >>>
> > > > >>> labelmask
> > > > >>>
> > > >
> > >
> >
> /Users/MiracleOz/Documents/improvervsdeclinermri/fsaverage/label/lh.cortex.label
> > > > >>>
> > > > >>> maskinv 0
> > > > >>>
> > > > >>> glmdir lh.thickness.glmdir
> > > > >>>
> > > > >>> IllCondOK 0
> > > > >>>
> > > > >>> ReScaleX 1
> > > > >>>
> > > > >>> DoFFx 0
> > > > >>>
> > > > >>> Creating output directory
> lh.thickness.glmdir
> > > > >>>
> > > > >>> Loading y from
> > > > >>>
> > > >
> > >
> >
> /Users/MiracleOz/Documents/improvervsdeclinermri/aparc_lh_thick_stats.txt
> > > > >>>
> > > > >>> Found 66 data colums
> > > > >>>
> > > > >>> Found 0 data rows
> > > > >>>
> > > > >>> INFO: gd2mtx_method is dods
> > > > >>>
> > > > >>> Saving design matrix to
> lh.thickness.glmdir/Xg.dat
> > > > >>>
> > > > >>> Computing normalized matrix
> > > > >>>
> > > > >>> Normalized matrix condition is 32.2165
> > > > >>>
> > > > >>> Matrix condition is 20734.7
> > > > >>>
> > > > >>> Found 149955 points in label.
> > > > >>>
> > > > >>> ERROR: mri_reshape: number of elements
> cannot
> > change
> > > > >>>
> > > > >>> nv1 = 163842, nv1 = 66
> > > > >>>
> > > > >>> search space = 82219.962936
> > > > >>>
> > > > >>> ERROR: dimension mismatch between y and X.
> > > > >>>
> > > > >>> y has 0 inputs, X has 32 rows."
> > > > >>>
> > > > >>> FSGD file: GroupDescriptorFile 1
> > > > >>>
> > > > >>> Title MOT
> > > > >>>
> > > > >>> Class Group1
> > > > >>>
> > > > >>> Class Group2
> > > > >>>
> > > > >>> Variables Age
> > > > >>>
> > > > >>> Input 01053p Group1 23
> > > > >>>
> > > > >>> Input 01054p Group1 43
> > > > >>>
> > > > >>> Input 01061p Group2 39
> > > > >>>
> > > > >>> Input 01062p Group2 19
> > > > >>>
> > > > >>> Input 01074p Group2 28
> > > > >>>
> > > > >>> .............. (I have more participants)
> > > > >>>
> > > > >>>
> > > > >>> CONTRAST MATRIX: 1 -1 0 0
> > > > >>>
> > > > >>>
> > > > >>>
> > > > >>> _______________________________________________
> > > > >>> Freesurfer mailing list
> > > > >>> Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>>
> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>
> > > > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>>
> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>>
> > > > >>>
> > >
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
> > >
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>>
> > > >
> > >
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
> > >
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>>>
> > > > >>>
> > >
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
> > >
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>>
> > > >
> > >
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
> > >
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>>>>
> > > > >>
> > > > >> _______________________________________________
> > > > >> Freesurfer mailing list
> > > > >> Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>>
> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>
> > > > >> <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>>
> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>>
> > > > >>
> > >
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
> > >
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>>
> > > >
> > >
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
> > >
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>>>
> > > > >>
> > >
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
> > >
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>>
> > > >
> > >
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
> > >
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>>>>
> > > > > _______________________________________________
> > Freesurfer
> > > > mailing
> > > > > list Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>>
> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>
> > > > > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>>
> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>>
> > > > >
> > >
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
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> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
> > >
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>>
> > > >
> > >
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
> > >
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>>>
> > > > >
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
> > >
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>>
> > > >
> > >
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
> > >
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <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>
> > <http://www.partners.org/complianceline
> <http://www.partners.org/complianceline>>
> > > <http://www.partners.org/complianceline
> <http://www.partners.org/complianceline>
> > <http://www.partners.org/complianceline
> <http://www.partners.org/complianceline>>>
> > > > <http://www.partners.org/complianceline
> <http://www.partners.org/complianceline>
> > <http://www.partners.org/complianceline
> <http://www.partners.org/complianceline>>
> > > <http://www.partners.org/complianceline
> <http://www.partners.org/complianceline>
> > <http://www.partners.org/complianceline
> <http://www.partners.org/complianceline>>>>
> > > > > <http://www.partners.org/complianceline
> <http://www.partners.org/complianceline>
> > <http://www.partners.org/complianceline
> <http://www.partners.org/complianceline>>
> > > <http://www.partners.org/complianceline
> <http://www.partners.org/complianceline>
> > <http://www.partners.org/complianceline
> <http://www.partners.org/complianceline>>>
> > > > <http://www.partners.org/complianceline
> <http://www.partners.org/complianceline>
> > <http://www.partners.org/complianceline
> <http://www.partners.org/complianceline>>
> > > <http://www.partners.org/complianceline
> <http://www.partners.org/complianceline>
> > <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>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>>
> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>
> > > > >
> > >
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
> > >
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>>
> > > >
> > >
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
> > >
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>>>
> > > > --
> > > > Douglas N. Greve, Ph.D.
> > > > MGH-NMR Center
> > > > greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>
> > <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>
> > <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>
> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> > <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>
> > <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>>>
> > > > Phone Number:617-724-2358 <tel:617-724-2358> <tel:617-724-2358
> <tel:617-724-2358>> <tel:617-724-2358 <tel:617-724-2358>
> <tel:617-724-2358 <tel:617-724-2358>>>
> > > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358
> <tel:617-724-2358>> <tel:617-724-2358 <tel:617-724-2358>
> > <tel:617-724-2358 <tel:617-724-2358>>>>
> > > > Fax: 617-726-7422 <tel:617-726-7422>
> <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422
> <tel:617-726-7422>
> > <tel:617-726-7422 <tel:617-726-7422>>> <tel:617-726-7422
> <tel:617-726-7422>
> > > <tel:617-726-7422 <tel:617-726-7422>>>
> > > >
> > > > Bugs:
> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>
> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>>
> > > >
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>
> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>>>
> > > > FileDrop:
> https://gate.nmr.mgh.harvard.edu/filedrop2
> <https://gate.nmr.mgh.harvard.edu/filedrop2>
> > <https://gate.nmr.mgh.harvard.edu/filedrop2
> <https://gate.nmr.mgh.harvard.edu/filedrop2>>
> > > <https://gate.nmr.mgh.harvard.edu/filedrop2
> <https://gate.nmr.mgh.harvard.edu/filedrop2>
> > <https://gate.nmr.mgh.harvard.edu/filedrop2
> <https://gate.nmr.mgh.harvard.edu/filedrop2>>>
> > > > <https://gate.nmr.mgh.harvard.edu/filedrop2
> <https://gate.nmr.mgh.harvard.edu/filedrop2>
> > <https://gate.nmr.mgh.harvard.edu/filedrop2
> <https://gate.nmr.mgh.harvard.edu/filedrop2>>
> > > <https://gate.nmr.mgh.harvard.edu/filedrop2
> <https://gate.nmr.mgh.harvard.edu/filedrop2>
> > <https://gate.nmr.mgh.harvard.edu/filedrop2
> <https://gate.nmr.mgh.harvard.edu/filedrop2>>>>
> > > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>
> > >
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>>
> > > >
> >
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>
> > >
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>>>
> > > > Outgoing:
> > > >
> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>
> >
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>>
> > >
> >
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>
> >
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>>>
> > > >
> >
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>
> >
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>>
> > >
> >
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>
> >
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>>>>
> > > > _______________________________________________
> > > > Freesurfer mailing list
> > > > Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>>
> > > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>
> > >
> >
> >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
> > >
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>>
> > > >
> > >
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
> > >
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>>>
> > > >
> > > >
> > > >
> > > >
> > > > _______________________________________________
> > > > Freesurfer mailing list
> > > > Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>>
> > > >
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
> > >
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>>
> > >
> > > --
> > > Douglas N. Greve, Ph.D.
> > > MGH-NMR Center
> > > greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>
> > <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>
> > > Phone Number: 617-724-2358 <tel:617-724-2358>
> > <tel:617-724-2358 <tel:617-724-2358>>
> > > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422
> > <tel:617-726-7422>>
> > >
> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>
> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>>
> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> <https://gate.nmr.mgh.harvard.edu/filedrop2>
> > <https://gate.nmr.mgh.harvard.edu/filedrop2
> <https://gate.nmr.mgh.harvard.edu/filedrop2>>
> > > <https://gate.nmr.mgh.harvard.edu/filedrop2
> <https://gate.nmr.mgh.harvard.edu/filedrop2>
> > <https://gate.nmr.mgh.harvard.edu/filedrop2
> <https://gate.nmr.mgh.harvard.edu/filedrop2>>>
> > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>
> > >
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>>
> > > Outgoing:
> > >
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>
> >
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>>
> > >
> >
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>
> >
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>>>
> > >
> > > _______________________________________________
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>>
> > >
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
> > >
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>>
> > >
> > >
> > >
> > >
> > > _______________________________________________
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > >
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>
> > Phone Number: 617-724-2358
> > Fax: 617-726-7422
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>
> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> <https://gate.nmr.mgh.harvard.edu/filedrop2>
> > <https://gate.nmr.mgh.harvard.edu/filedrop2
> <https://gate.nmr.mgh.harvard.edu/filedrop2>>
> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>
> > Outgoing:
> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>
> >
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>>
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
> >
> >
> >
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> <https://gate.nmr.mgh.harvard.edu/filedrop2>
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> Outgoing:
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <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: 5
Date: Thu, 20 Apr 2017 11:25:22 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] plot-twf-sess display error
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <825e6f41-0aea-10be-af32-005d2c9aa780@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed

display is an imagemagick program. It is used to display the images
created by gnuplot. If you have xv installed, you can add -xv to the
command line. Otherwise, install imagemagick

https://www.imagemagick.org/script/index.php

On 04/19/2017 04:03 PM, Xie, Wenting wrote:
> Hi all,
>
>
> I am trying to use plot-twf-sess to create the motion plots as
> specified in the FsFast Tutorial, but I keep getting the error of
> "cannot find display." The command was copy-pasted from the FsFast
> tutorial
> (https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/FsFastPreProc_freeview?highlight=%28plot\-twf\-sess%29),
> and Gnuplot works on this computer (CentOS 6.8; GNOME 2.28.2) with the
> default terminal type set to "wxt". I've looked at the plot-twf-sess
> code in an attempt to troubleshoot but do not entirely understand what
> "display" means here where this error is generated:
>
> which display > /dev/null
> if($status) then
> echo "ERROR: cannot find display"
> exit 1;
> endif
>
> I've searched the archives but it seems that no one has encountered
> this problem yet (or at least written about it), so I can't tell if
> I'm just missing something glaringly obvious. Thank you for your time
> and please let me know if any further information is needed to solve this!
>
>
> Thanks again,
>
> Wenting Xie
>
> Clinical Research Coordinator
>
> MGH Neurology | Boston, MA
>
>
>
>
> _______________________________________________
> 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: Thu, 20 Apr 2017 11:30:25 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] 5. Re: Selxavg3-sess Looking for (and can't
find) "fmc.sm0"
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <b8dfcdc4-2cc7-4255-30f1-6ac01c9bb09d@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed

What are the contents of the run list file?

On 04/19/2017 09:32 AM, Taylor, Johnmark wrote:
> Here's the contents of analysis.info <http://analysis.info>:
>
> # FSBUILD freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
> # MKAVERSION $Id: mkanalysis-sess,v 1.64.2.5 2013/01/22 21:52:07 greve
> Exp $
> # MKACMD /ncf/nrg/sw/apps/freesurfer/5.3.0/fsfast/bin/mkanalysis-sess
> -analysis glm_single_all_ps_0 -fsd bold -runlistfile
> runlist_single.txt -native -nuisreg mcprextreg 3 -fwhm 0
> -event-related -nconditions 8 -paradigm spiralpara.par -spmhrf 0
> -per-session -refeventdur 12 -TR 1.5 -polyfit 2 -force -nskip 8
> # DATE Sat Apr 1 18:30:53 EDT 2017
>
> analysis glm_single_all_ps_0
> mcstem fmc
> fsd bold
> runlistfile runlist_single.txt
> TR 1.5
> RegDOF 6
> PerSession 1
> RawSpace volume native
> mask brain
> RawFWHM 0
> RawSTC none
> UseB0DC 0
> ApplySubCortMask 1
> inorm 100
> acfbins 30
> fixacf 1
> acffwhm 20
> acfsvd 0
> designtype event-related
> nskip 8
> polyfit 2
> HPFCutoffHz 0
> HeteroGCor 0
> nconditions 8
> parname spiralpara.par
> RefEventDur 12
> timewindow 40.000000
> prestim 0
> TER 0.050000
> spmhrf 0
> stimulusdelay -.75000000000000000000
> Condition 1 Condition01
> Condition 2 Condition02
> Condition 3 Condition03
> Condition 4 Condition04
> Condition 5 Condition05
> Condition 6 Condition06
> Condition 7 Condition07
> Condition 8 Condition08
> nuisreg mcprextreg 3
>
>
> On Tue, Apr 18, 2017 at 9:49 PM,
> <freesurfer-request@nmr.mgh.harvard.edu
> <mailto:freesurfer-request@nmr.mgh.harvard.edu>> wrote:
>
> Send Freesurfer mailing list submissions toAl
> freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>
>
> To subscribe or unsubscribe via the World Wide Web, visit
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <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
> <mailto:freesurfer-request@nmr.mgh.harvard.edu>
>
> You can reach the person managing the list at
> freesurfer-owner@nmr.mgh.harvard.edu
> <mailto: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. Fwd: fix topology problem (miracle ozzoude)
> 2. mri_glmfit error with aparc table flag (miracle ozzoude)
> 3. Re: Any advices for hires surface reconstruction? (Douglas
> Greve)
> 4. Re: Inconsistency in SI axis coordinate between FreeSurfer
> recon-all seg image and BrainVoyager (Douglas Greve)
> 5. Re: Selxavg3-sess Looking for (and can't find) "fmc.sm0"
> (Douglas Greve)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 18 Apr 2017 21:06:00 -0400
> From: miracle ozzoude <miracooloz@gmail.com
> <mailto:miracooloz@gmail.com>>
> Subject: [Freesurfer] Fwd: fix topology problem
> To: Douglas N Greve <freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>
> Message-ID:
>
> <CANfOk0hQPdgzKMGQRRfFCvUZ8X+tmP=mL9r-mtQDMpWQVH4MyA@mail.gmail.com
> <mailto:mL9r-mtQDMpWQVH4MyA@mail.gmail.com>>
> Content-Type: text/plain; charset="utf-8"
>
> ---------- Forwarded message ----------
> From: miracle ozzoude <miracooloz@gmail.com
> <mailto:miracooloz@gmail.com>>
> Date: Mon, Apr 17, 2017 at 8:40 AM
> Subject: fix topology problem
> To: Douglas N Greve <freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>
>
>
> Hello freesurfer,
> I am running recon-all on a scan and for the past 4 days, it hasn't
> finished the fix topology step of recon-all. I have attached the
> recon.log
> in the email. Thanks
> Best,
> Paul
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>
> ------------------------------
>
> Message: 2
> Date: Tue, 18 Apr 2017 21:21:24 -0400
> From: miracle ozzoude <miracooloz@gmail.com
> <mailto:miracooloz@gmail.com>>
> Subject: [Freesurfer] mri_glmfit error with aparc table flag
> To: Douglas N Greve <freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>
> Message-ID:
>
> <CANfOk0gfUSYNBHqRPA1fMyadxSKi57=-02BYxvzL4nMVrTxFCw@mail.gmail.com
> <mailto:02BYxvzL4nMVrTxFCw@mail.gmail.com>>
> Content-Type: text/plain; charset="utf-8"
>
> Hello freesurfer,
> I am trying to run mri_glmfit with the --table flag. My
> aparc_lh_thick_stats.txt contain entorhinal and parahippocampal
> thickness
> values for 32 subjects. I ran the glm command and received an error.
> Please, how can i solve this issue? I have included my command,
> fsgd file,
> contrast matrix and error below. Thanks
> Best,
> Paul
>
> GLM command: mri_glmfit --table aparc_lh_thick_stats.txt --fsgd
> age.fsgd
> --C age1.mtx --C age2.mtx --surf fsaverage lh --cortex --glmdir
> lh.thickness.glmdir
>
>
> ERROR= "gdfRead(): reading age.fsgd
>
> INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
>
> Continuous Variable Means (all subjects)
>
> 0 Age 39.9375 17.3312
>
> Class Means of each Continuous Variable
>
> 1 Group1 35.6316
>
> 2 Group2 46.2308
>
> INFO: gd2mtx_method is dods
>
> Reading source surface
> /Users/MiracleOz/Documents/improvervsdeclinermri/fsaverage/surf/lh.white
>
> Number of vertices 163842
>
> Number of faces 327680
>
> Total area 65416.984375
>
> AvgVtxArea 0.399269
>
> AvgVtxDist 0.721953
>
> StdVtxDist 0.195470
>
>
> $Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $
>
> cwd /Users/MiracleOz/Documents/improvervsdeclinermri
>
> cmdline mri_glmfit.bin --table aparc_lh_thick_stats.txt --fsgd
> age.fsgd --C
> age1.mtx --C age2.mtx --surf fsaverage lh --cortex --glmdir
> lh.thickness.glmdir
>
> sysname Darwin
>
> hostname MacBook-Pro.local
>
> machine x86_64
>
> user MiracleOz
>
> FixVertexAreaFlag = 1
>
> UseMaskWithSmoothing 1
>
> OneSampleGroupMean 0
>
> y
> /Users/MiracleOz/Documents/improvervsdeclinermri/aparc_lh_thick_stats.txt
>
> logyflag 0
>
> usedti 0
>
> FSGD age.fsgd
>
> labelmask
> /Users/MiracleOz/Documents/improvervsdeclinermri/fsaverage/label/lh.cortex.label
>
> maskinv 0
>
> glmdir lh.thickness.glmdir
>
> IllCondOK 0
>
> ReScaleX 1
>
> DoFFx 0
>
> Creating output directory lh.thickness.glmdir
>
> Loading y from
> /Users/MiracleOz/Documents/improvervsdeclinermri/aparc_lh_thick_stats.txt
>
> Found 66 data colums
>
> Found 0 data rows
>
> INFO: gd2mtx_method is dods
>
> Saving design matrix to lh.thickness.glmdir/Xg.dat
>
> Computing normalized matrix
>
> Normalized matrix condition is 32.2165
>
> Matrix condition is 20734.7
>
> Found 149955 points in label.
>
> ERROR: mri_reshape: number of elements cannot change
>
> nv1 = 163842, nv1 = 66
>
> search space = 82219.962936
>
> ERROR: dimension mismatch between y and X.
>
> y has 0 inputs, X has 32 rows."
>
> FSGD file: GroupDescriptorFile 1
>
> Title MOT
>
> Class Group1
>
> Class Group2
>
> Variables Age
>
> Input 01053p Group1 23
>
> Input 01054p Group1 43
>
> Input 01061p Group2 39
>
> Input 01062p Group2 19
>
> Input 01074p Group2 28
>
> .............. (I have more participants)
>
>
> CONTRAST MATRIX: 1 -1 0 0
> -------------- next part --------------
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>
> ------------------------------
>
> Message: 3
> Date: Tue, 18 Apr 2017 21:41:17 -0400
> From: Douglas Greve <greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>
> Subject: Re: [Freesurfer] Any advices for hires surface
> reconstruction?
> To: freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> Message-ID:
> <dc190cc8-c70a-647c-6397-52c3834077ed@nmr.mgh.harvard.edu
> <mailto:dc190cc8-c70a-647c-6397-52c3834077ed@nmr.mgh.harvard.edu>>
> Content-Type: text/plain; charset="windows-1252"
>
> That looks pretty good to me considering the resolution and 7T. We
> will
> be re-evaluating the hires stream over the next year. If you want to
> contribute a problem data set to our test suite, that would be
> appreciated.
>
> doug
>
>
> On 4/17/17 1:45 PM, Damien MARIE wrote:
> > Hi,
> >
> > I have a project on 7T data. I processed 26 subjects with
> FreeSurfer6
> > recon-all with or without the hires flag. The input is MP2RAGE, 0.6
> > mm^3, bias corrected, skull strip was done despite a slight piece of
> > dura is still present.
> >
> > For the data processed at native resolution, with the hires flag, I
> > mainly used this: recon-all -subject -i -parallel -expert -hires
> > The expert file indicating only mris_inflate -n 50
> > As a result, skull strip had to be fixed for 5 subjects (missing
> brain
> > pieces). Bilateral temporal pole is missing in the reconstructed
> > surfaces in 19 subjects.
> >
> > For the downsampled data, without the hires flag : recon-all
> -subject
> > -i -parallel
> > Bilateral temporal pole is missing in the reconstructed surfaces in
> > only 1 subject. Surfaces are way smoother.
> >
> > I guess such differences between the classic pipeline and the
> pipeline
> > tuned for hires data are expected.
> > I was just wondering if I was missing something somewhere, some
> > additional options that I would need to tweak, to get better
> surfaces
> > with the hires data especially in the temporal pole. For now the
> only
> > things I see that I could do are adding checkpoints or play with
> this
> > command line: mris_make_surfaces -max_gray_at_csf_border X
> -max_csf Y
> >
> > Thank you and best,
> >
> > *Damien*
> >
> >
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
>
> -------------- next part --------------
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>
> ------------------------------
>
> Message: 4
> Date: Tue, 18 Apr 2017 21:44:20 -0400
> From: Douglas Greve <greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>
> Subject: Re: [Freesurfer] Inconsistency in SI axis coordinate between
> FreeSurfer recon-all seg image and BrainVoyager
> To: freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> Message-ID:
> <675dc490-9fc6-29d8-9744-ad57155e9a87@nmr.mgh.harvard.edu
> <mailto:675dc490-9fc6-29d8-9744-ad57155e9a87@nmr.mgh.harvard.edu>>
> Content-Type: text/plain; charset="windows-1252"
>
> recon-all will recenter the volume. But I thought you said they were
> both in native space? Try looking at
> https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
> <https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems> Use
> Case #6
>
>
> On 4/17/17 3:07 PM, Jerry Jeyachandra wrote:
> >
> > Hi Freesurfer support team,
> >
> >
> > I'm attempting to register coordinates between BrainVoyager
> anatomical
> > images and freesurfer segmented images with both in native space,
> > however I'm running into inconsistencies specifically along the
> > inferior/superior dimension that I hope you can help me with
> >
> >
> > BrainVoyager reports coordinates as voxel indices which I'm
> trying to
> > match with FreeView's T1fs_nu_conform coordinates which I assume are
> > in voxel indices as well. Both the AP and RL dimensions match in
> both
> > programs across all our participants, however the SI axis does not,
> > with offsets varying across participants.
> >
> >
> > Does the recon-all function crop the image such that the Z dimension
> > is no longer matched with native space? I've noticed that the images
> > are cropped specifically from the bottom segment below the neck and
> > was wondering if that was affecting the coordinate report in the SI
> > axis. If this is the case, is this stored in freesurfer such that I
> > can get coordinates relative to the uncropped image or just the
> offset
> > value for the Z coordinate to compensate for it?
> >
> >
> > Thanks,
> >
> > Jerry Jeyachandra
> >
> >
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
>
> -------------- next part --------------
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> URL:
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> <http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170418/9c72ea7e/attachment-0001.html>
>
> ------------------------------
>
> Message: 5
> Date: Tue, 18 Apr 2017 21:49:05 -0400
> From: Douglas Greve <greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>
> Subject: Re: [Freesurfer] Selxavg3-sess Looking for (and can't find)
> "fmc.sm0"
> To: freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> Message-ID:
> <baec3fa1-d908-fbbc-865e-0f277001216c@nmr.mgh.harvard.edu
> <mailto:baec3fa1-d908-fbbc-865e-0f277001216c@nmr.mgh.harvard.edu>>
> Content-Type: text/plain; charset="windows-1252"
>
> Can you send the contents of glm_double_all_ps_0/analysis.info
> <http://analysis.info> ?
>
>
> On 4/17/17 4:44 PM, Taylor, Johnmark wrote:
> > Apologies for delayed response--here is the full terminal output.
> > (error in bold)
> >
> > --------------------------------------------------------------
> > selxavg3-sess logfile is
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/scripts/glm/log/selxavg3-sess-bold-glm_double_all_ps_0-170417150715.log
> > --------------------------------------------------------------
> > preproc-sess -s 170322_xu_binding01_sub01 -d
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata
> > -a glm_double_all_ps_0 -nolog
> > --------------------------------------------------------------
> > preproc-sess logfile is /dev/null
> > --------------------------------------------------------------
> > $Id: preproc-sess,v 1.45.2.3 2013/01/22 22:09:10 greve Exp $
> > jtaylor
> > setenv FREESURFER_HOME /ncf/nrg/sw/apps/freesurfer/5.3.0
> > setenv SUBJECTS_DIR /ncf/vcn/jtaylor/mri-space/subjects
> > Linux ncf2705.rc.fas.harvard.edu
> <http://ncf2705.rc.fas.harvard.edu>
> <http://ncf2705.rc.fas.harvard.edu
> <http://ncf2705.rc.fas.harvard.edu>>
> > 2.6.32-642.6.2.el6.x86_64 #1 SMP Wed Oct 26 06:52:09 UTC 2016 x86_64
> > x86_64 x86_64 GNU/Linux
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/scripts/glm
> > /ncf/vcn/jtaylor/programs/batch_edits/preproc-sess
> > -s 170322_xu_binding01_sub01 -d
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata
> > -a glm_double_all_ps_0 -nolog
> > Mon Apr 17 15:07:18 EDT 2017
> > instem f
> > mc 1 f fmc
> > stc 0 fmc
> > sm 0 fmc
> > mask 1 brain
> > 170322_xu_binding01_sub01 Template -----------------------------
> > mktemplate-sess -s 170322_xu_binding01_sub01 -d
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata
> > -fsd bold -rlf runlist_double.txt -nolog -update
> >
> > Session:
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170322_xu_binding01_sub01
> > ----------------
> > Mon Apr 17 15:07:18 EDT 2017
> > Detected input format at nii.gz
> > 170322_xu_binding01_sub01 Update not needed
> > Run: 008 ----------------
> > Mon Apr 17 15:07:19 EDT 2017
> > 170322_xu_binding01_sub01 008 Update not needed
> > Run: 010 ----------------
> > Mon Apr 17 15:07:19 EDT 2017
> > 170322_xu_binding01_sub01 010 Update not needed
> > Run: 012 ----------------
> > Mon Apr 17 15:07:19 EDT 2017
> > 170322_xu_binding01_sub01 012 Update not needed
> > Run: 020 ----------------
> > Mon Apr 17 15:07:19 EDT 2017
> > 170322_xu_binding01_sub01 020 Update not needed
> > Run: 022 ----------------
> > Mon Apr 17 15:07:19 EDT 2017
> > 170322_xu_binding01_sub01 022 Update not needed
> > Run: 024 ----------------
> > Mon Apr 17 15:07:19 EDT 2017
> > 170322_xu_binding01_sub01 024 Update not needed
> > Run: 034 ----------------
> > Mon Apr 17 15:07:19 EDT 2017
> > 170322_xu_binding01_sub01 034 Update not needed
> > Run: 036 ----------------
> > Mon Apr 17 15:07:19 EDT 2017
> > 170322_xu_binding01_sub01 036 Update not needed
> > Run: 038 ----------------
> > Mon Apr 17 15:07:19 EDT 2017
> > 170322_xu_binding01_sub01 038 Update not needed
> > Run: 046 ----------------
> > Mon Apr 17 15:07:19 EDT 2017
> > 170322_xu_binding01_sub01 046 Update not needed
> > Run: 048 ----------------
> > Mon Apr 17 15:07:19 EDT 2017
> > 170322_xu_binding01_sub01 048 Update not needed
> > Run: 050 ----------------
> > Mon Apr 17 15:07:19 EDT 2017
> > 170322_xu_binding01_sub01 050 Update not needed
> > Mon Apr 17 15:07:19 EDT 2017
> > mktemplate-sess completed
> > 170322_xu_binding01_sub01 Mask ------------------------
> > mkbrainmask-sess -maskstem brain -fsd bold -s
> > 170322_xu_binding01_sub01 -d
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata
> > -rlf runlist_double.txt -nolog -update
> > ------------------------------------------------
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170322_xu_binding01_sub01
> >
> > Mon Apr 17 15:07:19 EDT 2017
> > 170322_xu_binding01_sub01 Update not needed for session-level mask
> > 170322_xu_binding01_sub01 Update not needed for run 008 mask
> > 170322_xu_binding01_sub01 Update not needed for run 008 meanval
> > 170322_xu_binding01_sub01 Update not needed for run 010 mask
> > 170322_xu_binding01_sub01 Update not needed for run 010 meanval
> > 170322_xu_binding01_sub01 Update not needed for run 012 mask
> > 170322_xu_binding01_sub01 Update not needed for run 012 meanval
> > 170322_xu_binding01_sub01 Update not needed for run 020 mask
> > 170322_xu_binding01_sub01 Update not needed for run 020 meanval
> > 170322_xu_binding01_sub01 Update not needed for run 022 mask
> > 170322_xu_binding01_sub01 Update not needed for run 022 meanval
> > 170322_xu_binding01_sub01 Update not needed for run 024 mask
> > 170322_xu_binding01_sub01 Update not needed for run 024 meanval
> > 170322_xu_binding01_sub01 Update not needed for run 034 mask
> > 170322_xu_binding01_sub01 Update not needed for run 034 meanval
> > 170322_xu_binding01_sub01 Update not needed for run 036 mask
> > 170322_xu_binding01_sub01 Update not needed for run 036 meanval
> > 170322_xu_binding01_sub01 Update not needed for run 038 mask
> > 170322_xu_binding01_sub01 Update not needed for run 038 meanval
> > 170322_xu_binding01_sub01 Update not needed for run 046 mask
> > 170322_xu_binding01_sub01 Update not needed for run 046 meanval
> > 170322_xu_binding01_sub01 Update not needed for run 048 mask
> > 170322_xu_binding01_sub01 Update not needed for run 048 meanval
> > 170322_xu_binding01_sub01 Update not needed for run 050 mask
> > 170322_xu_binding01_sub01 Update not needed for run 050 meanval
> > Mon Apr 17 15:07:21 EDT 2017
> > mkbrainmask-sess done
> > 170322_xu_binding01_sub01 Registration -----------------------------
> > register-sess -s 170322_xu_binding01_sub01 -d
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata
> > -fsd bold -dof 6 -rlf runlist_double.txt -per-session -nolog -update
> > --------------------------------------------------------------
> > register-sess logfile is /dev/null
> > --------------------------------------------------------------
> > Mon Apr 17 15:07:22 EDT 2017
> >
> > setenv SUBJECTS_DIR /ncf/vcn/jtaylor/mri-space/subjects
> > cd
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/scripts/glm
> > /ncf/nrg/sw/apps/freesurfer/5.3.0/fsfast/bin/register-sess -s
> > 170322_xu_binding01_sub01 -d
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata
> > -fsd bold -dof 6 -rlf runlist_double.txt -per-session -nolog -update
> >
> > freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
> > Linux ncf2705.rc.fas.harvard.edu
> <http://ncf2705.rc.fas.harvard.edu>
> <http://ncf2705.rc.fas.harvard.edu
> <http://ncf2705.rc.fas.harvard.edu>>
> > 2.6.32-642.6.2.el6.x86_64 #1 SMP Wed Oct 26 06:52:09 UTC 2016 x86_64
> > x86_64 x86_64 GNU/Linux
> >
> > Session:
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170322_xu_binding01_sub01
> > ----------------
> > Mon Apr 17 15:07:22 EDT 2017
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170322_xu_binding01_sub01
> > Mon Apr 17 15:07:22 EDT 2017
> > register-sess completed
> > 170322_xu_binding01_sub01 MC -----------------------------
> > mc-sess -fstem f -fmcstem fmc -s 170322_xu_binding01_sub01 -d
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata
> > -fsd bold -rlf runlist_double.txt -per-session -nolog -update
> > Logfile is /dev/null
> > -------------------------------------------
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170322_xu_binding01_sub01
> >
> > RunList: 008 010 012 020 022 024 034 036 038 046 048 050
> > 170322_xu_binding01_sub01 008 Update not needed
> > 170322_xu_binding01_sub01 010 Update not needed
> > 170322_xu_binding01_sub01 012 Update not needed
> > 170322_xu_binding01_sub01 020 Update not needed
> > 170322_xu_binding01_sub01 022 Update not needed
> > 170322_xu_binding01_sub01 024 Update not needed
> > 170322_xu_binding01_sub01 034 Update not needed
> > 170322_xu_binding01_sub01 036 Update not needed
> > 170322_xu_binding01_sub01 038 Update not needed
> > 170322_xu_binding01_sub01 046 Update not needed
> > 170322_xu_binding01_sub01 048 Update not needed
> > 170322_xu_binding01_sub01 050 Update not needed
> >
> >
> > Mon Apr 17 15:07:22 EDT 2017
> > mc-sess completed SUCCESSFULLY
> > ----------------------------------------
> > Started at Mon Apr 17 15:07:18 EDT 2017
> > Ended at Mon Apr 17 15:07:22 EDT 2017
> > preproc-sess done
> > preproc-sess -s 170329_xu_binding01_sub02 -d
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata
> > -a glm_double_all_ps_0 -nolog
> > --------------------------------------------------------------
> > preproc-sess logfile is /dev/null
> > --------------------------------------------------------------
> > $Id: preproc-sess,v 1.45.2.3 2013/01/22 22:09:10 greve Exp $
> > jtaylor
> > setenv FREESURFER_HOME /ncf/nrg/sw/apps/freesurfer/5.3.0
> > setenv SUBJECTS_DIR /ncf/vcn/jtaylor/mri-space/subjects
> > Linux ncf2705.rc.fas.harvard.edu
> <http://ncf2705.rc.fas.harvard.edu>
> <http://ncf2705.rc.fas.harvard.edu
> <http://ncf2705.rc.fas.harvard.edu>>
> > 2.6.32-642.6.2.el6.x86_64 #1 SMP Wed Oct 26 06:52:09 UTC 2016 x86_64
> > x86_64 x86_64 GNU/Linux
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/scripts/glm
> > /ncf/vcn/jtaylor/programs/batch_edits/preproc-sess
> > -s 170329_xu_binding01_sub02 -d
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata
> > -a glm_double_all_ps_0 -nolog
> > Mon Apr 17 15:07:23 EDT 2017
> > instem f
> > mc 1 f fmc
> > stc 0 fmc
> > sm 0 fmc
> > mask 1 brain
> > 170329_xu_binding01_sub02 Template -----------------------------
> > mktemplate-sess -s 170329_xu_binding01_sub02 -d
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata
> > -fsd bold -rlf runlist_double.txt -nolog -update
> >
> > Session:
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170329_xu_binding01_sub02
> > ----------------
> > Mon Apr 17 15:07:23 EDT 2017
> > Detected input format at nii.gz
> > 170329_xu_binding01_sub02 Update not needed
> > Run: 014 ----------------
> > Mon Apr 17 15:07:23 EDT 2017
> > 170329_xu_binding01_sub02 014 Update not needed
> > Run: 016 ----------------
> > Mon Apr 17 15:07:23 EDT 2017
> > 170329_xu_binding01_sub02 016 Update not needed
> > Run: 018 ----------------
> > Mon Apr 17 15:07:23 EDT 2017
> > 170329_xu_binding01_sub02 018 Update not needed
> > Run: 026 ----------------
> > Mon Apr 17 15:07:23 EDT 2017
> > 170329_xu_binding01_sub02 026 Update not needed
> > Run: 028 ----------------
> > Mon Apr 17 15:07:23 EDT 2017
> > 170329_xu_binding01_sub02 028 Update not needed
> > Run: 030 ----------------
> > Mon Apr 17 15:07:24 EDT 2017
> > 170329_xu_binding01_sub02 030 Update not needed
> > Run: 040 ----------------
> > Mon Apr 17 15:07:24 EDT 2017
> > 170329_xu_binding01_sub02 040 Update not needed
> > Run: 042 ----------------
> > Mon Apr 17 15:07:24 EDT 2017
> > 170329_xu_binding01_sub02 042 Update not needed
> > Run: 044 ----------------
> > Mon Apr 17 15:07:24 EDT 2017
> > 170329_xu_binding01_sub02 044 Update not needed
> > Run: 052 ----------------
> > Mon Apr 17 15:07:24 EDT 2017
> > 170329_xu_binding01_sub02 052 Update not needed
> > Run: 054 ----------------
> > Mon Apr 17 15:07:24 EDT 2017
> > 170329_xu_binding01_sub02 054 Update not needed
> > Run: 056 ----------------
> > Mon Apr 17 15:07:24 EDT 2017
> > 170329_xu_binding01_sub02 056 Update not needed
> > Mon Apr 17 15:07:24 EDT 2017
> > mktemplate-sess completed
> > 170329_xu_binding01_sub02 Mask ------------------------
> > mkbrainmask-sess -maskstem brain -fsd bold -s
> > 170329_xu_binding01_sub02 -d
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata
> > -rlf runlist_double.txt -nolog -update
> > ------------------------------------------------
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170329_xu_binding01_sub02
> >
> > Mon Apr 17 15:07:24 EDT 2017
> > 170329_xu_binding01_sub02 Update not needed for session-level mask
> > 170329_xu_binding01_sub02 Update not needed for run 014 mask
> > 170329_xu_binding01_sub02 Update not needed for run 014 meanval
> > 170329_xu_binding01_sub02 Update not needed for run 016 mask
> > 170329_xu_binding01_sub02 Update not needed for run 016 meanval
> > 170329_xu_binding01_sub02 Update not needed for run 018 mask
> > 170329_xu_binding01_sub02 Update not needed for run 018 meanval
> > 170329_xu_binding01_sub02 Update not needed for run 026 mask
> > 170329_xu_binding01_sub02 Update not needed for run 026 meanval
> > 170329_xu_binding01_sub02 Update not needed for run 028 mask
> > 170329_xu_binding01_sub02 Update not needed for run 028 meanval
> > 170329_xu_binding01_sub02 Update not needed for run 030 mask
> > 170329_xu_binding01_sub02 Update not needed for run 030 meanval
> > 170329_xu_binding01_sub02 Update not needed for run 040 mask
> > 170329_xu_binding01_sub02 Update not needed for run 040 meanval
> > 170329_xu_binding01_sub02 Update not needed for run 042 mask
> > 170329_xu_binding01_sub02 Update not needed for run 042 meanval
> > 170329_xu_binding01_sub02 Update not needed for run 044 mask
> > 170329_xu_binding01_sub02 Update not needed for run 044 meanval
> > 170329_xu_binding01_sub02 Update not needed for run 052 mask
> > 170329_xu_binding01_sub02 Update not needed for run 052 meanval
> > 170329_xu_binding01_sub02 Update not needed for run 054 mask
> > 170329_xu_binding01_sub02 Update not needed for run 054 meanval
> > 170329_xu_binding01_sub02 Update not needed for run 056 mask
> > 170329_xu_binding01_sub02 Update not needed for run 056 meanval
> > Mon Apr 17 15:07:27 EDT 2017
> > mkbrainmask-sess done
> > 170329_xu_binding01_sub02 Registration -----------------------------
> > register-sess -s 170329_xu_binding01_sub02 -d
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata
> > -fsd bold -dof 6 -rlf runlist_double.txt -per-session -nolog -update
> > --------------------------------------------------------------
> > register-sess logfile is /dev/null
> > --------------------------------------------------------------
> > Mon Apr 17 15:07:27 EDT 2017
> >
> > setenv SUBJECTS_DIR /ncf/vcn/jtaylor/mri-space/subjects
> > cd
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/scripts/glm
> > /ncf/nrg/sw/apps/freesurfer/5.3.0/fsfast/bin/register-sess -s
> > 170329_xu_binding01_sub02 -d
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata
> > -fsd bold -dof 6 -rlf runlist_double.txt -per-session -nolog -update
> >
> > freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
> > Linux ncf2705.rc.fas.harvard.edu
> <http://ncf2705.rc.fas.harvard.edu>
> <http://ncf2705.rc.fas.harvard.edu
> <http://ncf2705.rc.fas.harvard.edu>>
> > 2.6.32-642.6.2.el6.x86_64 #1 SMP Wed Oct 26 06:52:09 UTC 2016 x86_64
> > x86_64 x86_64 GNU/Linux
> >
> > Session:
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170329_xu_binding01_sub02
> > ----------------
> > Mon Apr 17 15:07:27 EDT 2017
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170329_xu_binding01_sub02
> > Mon Apr 17 15:07:27 EDT 2017
> > register-sess completed
> > 170329_xu_binding01_sub02 MC -----------------------------
> > mc-sess -fstem f -fmcstem fmc -s 170329_xu_binding01_sub02 -d
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata
> > -fsd bold -rlf runlist_double.txt -per-session -nolog -update
> > Logfile is /dev/null
> > -------------------------------------------
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170329_xu_binding01_sub02
> >
> > RunList: 014 016 018 026 028 030 040 042 044 052 054 056
> > 170329_xu_binding01_sub02 014 Update not needed
> > 170329_xu_binding01_sub02 016 Update not needed
> > 170329_xu_binding01_sub02 018 Update not needed
> > 170329_xu_binding01_sub02 026 Update not needed
> > 170329_xu_binding01_sub02 028 Update not needed
> > 170329_xu_binding01_sub02 030 Update not needed
> > 170329_xu_binding01_sub02 040 Update not needed
> > 170329_xu_binding01_sub02 042 Update not needed
> > 170329_xu_binding01_sub02 044 Update not needed
> > 170329_xu_binding01_sub02 052 Update not needed
> > 170329_xu_binding01_sub02 054 Update not needed
> > 170329_xu_binding01_sub02 056 Update not needed
> >
> >
> > Mon Apr 17 15:07:28 EDT 2017
> > mc-sess completed SUCCESSFULLY
> > ----------------------------------------
> > Started at Mon Apr 17 15:07:23 EDT 2017
> > Ended at Mon Apr 17 15:07:28 EDT 2017
> > preproc-sess done
> > preproc-sess -s 170402_xu_binding01_sub03 -d
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata
> > -a glm_double_all_ps_0 -nolog
> > --------------------------------------------------------------
> > preproc-sess logfile is /dev/null
> > --------------------------------------------------------------
> > $Id: preproc-sess,v 1.45.2.3 2013/01/22 22:09:10 greve Exp $
> > jtaylor
> > setenv FREESURFER_HOME /ncf/nrg/sw/apps/freesurfer/5.3.0
> > setenv SUBJECTS_DIR /ncf/vcn/jtaylor/mri-space/subjects
> > Linux ncf2705.rc.fas.harvard.edu
> <http://ncf2705.rc.fas.harvard.edu>
> <http://ncf2705.rc.fas.harvard.edu
> <http://ncf2705.rc.fas.harvard.edu>>
> > 2.6.32-642.6.2.el6.x86_64 #1 SMP Wed Oct 26 06:52:09 UTC 2016 x86_64
> > x86_64 x86_64 GNU/Linux
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/scripts/glm
> > /ncf/vcn/jtaylor/programs/batch_edits/preproc-sess
> > -s 170402_xu_binding01_sub03 -d
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata
> > -a glm_double_all_ps_0 -nolog
> > Mon Apr 17 15:07:28 EDT 2017
> > instem f
> > mc 1 f fmc
> > stc 0 fmc
> > sm 0 fmc
> > mask 1 brain
> > 170402_xu_binding01_sub03 Template -----------------------------
> > mktemplate-sess -s 170402_xu_binding01_sub03 -d
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata
> > -fsd bold -rlf runlist_double.txt -nolog -update
> >
> > Session:
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170402_xu_binding01_sub03
> > ----------------
> > Mon Apr 17 15:07:29 EDT 2017
> > Detected input format at nii.gz
> > 170402_xu_binding01_sub03 Update not needed
> > Run: 008 ----------------
> > Mon Apr 17 15:07:29 EDT 2017
> > 170402_xu_binding01_sub03 008 Update not needed
> > Run: 010 ----------------
> > Mon Apr 17 15:07:29 EDT 2017
> > 170402_xu_binding01_sub03 010 Update not needed
> > Run: 012 ----------------
> > Mon Apr 17 15:07:29 EDT 2017
> > 170402_xu_binding01_sub03 012 Update not needed
> > Run: 020 ----------------
> > Mon Apr 17 15:07:29 EDT 2017
> > 170402_xu_binding01_sub03 020 Update not needed
> > Run: 022 ----------------
> > Mon Apr 17 15:07:29 EDT 2017
> > 170402_xu_binding01_sub03 022 Update not needed
> > Run: 024 ----------------
> > Mon Apr 17 15:07:29 EDT 2017
> > 170402_xu_binding01_sub03 024 Update not needed
> > Run: 034 ----------------
> > Mon Apr 17 15:07:29 EDT 2017
> > 170402_xu_binding01_sub03 034 Update not needed
> > Run: 036 ----------------
> > Mon Apr 17 15:07:29 EDT 2017
> > 170402_xu_binding01_sub03 036 Update not needed
> > Run: 038 ----------------
> > Mon Apr 17 15:07:29 EDT 2017
> > 170402_xu_binding01_sub03 038 Update not needed
> > Run: 046 ----------------
> > Mon Apr 17 15:07:29 EDT 2017
> > 170402_xu_binding01_sub03 046 Update not needed
> > Run: 048 ----------------
> > Mon Apr 17 15:07:29 EDT 2017
> > 170402_xu_binding01_sub03 048 Update not needed
> > Run: 050 ----------------
> > Mon Apr 17 15:07:29 EDT 2017
> > 170402_xu_binding01_sub03 050 Update not needed
> > Mon Apr 17 15:07:29 EDT 2017
> > mktemplate-sess completed
> > 170402_xu_binding01_sub03 Mask ------------------------
> > mkbrainmask-sess -maskstem brain -fsd bold -s
> > 170402_xu_binding01_sub03 -d
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata
> > -rlf runlist_double.txt -nolog -update
> > ------------------------------------------------
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170402_xu_binding01_sub03
> >
> > Mon Apr 17 15:07:29 EDT 2017
> > 170402_xu_binding01_sub03 Update not needed for session-level mask
> > 170402_xu_binding01_sub03 Update not needed for run 008 mask
> > 170402_xu_binding01_sub03 Update not needed for run 008 meanval
> > 170402_xu_binding01_sub03 Update not needed for run 010 mask
> > 170402_xu_binding01_sub03 Update not needed for run 010 meanval
> > 170402_xu_binding01_sub03 Update not needed for run 012 mask
> > 170402_xu_binding01_sub03 Update not needed for run 012 meanval
> > 170402_xu_binding01_sub03 Update not needed for run 020 mask
> > 170402_xu_binding01_sub03 Update not needed for run 020 meanval
> > 170402_xu_binding01_sub03 Update not needed for run 022 mask
> > 170402_xu_binding01_sub03 Update not needed for run 022 meanval
> > 170402_xu_binding01_sub03 Update not needed for run 024 mask
> > 170402_xu_binding01_sub03 Update not needed for run 024 meanval
> > 170402_xu_binding01_sub03 Update not needed for run 034 mask
> > 170402_xu_binding01_sub03 Update not needed for run 034 meanval
> > 170402_xu_binding01_sub03 Update not needed for run 036 mask
> > 170402_xu_binding01_sub03 Update not needed for run 036 meanval
> > 170402_xu_binding01_sub03 Update not needed for run 038 mask
> > 170402_xu_binding01_sub03 Update not needed for run 038 meanval
> > 170402_xu_binding01_sub03 Update not needed for run 046 mask
> > 170402_xu_binding01_sub03 Update not needed for run 046 meanval
> > 170402_xu_binding01_sub03 Update not needed for run 048 mask
> > 170402_xu_binding01_sub03 Update not needed for run 048 meanval
> > 170402_xu_binding01_sub03 Update not needed for run 050 mask
> > 170402_xu_binding01_sub03 Update not needed for run 050 meanval
> > Mon Apr 17 15:07:32 EDT 2017
> > mkbrainmask-sess done
> > 170402_xu_binding01_sub03 Registration -----------------------------
> > register-sess -s 170402_xu_binding01_sub03 -d
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata
> > -fsd bold -dof 6 -rlf runlist_double.txt -per-session -nolog -update
> > --------------------------------------------------------------
> > register-sess logfile is /dev/null
> > --------------------------------------------------------------
> > Mon Apr 17 15:07:32 EDT 2017
> >
> > setenv SUBJECTS_DIR /ncf/vcn/jtaylor/mri-space/subjects
> > cd
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/scripts/glm
> > /ncf/nrg/sw/apps/freesurfer/5.3.0/fsfast/bin/register-sess -s
> > 170402_xu_binding01_sub03 -d
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata
> > -fsd bold -dof 6 -rlf runlist_double.txt -per-session -nolog -update
> >
> > freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
> > Linux ncf2705.rc.fas.harvard.edu
> <http://ncf2705.rc.fas.harvard.edu>
> <http://ncf2705.rc.fas.harvard.edu
> <http://ncf2705.rc.fas.harvard.edu>>
> > 2.6.32-642.6.2.el6.x86_64 #1 SMP Wed Oct 26 06:52:09 UTC 2016 x86_64
> > x86_64 x86_64 GNU/Linux
> >
> > Session:
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170402_xu_binding01_sub03
> > ----------------
> > Mon Apr 17 15:07:32 EDT 2017
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170402_xu_binding01_sub03
> > Mon Apr 17 15:07:32 EDT 2017
> > register-sess completed
> > 170402_xu_binding01_sub03 MC -----------------------------
> > mc-sess -fstem f -fmcstem fmc -s 170402_xu_binding01_sub03 -d
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata
> > -fsd bold -rlf runlist_double.txt -per-session -nolog -update
> > Logfile is /dev/null
> > -------------------------------------------
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170402_xu_binding01_sub03
> >
> > RunList: 008 010 012 020 022 024 034 036 038 046 048 050
> > 170402_xu_binding01_sub03 008 Update not needed
> > 170402_xu_binding01_sub03 010 Update not needed
> > 170402_xu_binding01_sub03 012 Update not needed
> > 170402_xu_binding01_sub03 020 Update not needed
> > 170402_xu_binding01_sub03 022 Update not needed
> > 170402_xu_binding01_sub03 024 Update not needed
> > 170402_xu_binding01_sub03 034 Update not needed
> > 170402_xu_binding01_sub03 036 Update not needed
> > 170402_xu_binding01_sub03 038 Update not needed
> > 170402_xu_binding01_sub03 046 Update not needed
> > 170402_xu_binding01_sub03 048 Update not needed
> > 170402_xu_binding01_sub03 050 Update not needed
> >
> >
> > Mon Apr 17 15:07:33 EDT 2017
> > mc-sess completed SUCCESSFULLY
> > ----------------------------------------
> > Started at Mon Apr 17 15:07:28 EDT 2017
> > Ended at Mon Apr 17 15:07:33 EDT 2017
> > preproc-sess done
> > preproc-sess -s 170402_xu_binding01_sub04 -d
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata
> > -a glm_double_all_ps_0 -nolog
> > --------------------------------------------------------------
> > preproc-sess logfile is /dev/null
> > --------------------------------------------------------------
> > $Id: preproc-sess,v 1.45.2.3 2013/01/22 22:09:10 greve Exp $
> > jtaylor
> > setenv FREESURFER_HOME /ncf/nrg/sw/apps/freesurfer/5.3.0
> > setenv SUBJECTS_DIR /ncf/vcn/jtaylor/mri-space/subjects
> > Linux ncf2705.rc.fas.harvard.edu
> <http://ncf2705.rc.fas.harvard.edu>
> <http://ncf2705.rc.fas.harvard.edu
> <http://ncf2705.rc.fas.harvard.edu>>
> > 2.6.32-642.6.2.el6.x86_64 #1 SMP Wed Oct 26 06:52:09 UTC 2016 x86_64
> > x86_64 x86_64 GNU/Linux
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/scripts/glm
> > /ncf/vcn/jtaylor/programs/batch_edits/preproc-sess
> > -s 170402_xu_binding01_sub04 -d
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata
> > -a glm_double_all_ps_0 -nolog
> > Mon Apr 17 15:07:33 EDT 2017
> > instem f
> > mc 1 f fmc
> > stc 0 fmc
> > sm 0 fmc
> > mask 1 brain
> > 170402_xu_binding01_sub04 Template -----------------------------
> > mktemplate-sess -s 170402_xu_binding01_sub04 -d
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata
> > -fsd bold -rlf runlist_double.txt -nolog -update
> >
> > Session:
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170402_xu_binding01_sub04
> > ----------------
> > Mon Apr 17 15:07:33 EDT 2017
> > Detected input format at nii.gz
> > 170402_xu_binding01_sub04 Update not needed
> > Run: 014 ----------------
> > Mon Apr 17 15:07:34 EDT 2017
> > 170402_xu_binding01_sub04 014 Update not needed
> > Run: 016 ----------------
> > Mon Apr 17 15:07:34 EDT 2017
> > 170402_xu_binding01_sub04 016 Update not needed
> > Run: 018 ----------------
> > Mon Apr 17 15:07:34 EDT 2017
> > 170402_xu_binding01_sub04 018 Update not needed
> > Run: 026 ----------------
> > Mon Apr 17 15:07:34 EDT 2017
> > 170402_xu_binding01_sub04 026 Update not needed
> > Run: 028 ----------------
> > Mon Apr 17 15:07:34 EDT 2017
> > 170402_xu_binding01_sub04 028 Update not needed
> > Run: 030 ----------------
> > Mon Apr 17 15:07:34 EDT 2017
> > 170402_xu_binding01_sub04 030 Update not needed
> > Run: 040 ----------------
> > Mon Apr 17 15:07:34 EDT 2017
> > 170402_xu_binding01_sub04 040 Update not needed
> > Run: 042 ----------------
> > Mon Apr 17 15:07:34 EDT 2017
> > 170402_xu_binding01_sub04 042 Update not needed
> > Run: 044 ----------------
> > Mon Apr 17 15:07:34 EDT 2017
> > 170402_xu_binding01_sub04 044 Update not needed
> > Run: 052 ----------------
> > Mon Apr 17 15:07:34 EDT 2017
> > 170402_xu_binding01_sub04 052 Update not needed
> > Run: 054 ----------------
> > Mon Apr 17 15:07:34 EDT 2017
> > 170402_xu_binding01_sub04 054 Update not needed
> > Run: 056 ----------------
> > Mon Apr 17 15:07:34 EDT 2017
> > 170402_xu_binding01_sub04 056 Update not needed
> > Mon Apr 17 15:07:34 EDT 2017
> > mktemplate-sess completed
> > 170402_xu_binding01_sub04 Mask ------------------------
> > mkbrainmask-sess -maskstem brain -fsd bold -s
> > 170402_xu_binding01_sub04 -d
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata
> > -rlf runlist_double.txt -nolog -update
> > ------------------------------------------------
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170402_xu_binding01_sub04
> >
> > Mon Apr 17 15:07:34 EDT 2017
> > 170402_xu_binding01_sub04 Update not needed for session-level mask
> > 170402_xu_binding01_sub04 Update not needed for run 014 mask
> > 170402_xu_binding01_sub04 Update not needed for run 014 meanval
> > 170402_xu_binding01_sub04 Update not needed for run 016 mask
> > 170402_xu_binding01_sub04 Update not needed for run 016 meanval
> > 170402_xu_binding01_sub04 Update not needed for run 018 mask
> > 170402_xu_binding01_sub04 Update not needed for run 018 meanval
> > 170402_xu_binding01_sub04 Update not needed for run 026 mask
> > 170402_xu_binding01_sub04 Update not needed for run 026 meanval
> > 170402_xu_binding01_sub04 Update not needed for run 028 mask
> > 170402_xu_binding01_sub04 Update not needed for run 028 meanval
> > 170402_xu_binding01_sub04 Update not needed for run 030 mask
> > 170402_xu_binding01_sub04 Update not needed for run 030 meanval
> > 170402_xu_binding01_sub04 Update not needed for run 040 mask
> > 170402_xu_binding01_sub04 Update not needed for run 040 meanval
> > 170402_xu_binding01_sub04 Update not needed for run 042 mask
> > 170402_xu_binding01_sub04 Update not needed for run 042 meanval
> > 170402_xu_binding01_sub04 Update not needed for run 044 mask
> > 170402_xu_binding01_sub04 Update not needed for run 044 meanval
> > 170402_xu_binding01_sub04 Update not needed for run 052 mask
> > 170402_xu_binding01_sub04 Update not needed for run 052 meanval
> > 170402_xu_binding01_sub04 Update not needed for run 054 mask
> > 170402_xu_binding01_sub04 Update not needed for run 054 meanval
> > 170402_xu_binding01_sub04 Update not needed for run 056 mask
> > 170402_xu_binding01_sub04 Update not needed for run 056 meanval
> > Mon Apr 17 15:07:36 EDT 2017
> > mkbrainmask-sess done
> > 170402_xu_binding01_sub04 Registration -----------------------------
> > register-sess -s 170402_xu_binding01_sub04 -d
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata
> > -fsd bold -dof 6 -rlf runlist_double.txt -per-session -nolog -update
> > --------------------------------------------------------------
> > register-sess logfile is /dev/null
> > --------------------------------------------------------------
> > Mon Apr 17 15:07:37 EDT 2017
> >
> > setenv SUBJECTS_DIR /ncf/vcn/jtaylor/mri-space/subjects
> > cd
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/scripts/glm
> > /ncf/nrg/sw/apps/freesurfer/5.3.0/fsfast/bin/register-sess -s
> > 170402_xu_binding01_sub04 -d
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata
> > -fsd bold -dof 6 -rlf runlist_double.txt -per-session -nolog -update
> >
> > freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
> > Linux ncf2705.rc.fas.harvard.edu
> <http://ncf2705.rc.fas.harvard.edu>
> <http://ncf2705.rc.fas.harvard.edu
> <http://ncf2705.rc.fas.harvard.edu>>
> > 2.6.32-642.6.2.el6.x86_64 #1 SMP Wed Oct 26 06:52:09 UTC 2016 x86_64
> > x86_64 x86_64 GNU/Linux
> >
> > Session:
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170402_xu_binding01_sub04
> > ----------------
> > Mon Apr 17 15:07:37 EDT 2017
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170402_xu_binding01_sub04
> > Mon Apr 17 15:07:37 EDT 2017
> > register-sess completed
> > 170402_xu_binding01_sub04 MC -----------------------------
> > mc-sess -fstem f -fmcstem fmc -s 170402_xu_binding01_sub04 -d
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata
> > -fsd bold -rlf runlist_double.txt -per-session -nolog -update
> > Logfile is /dev/null
> > -------------------------------------------
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170402_xu_binding01_sub04
> >
> > RunList: 014 016 018 026 028 030 040 042 044 052 054 056
> > 170402_xu_binding01_sub04 014 Update not needed
> > 170402_xu_binding01_sub04 016 Update not needed
> > 170402_xu_binding01_sub04 018 Update not needed
> > 170402_xu_binding01_sub04 026 Update not needed
> > 170402_xu_binding01_sub04 028 Update not needed
> > 170402_xu_binding01_sub04 030 Update not needed
> > 170402_xu_binding01_sub04 040 Update not needed
> > 170402_xu_binding01_sub04 042 Update not needed
> > 170402_xu_binding01_sub04 044 Update not needed
> > 170402_xu_binding01_sub04 052 Update not needed
> > 170402_xu_binding01_sub04 054 Update not needed
> > 170402_xu_binding01_sub04 056 Update not needed
> >
> >
> > Mon Apr 17 15:07:37 EDT 2017
> > mc-sess completed SUCCESSFULLY
> > ----------------------------------------
> > Started at Mon Apr 17 15:07:33 EDT 2017
> > Ended at Mon Apr 17 15:07:37 EDT 2017
> > preproc-sess done
> > preproc-sess -s 170412_xu_binding01_sub05 -d
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata
> > -a glm_double_all_ps_0 -nolog
> > --------------------------------------------------------------
> > preproc-sess logfile is /dev/null
> > --------------------------------------------------------------
> > $Id: preproc-sess,v 1.45.2.3 2013/01/22 22:09:10 greve Exp $
> > jtaylor
> > setenv FREESURFER_HOME /ncf/nrg/sw/apps/freesurfer/5.3.0
> > setenv SUBJECTS_DIR /ncf/vcn/jtaylor/mri-space/subjects
> > Linux ncf2705.rc.fas.harvard.edu
> <http://ncf2705.rc.fas.harvard.edu>
> <http://ncf2705.rc.fas.harvard.edu
> <http://ncf2705.rc.fas.harvard.edu>>
> > 2.6.32-642.6.2.el6.x86_64 #1 SMP Wed Oct 26 06:52:09 UTC 2016 x86_64
> > x86_64 x86_64 GNU/Linux
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/scripts/glm
> > /ncf/vcn/jtaylor/programs/batch_edits/preproc-sess
> > -s 170412_xu_binding01_sub05 -d
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata
> > -a glm_double_all_ps_0 -nolog
> > Mon Apr 17 15:07:38 EDT 2017
> > instem f
> > mc 1 f fmc
> > stc 0 fmc
> > sm 0 fmc
> > mask 1 brain
> > 170412_xu_binding01_sub05 Template -----------------------------
> > mktemplate-sess -s 170412_xu_binding01_sub05 -d
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata
> > -fsd bold -rlf runlist_double.txt -nolog -update
> >
> > Session:
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170412_xu_binding01_sub05
> > ----------------
> > Mon Apr 17 15:07:38 EDT 2017
> > Detected input format at nii.gz
> > 170412_xu_binding01_sub05 Update not needed
> > Run: 008 ----------------
> > Mon Apr 17 15:07:38 EDT 2017
> > 170412_xu_binding01_sub05 008 Update not needed
> > Run: 010 ----------------
> > Mon Apr 17 15:07:38 EDT 2017
> > 170412_xu_binding01_sub05 010 Update not needed
> > Run: 012 ----------------
> > Mon Apr 17 15:07:38 EDT 2017
> > 170412_xu_binding01_sub05 012 Update not needed
> > Run: 020 ----------------
> > Mon Apr 17 15:07:38 EDT 2017
> > 170412_xu_binding01_sub05 020 Update not needed
> > Run: 022 ----------------
> > Mon Apr 17 15:07:38 EDT 2017
> > 170412_xu_binding01_sub05 022 Update not needed
> > Run: 024 ----------------
> > Mon Apr 17 15:07:38 EDT 2017
> > 170412_xu_binding01_sub05 024 Update not needed
> > Run: 034 ----------------
> > Mon Apr 17 15:07:38 EDT 2017
> > 170412_xu_binding01_sub05 034 Update not needed
> > Run: 036 ----------------
> > Mon Apr 17 15:07:39 EDT 2017
> > 170412_xu_binding01_sub05 036 Update not needed
> > Run: 038 ----------------
> > Mon Apr 17 15:07:39 EDT 2017
> > 170412_xu_binding01_sub05 038 Update not needed
> > Run: 046 ----------------
> > Mon Apr 17 15:07:39 EDT 2017
> > 170412_xu_binding01_sub05 046 Update not needed
> > Run: 048 ----------------
> > Mon Apr 17 15:07:39 EDT 2017
> > 170412_xu_binding01_sub05 048 Update not needed
> > Run: 050 ----------------
> > Mon Apr 17 15:07:39 EDT 2017
> > 170412_xu_binding01_sub05 050 Update not needed
> > Mon Apr 17 15:07:39 EDT 2017
> > mktemplate-sess completed
> > 170412_xu_binding01_sub05 Mask ------------------------
> > mkbrainmask-sess -maskstem brain -fsd bold -s
> > 170412_xu_binding01_sub05 -d
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata
> > -rlf runlist_double.txt -nolog -update
> > ------------------------------------------------
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170412_xu_binding01_sub05
> >
> > Mon Apr 17 15:07:39 EDT 2017
> > 170412_xu_binding01_sub05 Update not needed for session-level mask
> > 170412_xu_binding01_sub05 Update not needed for run 008 mask
> > 170412_xu_binding01_sub05 Update not needed for run 008 meanval
> > 170412_xu_binding01_sub05 Update not needed for run 010 mask
> > 170412_xu_binding01_sub05 Update not needed for run 010 meanval
> > 170412_xu_binding01_sub05 Update not needed for run 012 mask
> > 170412_xu_binding01_sub05 Update not needed for run 012 meanval
> > 170412_xu_binding01_sub05 Update not needed for run 020 mask
> > 170412_xu_binding01_sub05 Update not needed for run 020 meanval
> > 170412_xu_binding01_sub05 Update not needed for run 022 mask
> > 170412_xu_binding01_sub05 Update not needed for run 022 meanval
> > 170412_xu_binding01_sub05 Update not needed for run 024 mask
> > 170412_xu_binding01_sub05 Update not needed for run 024 meanval
> > 170412_xu_binding01_sub05 Update not needed for run 034 mask
> > 170412_xu_binding01_sub05 Update not needed for run 034 meanval
> > 170412_xu_binding01_sub05 Update not needed for run 036 mask
> > 170412_xu_binding01_sub05 Update not needed for run 036 meanval
> > 170412_xu_binding01_sub05 Update not needed for run 038 mask
> > 170412_xu_binding01_sub05 Update not needed for run 038 meanval
> > 170412_xu_binding01_sub05 Update not needed for run 046 mask
> > 170412_xu_binding01_sub05 Update not needed for run 046 meanval
> > 170412_xu_binding01_sub05 Update not needed for run 048 mask
> > 170412_xu_binding01_sub05 Update not needed for run 048 meanval
> > 170412_xu_binding01_sub05 Update not needed for run 050 mask
> > 170412_xu_binding01_sub05 Update not needed for run 050 meanval
> > Mon Apr 17 15:07:41 EDT 2017
> > mkbrainmask-sess done
> > 170412_xu_binding01_sub05 Registration -----------------------------
> > register-sess -s 170412_xu_binding01_sub05 -d
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata
> > -fsd bold -dof 6 -rlf runlist_double.txt -per-session -nolog -update
> > --------------------------------------------------------------
> > register-sess logfile is /dev/null
> > --------------------------------------------------------------
> > Mon Apr 17 15:07:41 EDT 2017
> >
> > setenv SUBJECTS_DIR /ncf/vcn/jtaylor/mri-space/subjects
> > cd
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/scripts/glm
> > /ncf/nrg/sw/apps/freesurfer/5.3.0/fsfast/bin/register-sess -s
> > 170412_xu_binding01_sub05 -d
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata
> > -fsd bold -dof 6 -rlf runlist_double.txt -per-session -nolog -update
> >
> > freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
> > Linux ncf2705.rc.fas.harvard.edu
> <http://ncf2705.rc.fas.harvard.edu>
> <http://ncf2705.rc.fas.harvard.edu
> <http://ncf2705.rc.fas.harvard.edu>>
> > 2.6.32-642.6.2.el6.x86_64 #1 SMP Wed Oct 26 06:52:09 UTC 2016 x86_64
> > x86_64 x86_64 GNU/Linux
> >
> > Session:
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170412_xu_binding01_sub05
> > ----------------
> > Mon Apr 17 15:07:41 EDT 2017
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170412_xu_binding01_sub05
> > Mon Apr 17 15:07:42 EDT 2017
> > register-sess completed
> > 170412_xu_binding01_sub05 MC -----------------------------
> > mc-sess -fstem f -fmcstem fmc -s 170412_xu_binding01_sub05 -d
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata
> > -fsd bold -rlf runlist_double.txt -per-session -nolog -update
> > Logfile is /dev/null
> > -------------------------------------------
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170412_xu_binding01_sub05
> >
> > RunList: 008 010 012 020 022 024 034 036 038 046 048 050
> > 170412_xu_binding01_sub05 008 Update not needed
> > 170412_xu_binding01_sub05 010 Update not needed
> > 170412_xu_binding01_sub05 012 Update not needed
> > 170412_xu_binding01_sub05 020 Update not needed
> > 170412_xu_binding01_sub05 022 Update not needed
> > 170412_xu_binding01_sub05 024 Update not needed
> > 170412_xu_binding01_sub05 034 Update not needed
> > 170412_xu_binding01_sub05 036 Update not needed
> > 170412_xu_binding01_sub05 038 Update not needed
> > 170412_xu_binding01_sub05 046 Update not needed
> > 170412_xu_binding01_sub05 048 Update not needed
> > 170412_xu_binding01_sub05 050 Update not needed
> >
> >
> > Mon Apr 17 15:07:42 EDT 2017
> > mc-sess completed SUCCESSFULLY
> > ----------------------------------------
> > Started at Mon Apr 17 15:07:38 EDT 2017
> > Ended at Mon Apr 17 15:07:42 EDT 2017
> > preproc-sess done
> > preproc-sess -s 170416_xu_binding01_sub06 -d
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata
> > -a glm_double_all_ps_0 -nolog
> > --------------------------------------------------------------
> > preproc-sess logfile is /dev/null
> > --------------------------------------------------------------
> > $Id: preproc-sess,v 1.45.2.3 2013/01/22 22:09:10 greve Exp $
> > jtaylor
> > setenv FREESURFER_HOME /ncf/nrg/sw/apps/freesurfer/5.3.0
> > setenv SUBJECTS_DIR /ncf/vcn/jtaylor/mri-space/subjects
> > Linux ncf2705.rc.fas.harvard.edu
> <http://ncf2705.rc.fas.harvard.edu>
> <http://ncf2705.rc.fas.harvard.edu
> <http://ncf2705.rc.fas.harvard.edu>>
> > 2.6.32-642.6.2.el6.x86_64 #1 SMP Wed Oct 26 06:52:09 UTC 2016 x86_64
> > x86_64 x86_64 GNU/Linux
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/scripts/glm
> > /ncf/vcn/jtaylor/programs/batch_edits/preproc-sess
> > -s 170416_xu_binding01_sub06 -d
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata
> > -a glm_double_all_ps_0 -nolog
> > Mon Apr 17 15:07:43 EDT 2017
> > instem f
> > mc 1 f fmc
> > stc 0 fmc
> > sm 0 fmc
> > mask 1 brain
> > 170416_xu_binding01_sub06 Template -----------------------------
> > mktemplate-sess -s 170416_xu_binding01_sub06 -d
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata
> > -fsd bold -rlf runlist_double.txt -nolog -update
> >
> > Session:
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170416_xu_binding01_sub06
> > ----------------
> > Mon Apr 17 15:07:43 EDT 2017
> > Detected input format at nii.gz
> > 170416_xu_binding01_sub06 Update not needed
> > Run: 014 ----------------
> > Mon Apr 17 15:07:43 EDT 2017
> > 170416_xu_binding01_sub06 014 Update not needed
> > Run: 016 ----------------
> > Mon Apr 17 15:07:43 EDT 2017
> > 170416_xu_binding01_sub06 016 Update not needed
> > Run: 018 ----------------
> > Mon Apr 17 15:07:43 EDT 2017
> > 170416_xu_binding01_sub06 018 Update not needed
> > Run: 026 ----------------
> > Mon Apr 17 15:07:43 EDT 2017
> > 170416_xu_binding01_sub06 026 Update not needed
> > Run: 028 ----------------
> > Mon Apr 17 15:07:43 EDT 2017
> > 170416_xu_binding01_sub06 028 Update not needed
> > Run: 030 ----------------
> > Mon Apr 17 15:07:43 EDT 2017
> > 170416_xu_binding01_sub06 030 Update not needed
> > Run: 040 ----------------
> > Mon Apr 17 15:07:44 EDT 2017
> > 170416_xu_binding01_sub06 040 Update not needed
> > Run: 042 ----------------
> > Mon Apr 17 15:07:44 EDT 2017
> > 170416_xu_binding01_sub06 042 Update not needed
> > Run: 044 ----------------
> > Mon Apr 17 15:07:44 EDT 2017
> > 170416_xu_binding01_sub06 044 Update not needed
> > Run: 052 ----------------
> > Mon Apr 17 15:07:44 EDT 2017
> > 170416_xu_binding01_sub06 052 Update not needed
> > Run: 054 ----------------
> > Mon Apr 17 15:07:44 EDT 2017
> > 170416_xu_binding01_sub06 054 Update not needed
> > Run: 056 ----------------
> > Mon Apr 17 15:07:44 EDT 2017
> > 170416_xu_binding01_sub06 056 Update not needed
> > Mon Apr 17 15:07:44 EDT 2017
> > mktemplate-sess completed
> > 170416_xu_binding01_sub06 Mask ------------------------
> > mkbrainmask-sess -maskstem brain -fsd bold -s
> > 170416_xu_binding01_sub06 -d
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata
> > -rlf runlist_double.txt -nolog -update
> > ------------------------------------------------
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170416_xu_binding01_sub06
> >
> > Mon Apr 17 15:07:44 EDT 2017
> > 170416_xu_binding01_sub06 Update not needed for session-level mask
> > 170416_xu_binding01_sub06 Update not needed for run 014 mask
> > 170416_xu_binding01_sub06 Update not needed for run 014 meanval
> > 170416_xu_binding01_sub06 Update not needed for run 016 mask
> > 170416_xu_binding01_sub06 Update not needed for run 016 meanval
> > 170416_xu_binding01_sub06 Update not needed for run 018 mask
> > 170416_xu_binding01_sub06 Update not needed for run 018 meanval
> > 170416_xu_binding01_sub06 Update not needed for run 026 mask
> > 170416_xu_binding01_sub06 Update not needed for run 026 meanval
> > 170416_xu_binding01_sub06 Update not needed for run 028 mask
> > 170416_xu_binding01_sub06 Update not needed for run 028 meanval
> > 170416_xu_binding01_sub06 Update not needed for run 030 mask
> > 170416_xu_binding01_sub06 Update not needed for run 030 meanval
> > 170416_xu_binding01_sub06 Update not needed for run 040 mask
> > 170416_xu_binding01_sub06 Update not needed for run 040 meanval
> > 170416_xu_binding01_sub06 Update not needed for run 042 mask
> > 170416_xu_binding01_sub06 Update not needed for run 042 meanval
> > 170416_xu_binding01_sub06 Update not needed for run 044 mask
> > 170416_xu_binding01_sub06 Update not needed for run 044 meanval
> > 170416_xu_binding01_sub06 Update not needed for run 052 mask
> > 170416_xu_binding01_sub06 Update not needed for run 052 meanval
> > 170416_xu_binding01_sub06 Update not needed for run 054 mask
> > 170416_xu_binding01_sub06 Update not needed for run 054 meanval
> > 170416_xu_binding01_sub06 Update not needed for run 056 mask
> > 170416_xu_binding01_sub06 Update not needed for run 056 meanval
> > Mon Apr 17 15:07:47 EDT 2017
> > mkbrainmask-sess done
> > 170416_xu_binding01_sub06 Registration -----------------------------
> > register-sess -s 170416_xu_binding01_sub06 -d
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata
> > -fsd bold -dof 6 -rlf runlist_double.txt -per-session -nolog -update
> > --------------------------------------------------------------
> > register-sess logfile is /dev/null
> > --------------------------------------------------------------
> > Mon Apr 17 15:07:47 EDT 2017
> >
> > setenv SUBJECTS_DIR /ncf/vcn/jtaylor/mri-space/subjects
> > cd
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/scripts/glm
> > /ncf/nrg/sw/apps/freesurfer/5.3.0/fsfast/bin/register-sess -s
> > 170416_xu_binding01_sub06 -d
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata
> > -fsd bold -dof 6 -rlf runlist_double.txt -per-session -nolog -update
> >
> > freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
> > Linux ncf2705.rc.fas.harvard.edu
> <http://ncf2705.rc.fas.harvard.edu>
> <http://ncf2705.rc.fas.harvard.edu
> <http://ncf2705.rc.fas.harvard.edu>>
> > 2.6.32-642.6.2.el6.x86_64 #1 SMP Wed Oct 26 06:52:09 UTC 2016 x86_64
> > x86_64 x86_64 GNU/Linux
> >
> > Session:
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170416_xu_binding01_sub06
> > ----------------
> > Mon Apr 17 15:07:47 EDT 2017
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170416_xu_binding01_sub06
> > Mon Apr 17 15:07:47 EDT 2017
> > register-sess completed
> > 170416_xu_binding01_sub06 MC -----------------------------
> > mc-sess -fstem f -fmcstem fmc -s 170416_xu_binding01_sub06 -d
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata
> > -fsd bold -rlf runlist_double.txt -per-session -nolog -update
> > Logfile is /dev/null
> > -------------------------------------------
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170416_xu_binding01_sub06
> >
> > RunList: 014 016 018 026 028 030 040 042 044 052 054 056
> > 170416_xu_binding01_sub06 014 Update not needed
> > 170416_xu_binding01_sub06 016 Update not needed
> > 170416_xu_binding01_sub06 018 Update not needed
> > 170416_xu_binding01_sub06 026 Update not needed
> > 170416_xu_binding01_sub06 028 Update not needed
> > 170416_xu_binding01_sub06 030 Update not needed
> > 170416_xu_binding01_sub06 040 Update not needed
> > 170416_xu_binding01_sub06 042 Update not needed
> > 170416_xu_binding01_sub06 044 Update not needed
> > 170416_xu_binding01_sub06 052 Update not needed
> > 170416_xu_binding01_sub06 054 Update not needed
> > 170416_xu_binding01_sub06 056 Update not needed
> >
> >
> > Mon Apr 17 15:07:47 EDT 2017
> > mc-sess completed SUCCESSFULLY
> > ----------------------------------------
> > Started at Mon Apr 17 15:07:43 EDT 2017
> > Ended at Mon Apr 17 15:07:47 EDT 2017
> > preproc-sess done
> > -------------------------------------------
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170322_xu_binding01_sub01
> >
> > Mon Apr 17 15:07:48 EDT 2017
> > anadir =
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170322_xu_binding01_sub01/bold/glm_double_all_ps_0
> > *ERROR: cannot find
> >
> /net/rcss11/srv/export/ncf_vcn/share_root/jtaylor/mri-space/studies/binding01/unpackdata/170322_xu_binding01_sub01/bold/008/fmc.sm0*
> >
> >
> >
> > On Fri, Apr 7, 2017 at 12:00 PM,
> > <freesurfer-request@nmr.mgh.harvard.edu
> <mailto:freesurfer-request@nmr.mgh.harvard.edu>
> > <mailto:freesurfer-request@nmr.mgh.harvard.edu
> <mailto:freesurfer-request@nmr.mgh.harvard.edu>>> wrote:
> >
> > Send Freesurfer mailing list submissions to
> > freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <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
> <mailto:freesurfer-request@nmr.mgh.harvard.edu>
> > <mailto:freesurfer-request@nmr.mgh.harvard.edu
> <mailto:freesurfer-request@nmr.mgh.harvard.edu>>
> >
> > You can reach the person managing the list at
> > freesurfer-owner@nmr.mgh.harvard.edu
> <mailto:freesurfer-owner@nmr.mgh.harvard.edu>
> > <mailto:freesurfer-owner@nmr.mgh.harvard.edu
> <mailto: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. postdoctoral Research Fellow position at Mayo Clinic
> > (Senjem, Matthew L., M.S.)
> > 2. First-level GLM on externally-preprocessed functionals
> > (Christopher Markiewicz)
> > 3. Re: Custom color maps (Senften, Peter)
> > 4. Re: MRIread (load_nifti)- Out of memory (Bruce Fischl)
> > 5. Re: long mri_ca_register error (Bruce Fischl)
> > 6. Re: help (Bruce Fischl)
> > 7. Re: MRIread (load_nifti)- Out of memory (Ilaria Sani)
> > 8. Re: MRIread (load_nifti)- Out of memory (Douglas N Greve)
> > 9. Re: QDEC-volume, thickness and area (Douglas N Greve)
> > 10. Re: Help on "mris_anatomical_stats" (Douglas N Greve)
> > 11. Re: First-level GLM on externally-preprocessed functionals
> > (Douglas N Greve)
> > 12. Re: Custom color maps (Douglas N Greve)
> > 13. Re: Custom registration template (Douglas N Greve)
> > 14. Re: Selxavg3-sess Looking for (and can't find) "fmc.sm0"
> > (Douglas N Greve)
> > 15. Re: Ventricle-to-Brain Ratio (Douglas N Greve)
> > 16. Re: ROI seed size (Douglas N Greve)
> > 17. Re: correlation coefficient R (Douglas N Greve)
> > 18. Re: Custom color maps (Senften, Peter)
> > 19. Re: General QDEC clarification queastions (Douglas N
> Greve)
> > 20. QDEC and ROI drawing (Arnaud Bor?)
> > 21. Re: QDEC and ROI drawing (Douglas N Greve)
> > 22. Re: QDEC-volume, thickness and area (Lim, Lena)
> > 23. Re: QDEC-volume, thickness and area (Douglas N Greve)
> > 24. R: Re: R: R: Re: R: Re: Whole preprocessing with FAST
> without
> > to perform a seed based analysis (stdp82@virgilio.it
> <mailto:stdp82@virgilio.it>
> > <mailto:stdp82@virgilio.it <mailto:stdp82@virgilio.it>>)
> > 25. Re: R: Re: R: R: Re: R: Re: Whole preprocessing with FAST
> > without to perform a seed based analysis (Douglas N Greve)
> > 26. QDEC-Cortical Thickness (Limachia, Gaurang (NIH/NINDS)
> [F])
> > 27. Re: Custom registration template (Linda Zhang)
> > 28. Re: Ventricle-to-Brain Ratio (Gullickson, James)
> > 29. Re: MRIread (load_nifti)- Out of memory (Ilaria Sani)
> > 30. Re: long mri_ca_register error (Chris Adamson)
> > 31. Re: help (Dilip Puri)
> > 32. How to segment subnuclei of thalamus? (Shane S)
> > 33. withdrawing from the mailing list.
> > (kjunji@med.kanazawa-u.ac.jp
> <mailto:kjunji@med.kanazawa-u.ac.jp>
> <mailto:kjunji@med.kanazawa-u.ac.jp
> <mailto:kjunji@med.kanazawa-u.ac.jp>>)
> > 34. Re: QA Tools v1.2 and future release (Yong Li)
> > 35. Hippocampal subfield segmentation, file content (Nina
> Jacobsen)
> > 36. Re: Multiple Comparisons Correction thresh error (teodora
> > petrova)
> > 37. Longitudinal Pipeline (Arman Eshaghi)
> > 38. Re: Hippocampal subfield segmentation, file content
> > (Iglesias Gonzalez, Eugenio)
> > 39. Re: How to segment subnuclei of thalamus? (Bruce Fischl)
> > 40. Analyzing xhemi results (Marissa Pifer)
> > 41. Re: QDEC and ROI drawing (Arnaud Bor?)
> >
> >
> >
> ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Thu, 06 Apr 2017 16:17:30 +0000
> > From: "Senjem, Matthew L., M.S." <Senjem.Matthew1@mayo.edu
> <mailto:Senjem.Matthew1@mayo.edu>
> > <mailto:Senjem.Matthew1@mayo.edu
> <mailto:Senjem.Matthew1@mayo.edu>>>
> > Subject: [Freesurfer] postdoctoral Research Fellow position
> at Mayo
> > Clinic
> > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>>
> > Message-ID: <47cabe$66564f@ironport10.mayo.edu
> <mailto:66564f@ironport10.mayo.edu>
> > <mailto:66564f@ironport10.mayo.edu
> <mailto:66564f@ironport10.mayo.edu>>>
> > Content-Type: text/plain; charset="windows-1252"
> >
> > The Mayo Clinic Departments of Neurology and Diagnostic
> Radiology
> > in Rochester, Minnesota are seeking applications for a
> > fully-funded, two-year postdoctoral Research Fellow position to
> > begin in July of 2017. The Research Fellow position will
> > primarily work on developing advanced multi-modal molecular and
> > high-field (3T and 7T) neuroimaging to study connectomics in
> > pre-clinical and clinical Alzheimer?s disease. The resulting
> data
> > will be acquired and analyzed as part of a unique collaboration
> > between investigators at Mayo Clinic Alzheimer?s Disease
> Research
> > Center and the Center for Magnetic Resonance Research at the
> > University of Minnesota. Basic programing skills and familiarity
> > with widely used neuroimaging software platforms are
> required for
> > successful applicants. Familiarity with the Human Connectome
> > Project imaging and analyses protocols is preferred but not
> > required. No clinical or Alzheimer?s specific background is
> > required. Salary will be commensurate with postdoctoral
> > experience. The position will remain open until filled by a
> > successful candidate.
> >
> > Please send CV, three letters of recommendation, and any
> inquiries to:
> >
> > David T. Jones, M.D.
> > Mayo Clinic
> > Department of Neurology
> > Email: Jones.David@mayo.edu <mailto:Jones.David@mayo.edu>
> > <mailto:Jones.David@mayo.edu
> <mailto:Jones.David@mayo.edu>><mailto:Jones.David@mayo.edu
> <mailto:Jones.David@mayo.edu>
> > <mailto:Jones.David@mayo.edu <mailto:Jones.David@mayo.edu>>>
> >
> > A Research Fellow at Mayo Clinic is a temporary position
> intended
> > to provide training and education in research. Individuals will
> > train in the research program of a Mayo Clinic principal
> > investigator. Qualified individuals will demonstrate the
> potential
> > for research as evidenced by their training and peer-reviewed
> > publications and should become competitive for national research
> > grants. Proof of English proficiency is required for J-1
> > Short-Term Scholars, Research Scholars, Professors, Specialists,
> > and Student Interns sponsored by Mayo Clinic.
> >
> > Why Mayo Clinic? Learn and grow among the best in your field at
> > the nation?s top hospital (U.S. News & World Report, 2016-2017),
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> -------------------------------------------------------------------------------------------------------------------------------------------------------------------------
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
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> >
> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170406/8ab14f40/attachment-0001.html
> <http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170406/8ab14f40/attachment-0001.html>
> >
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> <http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170406/8ab14f40/attachment-0001.html>>
> >
> > ------------------------------
> >
> > Message: 2
> > Date: Thu, 6 Apr 2017 12:35:05 -0400
> > From: Christopher Markiewicz <effigies@bu.edu
> <mailto:effigies@bu.edu>
> > <mailto:effigies@bu.edu <mailto:effigies@bu.edu>>>
> > Subject: [Freesurfer] First-level GLM on externally-preprocessed
> > functionals
> > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>>
> > Message-ID:
> >
> >
> <CAHE-diMQn+WO5VdzmFYhoBm2C7kRCdU=4kOHrAL9hdFqhO1Wcw@mail.gmail.com
> <mailto:4kOHrAL9hdFqhO1Wcw@mail.gmail.com>
> > <mailto:4kOHrAL9hdFqhO1Wcw@mail.gmail.com
> <mailto:4kOHrAL9hdFqhO1Wcw@mail.gmail.com>>>
> > Content-Type: text/plain; charset="utf-8"
> >
> > Hi list,
> >
> > We're working on making a preprocessing stream that will be
> generally
> > accessible to different analysis streams, including
> FreeSurfer. One
> > component of this is sampling functional volumes to FreeSurfer
> > meshes, and
> > I want to test this component by running a simple
> first-level GLM in
> > FreeSurfer.
> >
> > I've always done this through the FSFAST pipeline, but that
> may be
> > a bit
> > much, given that I'm starting from surface time series (the
> > equivalent of
> >
> `$FUNCTIONALS_DIR/$SESS_ID/bold/$RUN/fmcpr.sm0.fsaverage.lh.nii.gz`,
> > but as
> > a GIFTI file).
> >
> > Supposing I have a paradigm file and the files described above,
> > what's the
> > best way to do a basic GLM? Would it be to `mri_surf2surf`
> our GIFTI
> > surfaces into `fmcpr.sm0.fsaverage.lh.nii.gz` files in a FSFAST
> > directory
> > structure, and pick up at `mkanalysis-sess`? Or is there a more
> > straightforward way to just get a simple set of contrasts to
> > compare with a
> > volumetric analysis?
> >
> > Thanks in advance,
> > Chris Markiewicz
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
> > URL:
> >
> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170406/eff39c3c/attachment-0001.html
> <http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170406/eff39c3c/attachment-0001.html>
> >
> <http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170406/eff39c3c/attachment-0001.html
> <http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170406/eff39c3c/attachment-0001.html>>
> >
> > ------------------------------
> >
> > Message: 3
> > Date: Thu, 6 Apr 2017 17:00:18 +0000
> > From: "Senften, Peter" <peter.senften@ubc.ca
> <mailto:peter.senften@ubc.ca>
> > <mailto:peter.senften@ubc.ca <mailto:peter.senften@ubc.ca>>>
> > Subject: Re: [Freesurfer] Custom color maps
> > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>>
> > Message-ID:
> >
> >
> <B6AC19D7BE198443A028636599CB88771E558248@exch-mbx08p.ead.ubc.ca
> <mailto:B6AC19D7BE198443A028636599CB88771E558248@exch-mbx08p.ead.ubc.ca>
> >
> <mailto:B6AC19D7BE198443A028636599CB88771E558248@exch-mbx08p.ead.ubc.ca
> <mailto:B6AC19D7BE198443A028636599CB88771E558248@exch-mbx08p.ead.ubc.ca>>>
> > Content-Type: text/plain; charset="us-ascii"
> >
> > hi,
> >
> > I've read through the list, and searched over the last few days,
> > and can't quite seem to find what I'm looking for. My first
> > message wasn't clear at all either (my apologies), it was one of
> > those days where your brain ends up in a bit of a fog.
> >
> > I am trying to get a heat map style visual output based on the
> > destrieux 72 region map using cortical thickness as our measure.
> > I'm using FS 6.0 and the edits and outputs have all gone
> great. We
> > are doing the analysis of the cortical thickness outside of
> FS and
> > would like to create a heat-map style visual output of the areas
> > that show a large effect size. My original idea was to create a
> > custom color map and somehow load that in place of the default
> > destrieux color map but I couldn't get that to work. Tried
> > replacing the FS LUT table as well and when loaded the colors
> > remained the same as well.
> >
> > Hope that clarifies what I'm trying to do.
> >
> > Thanks,
> >
> > Peter
> > ________________________________________
> > From: freesurfer-bounces@nmr.mgh.harvard.edu
> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>
> > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu
> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>>
> > [freesurfer-bounces@nmr.mgh.harvard.edu
> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>
> > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu
> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>>] on behalf of dg
> > wakeman [dgwakeman@gmail.com <mailto:dgwakeman@gmail.com>
> <mailto:dgwakeman@gmail.com <mailto:dgwakeman@gmail.com>>]
> > Sent: Tuesday, April 04, 2017 12:11 PM
> > To: Freesurfer support list
> > Subject: Re: [Freesurfer] Custom color maps
> >
> > Hi Peter,
> >
> > We will need a lot more details to help. I suggest you look
> through
> > the e-mail list a bit. I spent a lot of time helping a user
> or two
> > with a similar issue. The key details are what are you
> trying to show
> > (an annotation, a single label, or values)?
> >
> > hth
> > d
> >
> > On Wed, Mar 29, 2017 at 11:15 AM, Senften, Peter
> > <peter.senften@ubc.ca <mailto:peter.senften@ubc.ca>
> <mailto:peter.senften@ubc.ca <mailto:peter.senften@ubc.ca>>> wrote:
> > > Hello,
> > >
> > > I am wondering if it is possible to create a custom color map
> > that will be
> > > visible in freeview using the 3D viewer - not the coronal,
> > axial, or sagital
> > > views. I created a copy of the LUT file and then replaced the
> > RGB values the
> > > ones I wanted but haven't been able to get it to load at all.
> > >
> > > In the end I am trying to make pretty 3D pictures to see our
> > regions of
> > > interest better for our data. I am open to other ways of
> doing this.
> > >
> > > Thanks,
> > >
> > > Peter
> > >
> > > _______________________________________________
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > >
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <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>
> > <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>
> <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
> >
> >
> >
> > ------------------------------
> >
> > Message: 4
> > Date: Thu, 6 Apr 2017 13:35:31 -0400 (EDT)
> > From: Bruce Fischl <fischl@nmr.mgh.harvard.edu
> <mailto:fischl@nmr.mgh.harvard.edu>
> > <mailto:fischl@nmr.mgh.harvard.edu
> <mailto:fischl@nmr.mgh.harvard.edu>>>
> > Subject: Re: [Freesurfer] MRIread (load_nifti)- Out of memory
> > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>>
> > Message-ID:
> >
> >
> <alpine.LRH.2.20.1704061335010.29155@gate.nmr.mgh.harvard.edu
> <mailto:alpine.LRH.2.20.1704061335010.29155@gate.nmr.mgh.harvard.edu>
> >
> <mailto:alpine.LRH.2.20.1704061335010.29155@gate.nmr.mgh.harvard.edu
> <mailto:alpine.LRH.2.20.1704061335010.29155@gate.nmr.mgh.harvard.edu>>>
> > Content-Type: text/plain; charset="iso-8859-7"
> >
> > Hi Ilaria
> >
> > do you have any reason to believe that it isn't just out of
> > memory? If so,
> > there's not much to do other than get more RAM or use a
> different
> > machine
> >
> > cheers
> > Bruce
> >
> >
> > On Thu,
> > 6 Apr 2017, Ilaria Sani wrote:
> >
> > >
> > > Dear All,
> > >
> > > ?
> > >
> > > I?m trying to load a pretty big diffusion MRI dataset
> > (320x320x260x122).
> > >
> > > I?m running matlab 2015a 64bit on a linux machine.
> > >
> > > ?
> > >
> > > I?m using MRIread, which in turn calls load_nifti.
> > >
> > > I?m getting the following error:
> > >
> > > ?
> > >
> > > Error using? +
> > >
> > > Out of memory. Type HELP MEMORY for your options.
> > >
> > > ?
> > >
> > > Error in load_nifti (line 158)
> > >
> > > ? hdr.vol = hdr.vol * hdr.scl_slope? + hdr.scl_inter;
> > >
> > > ?
> > >
> > > Error in MRIread (line 158)
> > >
> > > hdr = load_nifti(fspec,headeronly);
> > >
> > > ?
> > >
> > > When I load half dataset (320x320x260x61) it works ok.
> > >
> > > I tried to increase the Maximum array size in Matalb (default
> > 1,000 - now 10,000), but I?m still getting the error.
> > >
> > > I tried to change machine (which runs matlab 2013a on
> linux) and
> > it worked fine.
> > >
> > > ?
> > >
> > > I think this is due to some matlab settings.
> > >
> > > Can anyone help?
> > >
> > > ?
> > >
> > > Thanks a lot,
> > >
> > > Ilaria
> > >
> > > ?
> > >
> > > ?
> > >
> > > -------------------------------------------
> > > Ilaria Sani, PhD
> > > Postdoctoral Fellow, Freiwald Lab
> > > The Rockefeller University
> > > 1230 York Ave., New York, NY 10065.
> > > Phone: (212) 327?7699
> > > Fax: ??? (212) 327 7698 <tel:%28212%29%20327-7698>
> > > Email:?isani01@rockefeller.edu
> <mailto:isani01@rockefeller.edu> <mailto:isani01@rockefeller.edu
> <mailto:isani01@rockefeller.edu>>
> > >
> > > ?
> > >
> > >
> > >
> >
> > ------------------------------
> >
> > Message: 5
> > Date: Thu, 6 Apr 2017 13:37:14 -0400 (EDT)
> > From: Bruce Fischl <fischl@nmr.mgh.harvard.edu
> <mailto:fischl@nmr.mgh.harvard.edu>
> > <mailto:fischl@nmr.mgh.harvard.edu
> <mailto:fischl@nmr.mgh.harvard.edu>>>
> > Subject: Re: [Freesurfer] long mri_ca_register error
> > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>>
> > Message-ID:
> >
> >
> <alpine.LRH.2.20.1704061336540.29155@gate.nmr.mgh.harvard.edu
> <mailto:alpine.LRH.2.20.1704061336540.29155@gate.nmr.mgh.harvard.edu>
> >
> <mailto:alpine.LRH.2.20.1704061336540.29155@gate.nmr.mgh.harvard.edu
> <mailto:alpine.LRH.2.20.1704061336540.29155@gate.nmr.mgh.harvard.edu>>>
> > Content-Type: text/plain; charset="iso-8859-7"
> >
> > Hi Chris
> >
> > it's possible we never looked at -bigventricle in the long
> stage. What
> > was your recon-all command line?
> >
> > cheers
> > Bruce
> > On Thu, 6 Apr 2017, Chris Adamson wrote:
> >
> > >
> > > It happens when I use -bigventricles.
> > >
> > > ?
> > >
> > > From: freesurfer-bounces@nmr.mgh.harvard.edu
> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>
> > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu
> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>>
> > [mailto:freesurfer-bounces@nmr.mgh.harvard.edu
> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>
> > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu
> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>>] On Behalf Of
> > Chris Adamson
> > > Sent: Thursday, 6 April 2017 12:27 PM
> > > To: freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>
> > > Subject: [Freesurfer] long mri_ca_register error
> > >
> > > ?
> > >
> > > Freesurfer devs,
> > >
> > > ?
> > >
> > > In freesurfer 6 stable I?m having a problem at the careg stage
> > of the long. The relevant recon-all log is pasted below.
> Could you
> > point me to where to debug this
> > > problem?
> > >
> > > ?
> > >
> > > Cheers,
> > >
> > > ?
> > >
> > > Chris.
> > >
> > > ?
> > >
> > > mri_ca_register -rusage
> >
> 136_S_0426_20070604.long.136_S_0426/touch/rusage.mri_ca_register.dat
> > -bigventricles -smoothness 0.5 -levels 2 -A 1 -l
> > > *base*/transforms/talairach.m3z identity.nofile -align-after
> > -mask brainmask.mgz norm.mgz
> > /usr/local/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca
> > > transforms/talairach.m3z
> > >
> > > ?
> > >
> > > handling expanded ventricles...
> > >
> > > l_smoothness = 0.50
> > >
> > > levels = 2
> > >
> > > smoothing gradient with 1 averages...
> > >
> > > reading previously computed atlas xform
> >
> /isilon/data/addo/ADNI3T/freesurfer6/136_S_0426/mri/transforms/talairach.m3z
> > and applying inverse registration identity.nofile
> > >
> > > renormalizing sequences with structure alignment,
> equivalent to:
> > >
> > > ??? -renormalize
> > >
> > > ??? -regularize_mean 0.500
> > >
> > > ??? -regularize 0.500
> > >
> > > using MR volume brainmask.mgz to mask input volume...
> > >
> > > ?
> > >
> > > == Number of threads available to mri_ca_register for
> OpenMP = 2 ==
> > >
> > > reading 1 input volumes...
> > >
> > > logging results to talairach.log
> > >
> > > reading input volume 'norm.mgz'...
> > >
> > > reading GCA
> >
> '/usr/local/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca'...
> > >
> > > label assignment complete, 0 changed (0.00%)
> > >
> > > TransformSample: gcam has not been inverted!
> > >
> > > freeing gibbs priors...done.
> > >
> > > average std[0] = 5.0
> > >
> > > setting orig areas to linear transform determinant scaled 8.40
> > >
> > > writing talairach.invalid.mgz
> > >
> > > writing talairach.status.mgz
> > >
> > > registering ventricular system...
> > >
> > > using threshold 45.0 from atlas ventricle (20.1 +- 5.0) and
> > caudate (70.0 +- 5.0) distributions for initial ventricular
> estimate
> > >
> > > No such file or directory
> > >
> > > TransformSample: gcam has not been inverted!
> > >
> > > No such file or directory
> > >
> > > TransformSample: gcam has not been inverted!
> > >
> > > No such file or directory
> > >
> > > TransformSample: gcam has not been inverted!
> > >
> > > No such file or directory
> > >
> > > TransformSample: gcam has not been inverted!
> > >
> > > No such file or directory
> > >
> > > TransformSample: gcam has not been inverted!
> > >
> > > No such file or directory
> > >
> > > TransformSample: gcam has not been inverted!
> > >
> > > No such file or directory
> > >
> > > TransformSample: gcam has not been inverted!
> > >
> > > No such file or directory
> > >
> > > TransformSample: gcam has not been inverted!
> > >
> > > No such file or directory
> > >
> > > TransformSample: gcam has not been inverted!
> > >
> > > No such file or directory
> > >
> > > TransformSample: gcam has not been inverted!
> > >
> > > No such file or directory
> > >
> > > TransformSample: gcam has not been inverted!
> > >
> > > No such file or directory
> > >
> > > ?
> > >
> > > Dr Chris Adamson
> > >
> > > Senior Research Officer
> > >
> > > Developmental Imaging, Clinical Sciences
> > >
> > > ?
> > >
> > > Murdoch Childrens Research Institute
> > >
> > > The Royal Children?s Hospital
> > >
> > > Flemington Road, Parkville, VIC 3052 Australia
> > >
> > > E?chris.adamson@mcri.edu.au
> <mailto:chris.adamson@mcri.edu.au>
> <mailto:chris.adamson@mcri.edu.au <mailto:chris.adamson@mcri.edu.au>>?
> > >
> > > www.mcri.edu.au <http://www.mcri.edu.au>
> <http://www.mcri.edu.au>
> > >
> > > ?
> > >
> > > ?
> > >
> > > This e-mail and any attachments to it (the
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> > >
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> ______________________________________________________________________
> > >
> > >
> >
> > ------------------------------
> >
> > Message: 6
> > Date: Thu, 6 Apr 2017 13:38:20 -0400 (EDT)
> > From: Bruce Fischl <fischl@nmr.mgh.harvard.edu
> <mailto:fischl@nmr.mgh.harvard.edu>
> > <mailto:fischl@nmr.mgh.harvard.edu
> <mailto:fischl@nmr.mgh.harvard.edu>>>
> > Subject: Re: [Freesurfer] help
> > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>>
> > Message-ID:
> >
> >
> <alpine.LRH.2.20.1704061338010.29155@gate.nmr.mgh.harvard.edu
> <mailto:alpine.LRH.2.20.1704061338010.29155@gate.nmr.mgh.harvard.edu>
> >
> <mailto:alpine.LRH.2.20.1704061338010.29155@gate.nmr.mgh.harvard.edu
> <mailto:alpine.LRH.2.20.1704061338010.29155@gate.nmr.mgh.harvard.edu>>>
> > Content-Type: text/plain; charset=US-ASCII; format=flowed
> >
> > Hi Dilip
> >
> > yes, freesurfer will do this for you, although the labels
> will be
> > 17 for
> > left hippocampus and 53 for right.
> >
> > cheers
> > Bruce
> > On Thu, 6 Apr 2017, Dilip Puri wrote:
> >
> > > Hi everyone,
> > >
> > > I am working on Hippocampus segmentation using Neural Networks
> > for that I need labeled images of Hippocampus corresponding to
> > original images.
> > >
> > > I am using OASIS Dataset for this. I want to generate labeled
> > images using FREESURFER. Is there any way to label each 3D
> co-ordinate
> > > HippoCampus -1
> > > Otherwise - 0
> > >
> > > Here are sample files link
> > >
> > > Kindly help me!
> > >
> > >
> > > Dilip Puri
> > > IIIT Vadodara
> > >
> > >
> >
> >
> > ------------------------------
> >
> > Message: 7
> > Date: Thu, 6 Apr 2017 18:53:34 +0000
> > From: Ilaria Sani <isani01@mail.rockefeller.edu
> <mailto:isani01@mail.rockefeller.edu>
> > <mailto:isani01@mail.rockefeller.edu
> <mailto:isani01@mail.rockefeller.edu>>>
> > Subject: Re: [Freesurfer] MRIread (load_nifti)- Out of memory
> > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>>
> > Message-ID:
> > <83430b6af8e142319c5cdbf9cb130b2a@RUMBX12.rockefeller.edu
> <mailto:83430b6af8e142319c5cdbf9cb130b2a@RUMBX12.rockefeller.edu>
> >
> <mailto:83430b6af8e142319c5cdbf9cb130b2a@RUMBX12.rockefeller.edu
> <mailto:83430b6af8e142319c5cdbf9cb130b2a@RUMBX12.rockefeller.edu>>>
> > Content-Type: text/plain; charset="iso-8859-7"
> >
> > Hi Bruce,
> >
> > Not sure this answer your question...
> >
> > In matlab workspace, I am able to load data in two halves:
> >
> > H1=MRIread(half1)
> > H2=MRIread(half2)
> >
> > And then concatenate the volumes
> > concatenate them var=cat(4,H1,H2).
> >
> > So, somehow matlab can handle...
> >
> > However, when those operations are embedded inside a function
> > (like in the case of load_nifti and MRIread) I get the error.
> >
> >
> > Thanks,
> > Ilaria
> >
> >
> > -----Original Message-----
> > From: freesurfer-bounces@nmr.mgh.harvard.edu
> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>
> > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu
> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>>
> > [mailto:freesurfer-bounces@nmr.mgh.harvard.edu
> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>
> > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu
> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>>] On Behalf Of
> > Bruce Fischl
> > Sent: Thursday, April 6, 2017 1:36 PM
> > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>>
> > Subject: Re: [Freesurfer] MRIread (load_nifti)- Out of memory
> >
> > Hi Ilaria
> >
> > do you have any reason to believe that it isn't just out of
> > memory? If so, there's not much to do other than get more RAM or
> > use a different machine
> >
> > cheers
> > Bruce
> >
> >
> > On Thu,
> > 6 Apr 2017, Ilaria Sani wrote:
> >
> > >
> > > Dear All,
> > >
> > > ?
> > >
> > > I?m trying to load a pretty big diffusion MRI dataset
> > (320x320x260x122).
> > >
> > > I?m running matlab 2015a 64bit on a linux machine.
> > >
> > > ?
> > >
> > > I?m using MRIread, which in turn calls load_nifti.
> > >
> > > I?m getting the following error:
> > >
> > > ?
> > >
> > > Error using? +
> > >
> > > Out of memory. Type HELP MEMORY for your options.
> > >
> > > ?
> > >
> > > Error in load_nifti (line 158)
> > >
> > > ? hdr.vol = hdr.vol * hdr.scl_slope? + hdr.scl_inter;
> > >
> > > ?
> > >
> > > Error in MRIread (line 158)
> > >
> > > hdr = load_nifti(fspec,headeronly);
> > >
> > > ?
> > >
> > > When I load half dataset (320x320x260x61) it works ok.
> > >
> > > I tried to increase the Maximum array size in Matalb (default
> > 1,000 - now 10,000), but I?m still getting the error.
> > >
> > > I tried to change machine (which runs matlab 2013a on
> linux) and
> > it worked fine.
> > >
> > > ?
> > >
> > > I think this is due to some matlab settings.
> > >
> > > Can anyone help?
> > >
> > > ?
> > >
> > > Thanks a lot,
> > >
> > > Ilaria
> > >
> > > ?
> > >
> > > ?
> > >
> > > -------------------------------------------
> > > Ilaria Sani, PhD
> > > Postdoctoral Fellow, Freiwald Lab
> > > The Rockefeller University
> > > 1230 York Ave., New York, NY 10065.
> > > Phone: (212) 327?7699
> > > Fax: ??? (212) 327 7698 <tel:%28212%29%20327-7698>
> > > Email:?isani01@rockefeller.edu
> <mailto:isani01@rockefeller.edu> <mailto:isani01@rockefeller.edu
> <mailto:isani01@rockefeller.edu>>
> > >
> > > ?
> > >
> > >
> > >
> >
> >
> >
> > ------------------------------
> >
> > Message: 8
> > Date: Thu, 6 Apr 2017 15:42:31 -0400
> > From: Douglas N Greve <greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>
> > <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>>
> > Subject: Re: [Freesurfer] MRIread (load_nifti)- Out of memory
> > To: freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>
> > Message-ID:
> > <9df0ba99-7c57-7370-e278-6f0a8ff9b0f8@nmr.mgh.harvard.edu
> <mailto:9df0ba99-7c57-7370-e278-6f0a8ff9b0f8@nmr.mgh.harvard.edu>
> >
> <mailto:9df0ba99-7c57-7370-e278-6f0a8ff9b0f8@nmr.mgh.harvard.edu
> <mailto:9df0ba99-7c57-7370-e278-6f0a8ff9b0f8@nmr.mgh.harvard.edu>>>
> > Content-Type: text/plain; charset=iso-8859-7; format=flowed
> >
> > is it a compressed nifti (nii.gz)? If so, try uncompressing
> it first
> >
> >
> > On 04/06/2017 02:53 PM, Ilaria Sani wrote:
> > > Hi Bruce,
> > >
> > > Not sure this answer your question...
> > >
> > > In matlab workspace, I am able to load data in two halves:
> > >
> > > H1=MRIread(half1)
> > > H2=MRIread(half2)
> > >
> > > And then concatenate the volumes
> > > concatenate them var=cat(4,H1,H2).
> > >
> > > So, somehow matlab can handle...
> > >
> > > However, when those operations are embedded inside a function
> > (like in the case of load_nifti and MRIread) I get the error.
> > >
> > >
> > > Thanks,
> > > Ilaria
> > >
> > >
> > > -----Original Message-----
> > > From: freesurfer-bounces@nmr.mgh.harvard.edu
> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>
> > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu
> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>>
> > [mailto:freesurfer-bounces@nmr.mgh.harvard.edu
> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>
> > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu
> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>>] On Behalf Of
> > Bruce Fischl
> > > Sent: Thursday, April 6, 2017 1:36 PM
> > > To: Freesurfer support list
> <freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>>
> > > Subject: Re: [Freesurfer] MRIread (load_nifti)- Out of memory
> > >
> > > Hi Ilaria
> > >
> > > do you have any reason to believe that it isn't just out of
> > memory? If so, there's not much to do other than get more RAM or
> > use a different machine
> > >
> > > cheers
> > > Bruce
> > >
> > >
> > > On Thu,
> > > 6 Apr 2017, Ilaria Sani wrote:
> > >
> > >> Dear All,
> > >>
> > >>
> > >>
> > >> I?m trying to load a pretty big diffusion MRI dataset
> > (320x320x260x122).
> > >>
> > >> I?m running matlab 2015a 64bit on a linux machine.
> > >>
> > >>
> > >>
> > >> I?m using MRIread, which in turn calls load_nifti.
> > >>
> > >> I?m getting the following error:
> > >>
> > >>
> > >>
> > >> Error using +
> > >>
> > >> Out of memory. Type HELP MEMORY for your options.
> > >>
> > >>
> > >>
> > >> Error in load_nifti (line 158)
> > >>
> > >> hdr.vol = hdr.vol * hdr.scl_slope + hdr.scl_inter;
> > >>
> > >>
> > >>
> > >> Error in MRIread (line 158)
> > >>
> > >> hdr = load_nifti(fspec,headeronly);
> > >>
> > >>
> > >>
> > >> When I load half dataset (320x320x260x61) it works ok.
> > >>
> > >> I tried to increase the Maximum array size in Matalb (default
> > 1,000 - now 10,000), but I?m still getting the error.
> > >>
> > >> I tried to change machine (which runs matlab 2013a on linux)
> > and it worked fine.
> > >>
> > >>
> > >>
> > >> I think this is due to some matlab settings.
> > >>
> > >> Can anyone help?
> > >>
> > >>
> > >>
> > >> Thanks a lot,
> > >>
> > >> Ilaria
> > >>
> > >>
> > >>
> > >>
> > >>
> > >> -------------------------------------------
> > >> Ilaria Sani, PhD
> > >> Postdoctoral Fellow, Freiwald Lab
> > >> The Rockefeller University
> > >> 1230 York Ave., New York, NY 10065.
> > >> Phone: (212) 327 7699 <tel:%28212%29%20327-7699>
> > >> Fax: (212) 327 7698 <tel:%28212%29%20327-7698>
> > >> Email: isani01@rockefeller.edu
> <mailto:isani01@rockefeller.edu> <mailto:isani01@rockefeller.edu
> <mailto:isani01@rockefeller.edu>>
> > >>
> > >>
> > >>
> > >>
> > >>
> > > _______________________________________________
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > >
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
> > >
> > >
> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>
> > Phone Number: 617-724-2358 <tel:617-724-2358>
> > Fax: 617-726-7422 <tel:617-726-7422>
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>
> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> <https://gate.nmr.mgh.harvard.edu/filedrop2>
> > <https://gate.nmr.mgh.harvard.edu/filedrop2
> <https://gate.nmr.mgh.harvard.edu/filedrop2>>
> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>
> > Outgoing:
> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>
> >
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>>
> >
> >
> >
> > ------------------------------
> >
> > Message: 9
> > Date: Thu, 6 Apr 2017 15:45:11 -0400
> > From: Douglas N Greve <greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>
> > <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>>
> > Subject: Re: [Freesurfer] QDEC-volume, thickness and area
> > To: freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>
> > Message-ID:
> > <d88bff3e-9ece-5b51-3e12-2ed44ebbc5c9@nmr.mgh.harvard.edu
> <mailto:d88bff3e-9ece-5b51-3e12-2ed44ebbc5c9@nmr.mgh.harvard.edu>
> >
> <mailto:d88bff3e-9ece-5b51-3e12-2ed44ebbc5c9@nmr.mgh.harvard.edu
> <mailto:d88bff3e-9ece-5b51-3e12-2ed44ebbc5c9@nmr.mgh.harvard.edu>>>
> > Content-Type: text/plain; charset=windows-1252; format=flowed
> >
> > what do you mean they do not differ in gender ratio? Just
> that the
> > relative number of M/F is the same in each group? If there
> is not a
> > significant interaction between gender and group, then you
> can usually
> > merge the genders.
> >
> >
> > On 04/05/2017 05:13 PM, Lim, Lena wrote:
> > >
> > > Dear Freesurfer Experts,
> > >
> > > 1) I have 2 groups (A & B), which do not differ in terms
> of gender
> > > ratio. If there were no significant regions for Group-Gender
> > > interaction in mean cortical thickness in the QDEC
> analysis, can I
> > > conclude that gender does not influence the effect of group on
> > > thickness? The differences between A and B on mean
> thickness is not
> > > affected by Gender? Is this valid or do I need to add
> Gender as a
> > > covariate even though the group do not differ on gender ratio?
> > >
> > > 2) A reviewer pointed that it is not right to test for group
> > > differences in volume once I have tested for thickness and
> area,
> > > especially when there is a cluster where A and B do not differ
> > > significantly in thickness and area but they differ
> significantly in
> > > volume?Is this right?
> > >
> > > Please kindly advise.
> > >
> > > Many thanks,
> > >
> > > Lena
> > >
> > >
> > >
> > > _______________________________________________
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > >
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>
> > Phone Number: 617-724-2358 <tel:617-724-2358>
> > Fax: 617-726-7422 <tel:617-726-7422>
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>
> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> <https://gate.nmr.mgh.harvard.edu/filedrop2>
> > <https://gate.nmr.mgh.harvard.edu/filedrop2
> <https://gate.nmr.mgh.harvard.edu/filedrop2>>
> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>
> > Outgoing:
> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>
> >
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>>
> >
> >
> >
> > ------------------------------
> >
> > Message: 10
> > Date: Thu, 6 Apr 2017 15:55:39 -0400
> > From: Douglas N Greve <greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>
> > <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>>
> > Subject: Re: [Freesurfer] Help on "mris_anatomical_stats"
> > To: freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>
> > Message-ID:
> > <f99aa257-7ad7-61e8-dd0f-7d63615b3aaa@nmr.mgh.harvard.edu
> <mailto:f99aa257-7ad7-61e8-dd0f-7d63615b3aaa@nmr.mgh.harvard.edu>
> >
> <mailto:f99aa257-7ad7-61e8-dd0f-7d63615b3aaa@nmr.mgh.harvard.edu
> <mailto:f99aa257-7ad7-61e8-dd0f-7d63615b3aaa@nmr.mgh.harvard.edu>>>
> > Content-Type: text/plain; charset=windows-1252; format=flowed
> >
> > I can't replicate. Try loading the white and pial surfaces into
> > freeview. If that works, please upload your subject so I can
> try to
> > replicate the error
> >
> >
> > On 12/08/2015 11:22 AM, Lim, Lena wrote:
> > >
> > > Dear Experts,
> > >
> > > I ran a group analysis in Qdec for the left volume and found a
> > region
> > > of significant group difference. I wanted to extract this
> ROI. I
> > > defined this label and used the ?map label to subjects? option
> > in Qdec
> > > and ran the following but encountered the following error.
> Please
> > > kindly help?
> > >
> > > [spjwker@nanlnx2 FSL]1% mris_anatomical_stats ?l
> > lh.HCA_vol.label \-b
> > > -f PAC07/stats/lh.HCA_vol.stats PAC07 lh
> > >
> > > limiting computations to label lh.HCA_vol.label.
> > >
> > > reading volume
> /home/spjwker_PAC/Lena/CT_SA/FSL/PAC07/mri/wm.mgz...
> > >
> > > reading input surface
> > > /home/spjwker_PAC/Lena/CT_SA/FSL/PAC07/surf/lh.white...
> > >
> > > reading input pial surface
> > > /home/spjwker_PAC/Lena/CT_SA/FSL/PAC07/surf/lh.pial...
> > >
> > > reading input white surface
> > > /home/spjwker_PAC/Lena/CT_SA/FSL/PAC07/surf/lh.white...
> > >
> > > Segmentation fault
> > >
> > > Many thanks,
> > >
> > > Lena
> > >
> > >
> > >
> > > _______________________________________________
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > >
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>
> > Phone Number: 617-724-2358 <tel:617-724-2358>
> > Fax: 617-726-7422 <tel:617-726-7422>
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>
> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> <https://gate.nmr.mgh.harvard.edu/filedrop2>
> > <https://gate.nmr.mgh.harvard.edu/filedrop2
> <https://gate.nmr.mgh.harvard.edu/filedrop2>>
> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>
> > Outgoing:
> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>
> >
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>>
> >
> >
> >
> > ------------------------------
> >
> > Message: 11
> > Date: Thu, 6 Apr 2017 15:58:47 -0400
> > From: Douglas N Greve <greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>
> > <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>>
> > Subject: Re: [Freesurfer] First-level GLM on
> externally-preprocessed
> > functionals
> > To: freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>
> > Message-ID:
> > <08302d8d-6dd8-9896-7072-4651d953a497@nmr.mgh.harvard.edu
> <mailto:08302d8d-6dd8-9896-7072-4651d953a497@nmr.mgh.harvard.edu>
> >
> <mailto:08302d8d-6dd8-9896-7072-4651d953a497@nmr.mgh.harvard.edu
> <mailto:08302d8d-6dd8-9896-7072-4651d953a497@nmr.mgh.harvard.edu>>>
> > Content-Type: text/plain; charset=windows-1252; format=flowed
> >
> > You should be able to do it that way. When you run
> mkanalysis, specify
> > -funcstem fmcpr.sm0.fsaverage.lh.nii.gz, and then
> selxavg3-sess will
> > then use that file as input. If you want to smooth, then do that
> > explicitly and pass the smoothed file to mkanalysis
> >
> >
> > On 04/06/2017 12:35 PM, Christopher Markiewicz wrote:
> > > Hi list,
> > >
> > > We're working on making a preprocessing stream that will be
> > generally
> > > accessible to different analysis streams, including
> FreeSurfer. One
> > > component of this is sampling functional volumes to FreeSurfer
> > meshes,
> > > and I want to test this component by running a simple
> > first-level GLM
> > > in FreeSurfer.
> > >
> > > I've always done this through the FSFAST pipeline, but
> that may be a
> > > bit much, given that I'm starting from surface time series
> (the
> > > equivalent of
> > >
> `$FUNCTIONALS_DIR/$SESS_ID/bold/$RUN/fmcpr.sm0.fsaverage.lh.nii.gz`,
> > > but as a GIFTI file).
> > >
> > > Supposing I have a paradigm file and the files described
> above,
> > what's
> > > the best way to do a basic GLM? Would it be to
> `mri_surf2surf` our
> > > GIFTI surfaces into `fmcpr.sm0.fsaverage.lh.nii.gz` files in a
> > FSFAST
> > > directory structure, and pick up at `mkanalysis-sess`? Or
> is there a
> > > more straightforward way to just get a simple set of
> contrasts to
> > > compare with a volumetric analysis?
> > >
> > > Thanks in advance,
> > > Chris Markiewicz
> > >
> > >
> > > _______________________________________________
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > >
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>
> > Phone Number: 617-724-2358 <tel:617-724-2358>
> > Fax: 617-726-7422 <tel:617-726-7422>
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>
> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> <https://gate.nmr.mgh.harvard.edu/filedrop2>
> > <https://gate.nmr.mgh.harvard.edu/filedrop2
> <https://gate.nmr.mgh.harvard.edu/filedrop2>>
> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>
> > Outgoing:
> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>
> >
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>>
> >
> >
> >
> > ------------------------------
> >
> > Message: 12
> > Date: Thu, 6 Apr 2017 16:00:08 -0400
> > From: Douglas N Greve <greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>
> > <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>>
> > Subject: Re: [Freesurfer] Custom color maps
> > To: freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>
> > Message-ID:
> > <fa3b5c5d-ed71-9b8a-7b13-5d101908bc91@nmr.mgh.harvard.edu
> <mailto:fa3b5c5d-ed71-9b8a-7b13-5d101908bc91@nmr.mgh.harvard.edu>
> >
> <mailto:fa3b5c5d-ed71-9b8a-7b13-5d101908bc91@nmr.mgh.harvard.edu
> <mailto:fa3b5c5d-ed71-9b8a-7b13-5d101908bc91@nmr.mgh.harvard.edu>>>
> > Content-Type: text/plain; charset=windows-1252; format=flowed
> >
> > See if annotval2surfoverlay.m does what you want. It is in
> v6. If you
> > have v5.x, I can send you the mfile separtely
> >
> >
> > On 04/06/2017 01:00 PM, Senften, Peter wrote:
> > > hi,
> > >
> > > I've read through the list, and searched over the last few
> days,
> > and can't quite seem to find what I'm looking for. My first
> > message wasn't clear at all either (my apologies), it was one of
> > those days where your brain ends up in a bit of a fog.
> > >
> > > I am trying to get a heat map style visual output based on the
> > destrieux 72 region map using cortical thickness as our measure.
> > I'm using FS 6.0 and the edits and outputs have all gone
> great. We
> > are doing the analysis of the cortical thickness outside of
> FS and
> > would like to create a heat-map style visual output of the areas
> > that show a large effect size. My original idea was to create a
> > custom color map and somehow load that in place of the default
> > destrieux color map but I couldn't get that to work. Tried
> > replacing the FS LUT table as well and when loaded the colors
> > remained the same as well.
> > >
> > > Hope that clarifies what I'm trying to do.
> > >
> > > Thanks,
> > >
> > > Peter
> > > ________________________________________
> > > From: freesurfer-bounces@nmr.mgh.harvard.edu
> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>
> > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu
> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>>
> > [freesurfer-bounces@nmr.mgh.harvard.edu
> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>
> > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu
> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>>] on behalf of dg
> > wakeman [dgwakeman@gmail.com <mailto:dgwakeman@gmail.com>
> <mailto:dgwakeman@gmail.com <mailto:dgwakeman@gmail.com>>]
> > > Sent: Tuesday, April 04, 2017 12:11 PM
> > > To: Freesurfer support list
> > > Subject: Re: [Freesurfer] Custom color maps
> > >
> > > Hi Peter,
> > >
> > > We will need a lot more details to help. I suggest you
> look through
> > > the e-mail list a bit. I spent a lot of time helping a
> user or two
> > > with a similar issue. The key details are what are you
> trying to
> > show
> > > (an annotation, a single label, or values)?
> > >
> > > hth
> > > d
> > >
> > > On Wed, Mar 29, 2017 at 11:15 AM, Senften, Peter
> > <peter.senften@ubc.ca <mailto:peter.senften@ubc.ca>
> <mailto:peter.senften@ubc.ca <mailto:peter.senften@ubc.ca>>> wrote:
> > >> Hello,
> > >>
> > >> I am wondering if it is possible to create a custom color map
> > that will be
> > >> visible in freeview using the 3D viewer - not the coronal,
> > axial, or sagital
> > >> views. I created a copy of the LUT file and then replaced the
> > RGB values the
> > >> ones I wanted but haven't been able to get it to load at all.
> > >>
> > >> In the end I am trying to make pretty 3D pictures to see our
> > regions of
> > >> interest better for our data. I am open to other ways of
> doing
> > this.
> > >>
> > >> Thanks,
> > >>
> > >> Peter
> > >>
> > >> _______________________________________________
> > >> Freesurfer mailing list
> > >> Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > >>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <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>
> > <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>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > >
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
> > >
> > > _______________________________________________
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > >
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
> > >
> > >
> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>
> > Phone Number: 617-724-2358 <tel:%28617%29%20724-2358>
> > Fax: 617-726-7422 <tel:%28617%29%20726-7422>
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>
> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> <https://gate.nmr.mgh.harvard.edu/filedrop2>
> > <https://gate.nmr.mgh.harvard.edu/filedrop2
> <https://gate.nmr.mgh.harvard.edu/filedrop2>>
> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>
> > Outgoing:
> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>
> >
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>>
> >
> >
> >
> > ------------------------------
> >
> > Message: 13
> > Date: Thu, 6 Apr 2017 16:06:51 -0400
> > From: Douglas N Greve <greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>
> > <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>>
> > Subject: Re: [Freesurfer] Custom registration template
> > To: freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>
> > Message-ID:
> > <3d80e2cd-55ca-10fa-a366-94079de995cf@nmr.mgh.harvard.edu
> <mailto:3d80e2cd-55ca-10fa-a366-94079de995cf@nmr.mgh.harvard.edu>
> >
> <mailto:3d80e2cd-55ca-10fa-a366-94079de995cf@nmr.mgh.harvard.edu
> <mailto:3d80e2cd-55ca-10fa-a366-94079de995cf@nmr.mgh.harvard.edu>>>
> > Content-Type: text/plain; charset=windows-1252; format=flowed
> >
> > 1. The "..." means to include the other options needed for
> the command
> > to run. Looks like you figured it out. Using -f as you have is
> > correct.
> >
> > 2. can you send the full terminal output?
> >
> >
> > On 04/06/2017 08:55 AM, Linda Zhang wrote:
> > > Dear all,
> > >
> > > I've been following the instructions for building a custom
> > > registration template as written here
> > >
> (http://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates
> <http://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates>
> >
> <http://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates
> <http://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates>>)
> and
> > > here
> > >
> >
> (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-May/018345.html
> <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-May/018345.html>
> >
> <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-May/018345.html
> <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-May/018345.html>>).
> > >
> > >
> > > I'm now at the mris_preproc stage and according to the
> instructions,
> > > the command should be:
> > >
> > > # Get thickness values in the newtemplate space for GLM
> analysis
> > > mris_preproc --surfreg sphere.reg.newtemplate --s subj1 --s
> > subj2 --s
> > > subj3 ...
> > >
> > > I put my subject list into a text file and replaced --s
> with --f
> > > [subjlist] but kept everything else the same. I got two
> errors
> > for no
> > > source hemi specified and no output specified, so I added
> --hemi lh
> > > and --out lh.surfreg.newtemplate.thick --meas thickness. Am I
> > > supposed to do this, and will the output file be used for
> anything
> > > else down the line, i.e., should it be named something more
> > specific?
> > > I see that the next step is to rerun the
> make_average_subject, but I
> > > don't see where the output from the mris_preproc step would
> > figure in.
> > >
> > > On a (maybe) separate issue, when I finally ran my command
> line:
> > >
> > > mris_preproc --surfreg sphere.reg.newtemplate --f subjlist
> --hemi lh
> > > --out lh.surfreg.newtemplate.thick --meas thickness
> > >
> > > I got the following error:
> > >
> > > nsubjects=100
> > > tmpdir is ./tmp.mris_preproc.25619
> > > /home/fsuser/data
> > > set: Variable name must contain alphanumeric characters.
> > >
> > > I'm not sure where the problem might be here. I'm running
> > FreeSurfer
> > > v.5.3 in Virtualbox, and I haven't had any problems while
> running
> > > recon-all on the subjects previously.
> > >
> > > Any insight would be greatly appreciated, thank you!
> > >
> > > Cheers,
> > > Linda
> > >
> > >
> > >
> > > _______________________________________________
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > >
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>
> > Phone Number: 617-724-2358 <tel:%28617%29%20724-2358>
> > Fax: 617-726-7422 <tel:%28617%29%20726-7422>
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>
> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> <https://gate.nmr.mgh.harvard.edu/filedrop2>
> > <https://gate.nmr.mgh.harvard.edu/filedrop2
> <https://gate.nmr.mgh.harvard.edu/filedrop2>>
> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>
> > Outgoing:
> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>
> >
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>>
> >
> >
> >
> > ------------------------------
> >
> > Message: 14
> > Date: Thu, 6 Apr 2017 16:12:31 -0400
> > From: Douglas N Greve <greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>
> > <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>>
> > Subject: Re: [Freesurfer] Selxavg3-sess Looking for (and
> can't find)
> > "fmc.sm0"
> > To: freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>
> > Message-ID:
> > <57429858-c90b-3267-23d5-773c1d49275d@nmr.mgh.harvard.edu
> <mailto:57429858-c90b-3267-23d5-773c1d49275d@nmr.mgh.harvard.edu>
> >
> <mailto:57429858-c90b-3267-23d5-773c1d49275d@nmr.mgh.harvard.edu
> <mailto:57429858-c90b-3267-23d5-773c1d49275d@nmr.mgh.harvard.edu>>>
> > Content-Type: text/plain; charset=windows-1252; format=flowed
> >
> > can you send the full terminal output?
> >
> >
> > On 04/05/2017 04:02 PM, Taylor, Johnmark wrote:
> > > Hello,
> > >
> > > I am getting an odd bug on selxavg3-sess. I am getting the
> error
> > message,
> > >
> > > *ERROR: cannot find [rest of file path]/fmc.sm0*
> > >
> > > I am indicating zero smoothing in mkanalysis-sess ("-fwhm
> 0"). I am
> > > confused because the output of preproc-sess for no
> smoothing is
> > > fmc.nii.gz, *NOT *fmc.sm0.nii.gz when doing analyses in native
> > volume
> > > space, so I am not sure why selxavg-sess is looking for the
> > wrong file
> > > path. For reference, here is my call to mkanalysis-sess:
> > >
> > > mkanalysis-sess -analysis analysis_name -fsd bold -runlistfile
> > runlist.txt
> > > -native -nuisreg mcextreg 3 -fwhm 0 -event-related
> -nconditions 8
> > > -paradigm spiralpara.par -spmhrf 0 -refeventdur 12 -TR 1.5
> > > -polyfit 2 -nskip 8
> > >
> > > I am using Freesurfer 5.3, if that helps. The analysis works
> > fine when
> > > I apply 3mm smoothing (I've done preprocessing for both
> the 0mm and
> > > 3mm options).
> > >
> > > Thank you very much, and cheers,
> > >
> > > JohnMark
> > >
> > >
> > > _______________________________________________
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > >
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>
> > Phone Number: 617-724-2358 <tel:%28617%29%20724-2358>
> > Fax: 617-726-7422 <tel:%28617%29%20726-7422>
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>
> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> <https://gate.nmr.mgh.harvard.edu/filedrop2>
> > <https://gate.nmr.mgh.harvard.edu/filedrop2
> <https://gate.nmr.mgh.harvard.edu/filedrop2>>
> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>
> > Outgoing:
> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>
> >
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>>
> >
> >
> >
> > ------------------------------
> >
> > Message: 15
> > Date: Thu, 6 Apr 2017 16:17:55 -0400
> > From: Douglas N Greve <greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>
> > <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>>
> > Subject: Re: [Freesurfer] Ventricle-to-Brain Ratio
> > To: freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>
> > Message-ID:
> > <b00cc093-33a4-9ae1-2e0f-637867719a68@nmr.mgh.harvard.edu
> <mailto:b00cc093-33a4-9ae1-2e0f-637867719a68@nmr.mgh.harvard.edu>
> >
> <mailto:b00cc093-33a4-9ae1-2e0f-637867719a68@nmr.mgh.harvard.edu
> <mailto:b00cc093-33a4-9ae1-2e0f-637867719a68@nmr.mgh.harvard.edu>>>
> > Content-Type: text/plain; charset=windows-1252; format=flowed
> >
> > that looks right. how different are the values?
> >
> >
> > On 04/05/2017 10:58 AM, Gullickson, James wrote:
> > > Hello all,
> > >
> > > I want to calculate a Ventricle-to-Brain ratio (VBR) as a
> measure of
> > > parenchymal atrophy using Freesurfer version 5.3.0. I have
> tried
> > to go
> > > about this using the aseg.stats output (using
> asegstats2table),
> > but am
> > > running into inconsistencies.
> > >
> > > The basic calculation for VBR is:
> > >
> > > (Total Ventricular Volume/Total Brain Volume) * 100
> > >
> > > i.e. Bigler, E. D. (2013). Traumatic brain injury,
> neuroimaging, and
> > > neurodegeneration. /Frontiers in human neuroscience/, /7/,
> 395.
> > >
> > >
> > > What is the best way to get Total Ventricular Volume (TVV)
> and Total
> > > Brain Volume (TBV) for this calculation? I have tried
> several ways,
> > > which lead to different values:
> > >
> > > TVV = left lateral ventricle + left inf lateral ventricle
> + right
> > > lateral ventricle + right inf lateral ventricle + 3rd
> ventricle
> > + 4th
> > > ventricle + 5th ventricle + choroid plexus
> > >
> > > which gives me a different result than
> > >
> > > TVV = BrainSegVol - BrainSegVolNotVent
> > >
> > >
> > > and for TBV
> > >
> > > TBV = TotalGrayVol + CorticalWhiteMatterVol
> > >
> > > which differs from
> > >
> > > TBV = BrainSegVolNotVent
> > >
> > >
> > > Thank you for your help,
> > >
> > > James Gullickson
> > >
> > >
> > >
> > >
> > >
> > > _______________________________________________
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > >
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>
> > Phone Number: 617-724-2358 <tel:%28617%29%20724-2358>
> > Fax: 617-726-7422 <tel:%28617%29%20726-7422>
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>
> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> <https://gate.nmr.mgh.harvard.edu/filedrop2>
> > <https://gate.nmr.mgh.harvard.edu/filedrop2
> <https://gate.nmr.mgh.harvard.edu/filedrop2>>
> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>
> > Outgoing:
> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>
> >
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>>
> >
> >
> >
> > ------------------------------
> >
> > Message: 16
> > Date: Thu, 6 Apr 2017 16:27:29 -0400
> > From: Douglas N Greve <greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>
> > <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>>
> > Subject: Re: [Freesurfer] ROI seed size
> > To: freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>
> > Message-ID:
> > <a48d0f59-ffee-e425-f352-e382a8362116@nmr.mgh.harvard.edu
> <mailto:a48d0f59-ffee-e425-f352-e382a8362116@nmr.mgh.harvard.edu>
> >
> <mailto:a48d0f59-ffee-e425-f352-e382a8362116@nmr.mgh.harvard.edu
> <mailto:a48d0f59-ffee-e425-f352-e382a8362116@nmr.mgh.harvard.edu>>>
> > Content-Type: text/plain; charset=utf-8; format=flowed
> >
> > these are good questions without good answers. It is hard to
> compare
> > surface-based vs volume-based. The surface-based may be smaller,
> > but it
> > will only include gray matter whereas a volume-based sphere
> will be
> > bigger but will include WM and CSF. If you're voxel size is
> small,
> > then
> > 3mm radius might not get more than one or two of them
> >
> >
> > On 04/03/2017 09:53 PM, ERIK JAHNER wrote:
> > > What is the appropriate size for a surface based seed?
> > >
> > > I am referencing a study with volumetric based seeds with
> > spheres with a radius of 3mm (in fMRI data). I would like to
> do a
> > similar study using surface based representations. In a
> volumetric
> > based analysis folding may actually increase the amount of
> > cortical surface represented in a sphere. Using a circle on the
> > surface with a 3 mm radius therefore would not be the same.
> But?.
> > is the difference so minimal and variable across the cortex that
> > it is not worth considering especially since the seeds are
> derived
> > from published work and not using a localizer?
> > >
> > > Do you know of any published guidelines on generating seed
> sizes
> > in surface based models, not based on a localizer.
> > > Or is this the completely wrong approach? Should I be
> using the
> > tal coordinates to locate which parcellation of the available
> > atlases that the seed was located in? (for example i have a
> > fusiform face area seed which I have set as a circle 3mm radius)
> > >
> > > many thanks for your continued help
> > > Erik
> > >
> > >
> > >
> > > _______________________________________________
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > >
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
> > >
> > >
> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>
> > Phone Number: 617-724-2358 <tel:%28617%29%20724-2358>
> > Fax: 617-726-7422 <tel:%28617%29%20726-7422>
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>
> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> <https://gate.nmr.mgh.harvard.edu/filedrop2>
> > <https://gate.nmr.mgh.harvard.edu/filedrop2
> <https://gate.nmr.mgh.harvard.edu/filedrop2>>
> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>
> > Outgoing:
> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>
> >
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>>
> >
> >
> >
> > ------------------------------
> >
> > Message: 17
> > Date: Thu, 6 Apr 2017 16:31:27 -0400
> > From: Douglas N Greve <greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>
> > <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>>
> > Subject: Re: [Freesurfer] correlation coefficient R
> > To: freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>
> > Message-ID:
> > <20326815-9122-4dd5-e0fa-bce6d0373e7f@nmr.mgh.harvard.edu
> <mailto:20326815-9122-4dd5-e0fa-bce6d0373e7f@nmr.mgh.harvard.edu>
> >
> <mailto:20326815-9122-4dd5-e0fa-bce6d0373e7f@nmr.mgh.harvard.edu
> <mailto:20326815-9122-4dd5-e0fa-bce6d0373e7f@nmr.mgh.harvard.edu>>>
> > Content-Type: text/plain; charset=windows-1252; format=flowed
> >
> > I guess you could average it over space (eg, over a
> cluster). Let me
> > know if you want instructions. Otherwise, I'm not sure what
> to say.
> >
> >
> > On 04/04/2017 06:49 AM, tom parker wrote:
> > > Hi Doug,
> > > Thanks! I realize now I didn't explain myself properly.
> > > I need one single R value for the correlation analysis I made,
> > > similarly to when I correlate two variables with Pearson's
> R in a
> > > statistical package. I have a referee asking me to put it
> on a table
> > > with the freesurfer results. Is there a way to get a single
> > average R
> > > value from the pcc.mgh file?
> > > Thank you so much!
> > >
> > > Douglas Greve
> > >
> >
> <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Douglas+Greve%22
> <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Douglas+Greve%22>
> >
> <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Douglas+Greve%22
> <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Douglas+Greve%22>>>
> > > Mon, 03 Apr 2017 18:46:46 -0700
> > >
> >
> <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20170403
> <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20170403>
> >
> <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20170403
> <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20170403>>>
> > >
> > >
> > > Each vertex is a correlation value.
> > >
> > > 2017-04-04 1:09 GMT+01:00 tom parker
> <tomparker540@gmail.com <mailto:tomparker540@gmail.com>
> > <mailto:tomparker540@gmail.com <mailto:tomparker540@gmail.com>>
> > > <mailto:tomparker540@gmail.com
> <mailto:tomparker540@gmail.com> <mailto:tomparker540@gmail.com
> <mailto:tomparker540@gmail.com>>>>:
> > >
> > > Thanks Doug!
> > >
> > > I have version 6 and got a pcc.mgh file.
> > >
> > > How can I get a correlation R value from this file?
> > >
> > > Thanks again
> > >
> > > Douglas N Greve
> > >
> >
> <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Douglas+N+Greve%22
> <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Douglas+N+Greve%22>
> >
> <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Douglas+N+Greve%22
> <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Douglas+N+Greve%22>>>
> > > Mon, 03 Apr 2017 09:41:41 -0700
> > >
> >
> <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20170403
> <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20170403>
> >
> <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20170403
> <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20170403>>>
> > >
> > >
> > > if you are using version 6, then it should have produced a
> > file called
> > > pcc.mgh. This the partial pearson correlation coef.
> > >
> > >
> > >
> > > 2017-04-03 15:40 GMT+01:00 tom parker
> > <tomparker540@gmail.com <mailto:tomparker540@gmail.com>
> <mailto:tomparker540@gmail.com <mailto:tomparker540@gmail.com>>
> > > <mailto:tomparker540@gmail.com
> <mailto:tomparker540@gmail.com>
> > <mailto:tomparker540@gmail.com
> <mailto:tomparker540@gmail.com>>>>:
> > >
> > > Dear Freesurfers,
> > >
> > > I made some correlations between cortical
> thickness and
> > age in
> > > qdec.
> > >
> > > Is it possible to get the correlation coefficient
> value of
> > > this analysis?
> > >
> > > I just need to put it in a table with the significant
> > results.
> > >
> > > Thank you so much!
> > >
> > >
> > >
> > >
> > >
> > > _______________________________________________
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > >
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>
> > Phone Number: 617-724-2358 <tel:%28617%29%20724-2358>
> > Fax: 617-726-7422 <tel:%28617%29%20726-7422>
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>
> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> <https://gate.nmr.mgh.harvard.edu/filedrop2>
> > <https://gate.nmr.mgh.harvard.edu/filedrop2
> <https://gate.nmr.mgh.harvard.edu/filedrop2>>
> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>
> > Outgoing:
> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>
> >
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>>
> >
> >
> >
> > ------------------------------
> >
> > Message: 18
> > Date: Thu, 6 Apr 2017 20:35:28 +0000
> > From: "Senften, Peter" <peter.senften@ubc.ca
> <mailto:peter.senften@ubc.ca>
> > <mailto:peter.senften@ubc.ca <mailto:peter.senften@ubc.ca>>>
> > Subject: Re: [Freesurfer] Custom color maps
> > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>>
> > Message-ID:
> >
> >
> <B6AC19D7BE198443A028636599CB88771E559AA9@exch-mbx08p.ead.ubc.ca
> <mailto:B6AC19D7BE198443A028636599CB88771E559AA9@exch-mbx08p.ead.ubc.ca>
> >
> <mailto:B6AC19D7BE198443A028636599CB88771E559AA9@exch-mbx08p.ead.ubc.ca
> <mailto:B6AC19D7BE198443A028636599CB88771E559AA9@exch-mbx08p.ead.ubc.ca>>>
> > Content-Type: text/plain; charset="us-ascii"
> >
> > Thanks, I'll take a look at it and let you know how it goes.
> >
> > Peter
> > ________________________________________
> > From: freesurfer-bounces@nmr.mgh.harvard.edu
> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>
> > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu
> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>>
> > [freesurfer-bounces@nmr.mgh.harvard.edu
> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>
> > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu
> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>>] on behalf of
> > Douglas N Greve [greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>
> > <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>]
> > Sent: Thursday, April 06, 2017 1:00 PM
> > To: freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>
> > Subject: Re: [Freesurfer] Custom color maps
> >
> > See if annotval2surfoverlay.m does what you want. It is in
> v6. If you
> > have v5.x, I can send you the mfile separtely
> >
> >
> > On 04/06/2017 01:00 PM, Senften, Peter wrote:
> > > hi,
> > >
> > > I've read through the list, and searched over the last few
> days,
> > and can't quite seem to find what I'm looking for. My first
> > message wasn't clear at all either (my apologies), it was one of
> > those days where your brain ends up in a bit of a fog.
> > >
> > > I am trying to get a heat map style visual output based on the
> > destrieux 72 region map using cortical thickness as our measure.
> > I'm using FS 6.0 and the edits and outputs have all gone
> great. We
> > are doing the analysis of the cortical thickness outside of
> FS and
> > would like to create a heat-map style visual output of the areas
> > that show a large effect size. My original idea was to create a
> > custom color map and somehow load that in place of the default
> > destrieux color map but I couldn't get that to work. Tried
> > replacing the FS LUT table as well and when loaded the colors
> > remained the same as well.
> > >
> > > Hope that clarifies what I'm trying to do.
> > >
> > > Thanks,
> > >
> > > Peter
> > > ________________________________________
> > > From: freesurfer-bounces@nmr.mgh.harvard.edu
> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>
> > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu
> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>>
> > [freesurfer-bounces@nmr.mgh.harvard.edu
> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>
> > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu
> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>>] on behalf of dg
> > wakeman [dgwakeman@gmail.com <mailto:dgwakeman@gmail.com>
> <mailto:dgwakeman@gmail.com <mailto:dgwakeman@gmail.com>>]
> > > Sent: Tuesday, April 04, 2017 12:11 PM
> > > To: Freesurfer support list
> > > Subject: Re: [Freesurfer] Custom color maps
> > >
> > > Hi Peter,
> > >
> > > We will need a lot more details to help. I suggest you
> look through
> > > the e-mail list a bit. I spent a lot of time helping a
> user or two
> > > with a similar issue. The key details are what are you
> trying to
> > show
> > > (an annotation, a single label, or values)?
> > >
> > > hth
> > > d
> > >
> > > On Wed, Mar 29, 2017 at 11:15 AM, Senften, Peter
> > <peter.senften@ubc.ca <mailto:peter.senften@ubc.ca>
> <mailto:peter.senften@ubc.ca <mailto:peter.senften@ubc.ca>>> wrote:
> > >> Hello,
> > >>
> > >> I am wondering if it is possible to create a custom color map
> > that will be
> > >> visible in freeview using the 3D viewer - not the coronal,
> > axial, or sagital
> > >> views. I created a copy of the LUT file and then replaced the
> > RGB values the
> > >> ones I wanted but haven't been able to get it to load at all.
> > >>
> > >> In the end I am trying to make pretty 3D pictures to see our
> > regions of
> > >> interest better for our data. I am open to other ways of
> doing
> > this.
> > >>
> > >> Thanks,
> > >>
> > >> Peter
> > >>
> > >> _______________________________________________
> > >> Freesurfer mailing list
> > >> Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > >>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <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>
> > <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>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > >
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
> > >
> > > _______________________________________________
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > >
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
> > >
> > >
> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>
> > Phone Number: 617-724-2358 <tel:%28617%29%20724-2358>
> > Fax: 617-726-7422 <tel:%28617%29%20726-7422>
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>
> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> <https://gate.nmr.mgh.harvard.edu/filedrop2>
> > <https://gate.nmr.mgh.harvard.edu/filedrop2
> <https://gate.nmr.mgh.harvard.edu/filedrop2>>
> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>
> > Outgoing:
> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>
> >
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>>
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
> >
> >
> >
> > ------------------------------
> >
> > Message: 19
> > Date: Thu, 6 Apr 2017 16:37:11 -0400
> > From: Douglas N Greve <greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>
> > <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>>
> > Subject: Re: [Freesurfer] General QDEC clarification queastions
> > To: freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>
> > Message-ID:
> > <e3752bc0-b24c-284f-a6a2-6cc5adb682b7@nmr.mgh.harvard.edu
> <mailto:e3752bc0-b24c-284f-a6a2-6cc5adb682b7@nmr.mgh.harvard.edu>
> >
> <mailto:e3752bc0-b24c-284f-a6a2-6cc5adb682b7@nmr.mgh.harvard.edu
> <mailto:e3752bc0-b24c-284f-a6a2-6cc5adb682b7@nmr.mgh.harvard.edu>>>
> > Content-Type: text/plain; charset=windows-1252; format=flowed
> >
> >
> >
> > On 04/03/2017 01:45 PM, Veggeberg, Rosanna wrote:
> > > Hello,
> > > I am using QDEC to analyze cortical structural data and am
> > looking for
> > > some clarification on some questions that have come up.
> > >
> > > 1. _Design tab_: In the "Measure" drop-down selection, I
> understand
> > > what we are getting when looking at thickness but the other
> > > measurements I am unclear on. Is there information or
> > publications on
> > > the other 12 possible measures (how they are measured,
> what they
> > mean,
> > > applications for using them). In particular, I am
> interested in
> > > learning more about area, area.pial, volume, sulc, and
> curv but
> > would
> > > like to understand what the others mean as well to
> determine if they
> > > would be applicable to our study questions.
> > There is not a specific pub on this. The area is the area of
> a vertex
> > (the average of the triangles around it), same interpreation
> for the
> > volume. These are kind of like VBM analysis. area.pial is
> the area of
> > the pial surface whereas simple area is the area of the
> white. curv is
> > the curvature; sulc is the sulcal depth. These are used for
> > registration
> > and generally not that interesting.
> > >
> > > 2. _Design tab_: I am a little unclear on why the model
> factors are
> > > labeled the way they are and wanted to see if I am using them
> > correctly.
> > > -Discrete (Fixed Factors): this is pretty straight forward
> to be
> > used
> > > as independent categorical variables, correct?
> > yes
> > > -Continuous (Covariate): even though it says covariate,
> should these
> > > variables just be treated as independent continuous varaibles?
> > correct
> > > -Nuisance Factors: should these just be treated as the
> covariates we
> > > wish to control for?
> > yes. it allows you to have more continuous variable, but you
> won't get
> > tests that include them
> > >
> > > 3. _Results_: When I am doing a group comparison (i.e.
> disease vs.
> > > control), does QDEC run the comparison based off of which
> order the
> > > labels appear in the table: disease vs. control, or does
> it run the
> > > comparison based off of which label comes first
> alphabetically:
> > > control vs. disease?
> > The order in your levels file
> > >
> > > 4. _Results_: When viewing the results in freeview, if I
> click on a
> > > significant cluster, in the bottom panel, does a negative
> value next
> > > to the mc-z.abs.th13.sig.cluster.mgh label indicate a
> decrease in
> > > cortical thickness (i.e. disease vs. control: negative value
> > indicates
> > > control is greater than disease)?
> > It depends on the order above. It will be contrast = first -
> second.
> > >
> > > 5. Finally, once you have closed QDEC, is it possible to
> reopen the
> > > files again in the Gui? Or would you have to rerun the
> analysis?
> > sorry, not sure
> > >
> > > Thank you for help and please let me know if you need any
> further
> > > clarification.
> > >
> > >
> > > _______________________________________________
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > >
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>
> > Phone Number: 617-724-2358 <tel:%28617%29%20724-2358>
> > Fax: 617-726-7422 <tel:%28617%29%20726-7422>
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>
> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> <https://gate.nmr.mgh.harvard.edu/filedrop2>
> > <https://gate.nmr.mgh.harvard.edu/filedrop2
> <https://gate.nmr.mgh.harvard.edu/filedrop2>>
> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>
> > Outgoing:
> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>
> >
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>>
> >
> >
> >
> > ------------------------------
> >
> > Message: 20
> > Date: Thu, 6 Apr 2017 16:52:33 -0400
> > From: Arnaud Bor? <arnaud.bore@gmail.com
> <mailto:arnaud.bore@gmail.com>
> > <mailto:arnaud.bore@gmail.com <mailto:arnaud.bore@gmail.com>>>
> > Subject: [Freesurfer] QDEC and ROI drawing
> > To: freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>
> > Message-ID:
> >
> >
> <CAPA8YjZO-wfJ1h19QZK5JNnA7G+fmXEUsQ+YjQDcC-3S9mWUXA@mail.gmail.com
> <mailto:CAPA8YjZO-wfJ1h19QZK5JNnA7G%2BfmXEUsQ%2BYjQDcC-3S9mWUXA@mail.gmail.com>
> >
> <mailto:CAPA8YjZO-wfJ1h19QZK5JNnA7G%2BfmXEUsQ%2BYjQDcC-3S9mWUXA@mail.gmail.com
> <mailto:CAPA8YjZO-wfJ1h19QZK5JNnA7G%252BfmXEUsQ%252BYjQDcC-3S9mWUXA@mail.gmail.com>>>
> > Content-Type: text/plain; charset="utf-8"
> >
> > Dear Freesurfer's experts,
> > I draw a specific region on fsaverage using QDEC, then I mapped
> > this label
> > on each subject using mri_label2label. I looked at these
> > registered labels
> > using freeview. Most of them are perfect but for some of them I
> > would like
> > to correct the segmentation. I would like to modify it using
> QDEC
> > but when
> > I overlay this label on the surface of my subject it has been
> > shifted. I
> > think this shift is because QDEC is using fsaverage as the
> > standard space.
> > I try opening QDEC using the "average" option and use the
> subject
> > I want
> > but I still get this shift. am I missing something ?
> > Thank you in advance for your help.
> > Arnaud Bore
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
> > URL:
> >
> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170406/c45e3871/attachment-0001.html
> <http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170406/c45e3871/attachment-0001.html>
> >
> <http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170406/c45e3871/attachment-0001.html
> <http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170406/c45e3871/attachment-0001.html>>
> >
> > ------------------------------
> >
> > Message: 21
> > Date: Thu, 6 Apr 2017 16:53:32 -0400
> > From: Douglas N Greve <greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>
> > <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>>
> > Subject: Re: [Freesurfer] QDEC and ROI drawing
> > To: freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>
> > Message-ID:
> > <793cd266-aae2-0b71-638e-cb620c08a3b6@nmr.mgh.harvard.edu
> <mailto:793cd266-aae2-0b71-638e-cb620c08a3b6@nmr.mgh.harvard.edu>
> >
> <mailto:793cd266-aae2-0b71-638e-cb620c08a3b6@nmr.mgh.harvard.edu
> <mailto:793cd266-aae2-0b71-638e-cb620c08a3b6@nmr.mgh.harvard.edu>>>
> > Content-Type: text/plain; charset=windows-1252; format=flowed
> >
> > what is your label2label command line?
> >
> >
> > On 04/06/2017 04:52 PM, Arnaud Bor? wrote:
> > > Dear Freesurfer's experts,
> > > I draw a specific region on fsaverage using QDEC, then I
> mapped this
> > > label on each subject using mri_label2label. I looked at these
> > > registered labels using freeview. Most of them are perfect
> but for
> > > some of them I would like to correct the segmentation. I would
> > like to
> > > modify it using QDEC but when I overlay this label on the
> surface of
> > > my subject it has been shifted. I think this shift is because
> > QDEC is
> > > using fsaverage as the standard space. I try opening QDEC
> using the
> > > "average" option and use the subject I want but I still
> get this
> > > shift. am I missing something ?
> > > Thank you in advance for your help.
> > > Arnaud Bore
> > >
> > >
> > >
> > > _______________________________________________
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > >
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>
> > Phone Number: 617-724-2358 <tel:%28617%29%20724-2358>
> > Fax: 617-726-7422 <tel:%28617%29%20726-7422>
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>
> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> <https://gate.nmr.mgh.harvard.edu/filedrop2>
> > <https://gate.nmr.mgh.harvard.edu/filedrop2
> <https://gate.nmr.mgh.harvard.edu/filedrop2>>
> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>
> > Outgoing:
> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>
> >
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>>
> >
> >
> >
> > ------------------------------
> >
> > Message: 22
> > Date: Thu, 6 Apr 2017 21:08:19 +0000
> > From: "Lim, Lena" <lena.lim@kcl.ac.uk
> <mailto:lena.lim@kcl.ac.uk> <mailto:lena.lim@kcl.ac.uk
> <mailto:lena.lim@kcl.ac.uk>>>
> > Subject: Re: [Freesurfer] QDEC-volume, thickness and area
> > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>>
> > Message-ID:
> >
> >
> <HE1PR0301MB2233E43DFD8B11E3CE0A0016C20D0@HE1PR0301MB2233.eurprd03.prod.outlook.com
> <mailto:HE1PR0301MB2233E43DFD8B11E3CE0A0016C20D0@HE1PR0301MB2233.eurprd03.prod.outlook.com>
> >
> <mailto:HE1PR0301MB2233E43DFD8B11E3CE0A0016C20D0@HE1PR0301MB2233.eurprd03.prod.outlook.com
> <mailto:HE1PR0301MB2233E43DFD8B11E3CE0A0016C20D0@HE1PR0301MB2233.eurprd03.prod.outlook.com>>>
> >
> > Content-Type: text/plain; charset="windows-1252"
> >
> > Thanks, Doug.
> >
> >
> > There is no significant interaction and I merged the males and
> > females within each group, but the reviewer wants me to include
> > gender as a covariate. Do we always need to control for gender
> > esp. when the group x gender is insignificant? Will that be
> > "over-controlled"?
> >
> >
> > ________________________________
> > From: freesurfer-bounces@nmr.mgh.harvard.edu
> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>
> > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu
> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>>
> > <freesurfer-bounces@nmr.mgh.harvard.edu
> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>
> > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu
> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>>> on behalf of
> > Douglas N Greve <greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>
> > <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>>
> > Sent: 06 April 2017 20:45
> > To: freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>
> > Subject: Re: [Freesurfer] QDEC-volume, thickness and area
> >
> > what do you mean they do not differ in gender ratio? Just
> that the
> > relative number of M/F is the same in each group? If there
> is not a
> > significant interaction between gender and group, then you
> can usually
> > merge the genders.
> >
> >
> > On 04/05/2017 05:13 PM, Lim, Lena wrote:
> > >
> > > Dear Freesurfer Experts,
> > >
> > > 1) I have 2 groups (A & B), which do not differ in terms
> of gender
> > > ratio. If there were no significant regions for Group-Gender
> > > interaction in mean cortical thickness in the QDEC
> analysis, can I
> > > conclude that gender does not influence the effect of group on
> > > thickness? The differences between A and B on mean
> thickness is not
> > > affected by Gender? Is this valid or do I need to add
> Gender as a
> > > covariate even though the group do not differ on gender ratio?
> > >
> > > 2) A reviewer pointed that it is not right to test for group
> > > differences in volume once I have tested for thickness and
> area,
> > > especially when there is a cluster where A and B do not differ
> > > significantly in thickness and area but they differ
> significantly in
> > > volume?Is this right?
> > >
> > > Please kindly advise.
> > >
> > > Many thanks,
> > >
> > > Lena
> > >
> > >
> > >
> > > _______________________________________________
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > >
> >
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> >
> <https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=01%7C01%7Clena.lim%40kcl.ac.uk%7C1a7a3062e8634c0e8d1c08d47d2577ca%7C8370cf1416f34c16b83c724071654356%7C0&sdata=PhNkIdT%2Fj8FHEIG2Wo1UjfG65ns90Ao7ajxUX7ErJus%3D&reserved=0
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> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>
> > Phone Number: 617-724-2358 <tel:%28617%29%20724-2358>
> > Fax: 617-726-7422 <tel:%28617%29%20726-7422>
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>
> > FileDrop:
> >
> https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgate.nmr.mgh.harvard.edu%2Ffiledrop2&data=01%7C01%7Clena.lim%40kcl.ac.uk%7C1a7a3062e8634c0e8d1c08d47d2577ca%7C8370cf1416f34c16b83c724071654356%7C0&sdata=sLX6wB91T%2FSYsH2ihNMK39jOGhYZgcSWos3D2cfO0RE%3D&reserved=0
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> >
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> >
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> >
> <https://emea01.safelinks.protection.outlook.com/?url=www.nmr.mgh.harvard.edu%2Ffacility%2Ffiledrop%2Findex.html&data=01%7C01%7Clena.lim%40kcl.ac.uk%7C1a7a3062e8634c0e8d1c08d47d2577ca%7C8370cf1416f34c16b83c724071654356%7C0&sdata=uCgDjaHFBNRCI0uSukR9fcgOVVo6Fhr5gGZIJslPy4E%3D&reserved=0
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> > Outgoing:
> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>
> >
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>>
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> >
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> >
> >
> > The information in this e-mail is intended only for the
> person to
> > whom it is
> > addressed. If you believe this e-mail was sent to you in
> error and
> > the e-mail
> > contains patient information, please contact the Partners
> > Compliance HelpLine at
> >
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> >
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> > . 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...
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> >
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> >
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> >
> > ------------------------------
> >
> > Message: 23
> > Date: Thu, 6 Apr 2017 17:17:04 -0400
> > From: Douglas N Greve <greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>
> > <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>>
> > Subject: Re: [Freesurfer] QDEC-volume, thickness and area
> > To: freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>
> > Message-ID:
> > <989131f9-3095-bde5-437e-36794a25df65@nmr.mgh.harvard.edu
> <mailto:989131f9-3095-bde5-437e-36794a25df65@nmr.mgh.harvard.edu>
> >
> <mailto:989131f9-3095-bde5-437e-36794a25df65@nmr.mgh.harvard.edu
> <mailto:989131f9-3095-bde5-437e-36794a25df65@nmr.mgh.harvard.edu>>>
> > Content-Type: text/plain; charset=windows-1252; format=flowed
> >
> > probably so. It is up to you whether you want to fight the
> > reviewer or not.
> >
> >
> > On 04/06/2017 05:08 PM, Lim, Lena wrote:
> > >
> > > Thanks, Doug.
> > >
> > >
> > > There is no significant interaction and I merged the males and
> > females
> > > within each group, but the reviewer wants me to include
> gender as a
> > > covariate. Do we always need to control for gender esp.
> when the
> > group
> > > x gender is insignificant? Will that be "over-controlled"?
> > >
> > >
> > >
> > >
> >
> ------------------------------------------------------------------------
> > > *From:* freesurfer-bounces@nmr.mgh.harvard.edu
> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>
> > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu
> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>>
> > > <freesurfer-bounces@nmr.mgh.harvard.edu
> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>
> > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu
> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>>> on behalf of
> > Douglas N Greve
> > > <greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>
> > > *Sent:* 06 April 2017 20:45
> > > *To:* freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>
> > > *Subject:* Re: [Freesurfer] QDEC-volume, thickness and area
> > > what do you mean they do not differ in gender ratio? Just
> that the
> > > relative number of M/F is the same in each group? If there
> is not a
> > > significant interaction between gender and group, then you can
> > usually
> > > merge the genders.
> > >
> > >
> > > On 04/05/2017 05:13 PM, Lim, Lena wrote:
> > > >
> > > > Dear Freesurfer Experts,
> > > >
> > > > 1) I have 2 groups (A & B), which do not differ in terms
> of gender
> > > > ratio. If there were no significant regions for Group-Gender
> > > > interaction in mean cortical thickness in the QDEC
> analysis, can I
> > > > conclude that gender does not influence the effect of
> group on
> > > > thickness? The differences between A and B on mean thickness
> > is not
> > > > affected by Gender? Is this valid or do I need to add
> Gender as a
> > > > covariate even though the group do not differ on gender
> ratio?
> > > >
> > > > 2) A reviewer pointed that it is not right to test for group
> > > > differences in volume once I have tested for thickness
> and area,
> > > > especially when there is a cluster where A and B do not
> differ
> > > > significantly in thickness and area but they differ
> > significantly in
> > > > volume?Is this right?
> > > >
> > > > Please kindly advise.
> > > >
> > > > Many thanks,
> > > >
> > > > Lena
> > > >
> > > >
> > > >
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> > >
> > > --
> > > Douglas N. Greve, Ph.D.
> > > MGH-NMR Center
> > > greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>
> > > Phone Number: 617-724-2358 <tel:%28617%29%20724-2358>
> > > Fax: 617-726-7422 <tel:%28617%29%20726-7422>
> > >
> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>
> > > FileDrop:
> > >
> >
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> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>
> > Phone Number: 617-724-2358 <tel:%28617%29%20724-2358>
> > Fax: 617-726-7422 <tel:%28617%29%20726-7422>
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>
> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> <https://gate.nmr.mgh.harvard.edu/filedrop2>
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> <https://gate.nmr.mgh.harvard.edu/filedrop2>>
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> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>
> > Outgoing:
> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>
> >
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>>
> >
> >
> >
> > ------------------------------
> >
> > Message: 24
> > Date: Thu, 6 Apr 2017 23:26:38 +0200 (CEST)
> > From: <stdp82@virgilio.it <mailto:stdp82@virgilio.it>
> <mailto:stdp82@virgilio.it <mailto:stdp82@virgilio.it>>>
> > Subject: [Freesurfer] R: Re: R: R: Re: R: Re: Whole
> preprocessing with
> > FAST without to perform a seed based analysis
> > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>>
> > Message-ID:
> >
> >
> <279193799.11183291491513998781.JavaMail.httpd@fep-webmail-07.iol.local>
> >
> > Content-Type: text/plain; charset="utf-8"
> >
> > Thanks.The file could not be open by fslview.I presume that
> it is
> > inflated.How can I do to transform it?Stefano
> >
> >
> >
> >
> > ----Messaggio originale----
> >
> > Da: "Douglas Greve" <greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>
> > <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>>
> >
> > Data: 6-apr-2017 17.56
> >
> > A: <freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>>
> >
> > Ogg: Re: [Freesurfer] R: R: Re: R: Re: Whole preprocessing with
> > FAST without to perform a seed based analysis
> >
> >
> >
> >
> >
> >
> >
> > It will be in the space that you analyzed it in. If you want the
> > native space, then use -native when running
> preproc-sess and
> > mkanalysis
> >
> >
> >
> >
> > On 4/6/17 2:34 AM, stdp82@virgilio.it
> <mailto:stdp82@virgilio.it> <mailto:stdp82@virgilio.it
> <mailto:stdp82@virgilio.it>>
> > wrote:
> >
> >
> > Furthermore, the res-001.nii which is produce in
> > produced in the res folder in not the same dimension
> of f.nii.
> > I would do the whole FAST preprocessing on f.nii.,
> > maintaining the same dimension and open it with FSL.
> > Thanks
> > Stefano
> >
> >
> >
> >
> > ----Messaggio originale----
> >
> > Da: stdp82@virgilio.it <mailto:stdp82@virgilio.it>
> <mailto:stdp82@virgilio.it <mailto:stdp82@virgilio.it>>
> >
> > Data: 5-apr-2017 23.39
> >
> > A: "Freesurfer support
> > list"<freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>>
> >
> > Ogg: [Freesurfer] R: Re: R: Re: Whole
> preprocessing with
> > FAST
> > without to perform a seed based analysis
> >
> >
> >
> > Hi,
> >
> >
> >
> > as you advise I have run selxavg3-sess with the -svres
> > option.
> > I found a folder called "res" which contain
> > "res-001.nii". Is it the f.nii fully processed?
> > Thanks
> > Stefano
> >
> >
> >
> >
> > ----Messaggio originale----
> >
> > Da: "Douglas Greve" <greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>
> > <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>>
> >
> > Data: 14-mar-2017 17.38
> >
> > A: <freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>>
> >
> > Ogg: Re: [Freesurfer] R: Re: Whole preprocessing
> > with FAST
> > without to perform a seed based analysis
> >
> >
> >
> >
> >
> > You can't on either occasion just using preproc-sess.
> > You can create an analysis with those
> components, then
> > run selxavg3-sess with the -svres option.
> This will
> > create a folder called eres with volumes
> that have had
> > all the nuisance variables and low freqeuncies
> > regressed
> > out
> >
> >
> >
> >
> > On 3/14/17 12:32 PM, stdp82@virgilio.it
> <mailto:stdp82@virgilio.it>
> > <mailto:stdp82@virgilio.it <mailto:stdp82@virgilio.it>>
> > wrote:
> >
> >
> >
> > Thanks.
> > 1- By using only preproc-sess, how can I perform
> > "band pass filtering"?
> > 2- And how can I take in account the nuisance
> > variables: the CSF from which the top 5
> principle
> > components, the white matter from which
> the top 5
> > principle components, motion correction
> parameters
> > (-mcextreg), 5th order polynomial. How can I
> > eliminate
> > the first 4 time points?
> > Regards
> > Stefano
> >
> > ----Messaggio originale----
> >
> > Da: "Douglas Greve"
> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> > <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>>
> >
> > Data: 14-mar-2017 16.14
> >
> > A: <freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>>
> >
> > Ogg: Re: [Freesurfer] Whole
> preprocessing with
> > FAST
> > without to perform a seed based analysis
> >
> >
> >
> >
> >
> > just use preproc-sess
> >
> >
> >
> >
> > On 3/14/17 10:45 AM, stdp82@virgilio.it
> <mailto:stdp82@virgilio.it>
> > <mailto:stdp82@virgilio.it <mailto:stdp82@virgilio.it>>
> > wrote:
> >
> >
> >
> >
> > Hi list,
> > in FS-FAST, on rs-fMRI data, is
> possible to
> > run selxavg3-sess without -a option?
> > I would use whole the FS-FAST to
> preprocess
> > my data. I would include the
> mkanalysis-sess
> > step but I would not perform a
> seed-based
> > analysis.
> > Thanks
> > Stefano
> >
> >
> >
> >
> >
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
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> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
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> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > _______________________________________________
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> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
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> >
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> >
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> <http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170406/552e2148/attachment-0001.html>>
> >
> > ------------------------------
> >
> > Message: 25
> > Date: Thu, 6 Apr 2017 17:29:20 -0400
> > From: Douglas N Greve <greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>
> > <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>>
> > Subject: Re: [Freesurfer] R: Re: R: R: Re: R: Re: Whole
> preprocessing
> > with FAST without to perform a seed based analysis
> > To: freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>
> > Message-ID:
> > <46c40ef7-d760-d3da-9a07-c88ab943b1fa@nmr.mgh.harvard.edu
> <mailto:46c40ef7-d760-d3da-9a07-c88ab943b1fa@nmr.mgh.harvard.edu>
> >
> <mailto:46c40ef7-d760-d3da-9a07-c88ab943b1fa@nmr.mgh.harvard.edu
> <mailto:46c40ef7-d760-d3da-9a07-c88ab943b1fa@nmr.mgh.harvard.edu>>>
> > Content-Type: text/plain; charset=windows-1252; format=flowed
> >
> > depends on your analysis but probably so
> >
> >
> > On 04/06/2017 05:26 PM, stdp82@virgilio.it
> <mailto:stdp82@virgilio.it>
> > <mailto:stdp82@virgilio.it <mailto:stdp82@virgilio.it>> wrote:
> > > Thanks.
> > > The file could not be open by fslview.
> > > I presume that it is inflated.
> > > How can I do to transform it?
> > > Stefano
> > >
> > > ----Messaggio originale----
> > > Da: "Douglas Greve" <greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>
> > <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>>
> > > Data: 6-apr-2017 17.56
> > > A: <freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>>
> > > Ogg: Re: [Freesurfer] R: R: Re: R: Re: Whole
> preprocessing with
> > > FAST without to perform a seed based analysis
> > >
> > > It will be in the space that you analyzed it in. If
> you want the
> > > native space, then use -native when running
> preproc-sess and
> > > mkanalysis
> > >
> > >
> > > On 4/6/17 2:34 AM, stdp82@virgilio.it
> <mailto:stdp82@virgilio.it>
> > <mailto:stdp82@virgilio.it <mailto:stdp82@virgilio.it>> wrote:
> > >> Furthermore, the res-001.nii which is produce in produced
> > in the
> > >> res folder in not the same dimension of f.nii.
> > >> I would do the whole FAST preprocessing on f.nii.,
> maintaining
> > >> the same dimension and open it with FSL.
> > >> Thanks
> > >> Stefano
> > >>
> > >> ----Messaggio originale----
> > >> Da: stdp82@virgilio.it
> <mailto:stdp82@virgilio.it> <mailto:stdp82@virgilio.it
> <mailto:stdp82@virgilio.it>>
> > >> Data: 5-apr-2017 23.39
> > >> A: "Freesurfer support
> > list"<freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>>
> > >> Ogg: [Freesurfer] R: Re: R: Re: Whole preprocessing
> > with FAST
> > >> without to perform a seed based analysis
> > >>
> > >> Hi,
> > >>
> > >> as you advise I have run selxavg3-sess with the
> -svres
> > option.
> > >> I found a folder called "res" which contain
> > "res-001.nii". Is
> > >> it the f.nii fully processed?
> > >> Thanks
> > >> Stefano
> > >>
> > >> ----Messaggio originale----
> > >> Da: "Douglas Greve"
> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> > <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>>
> > >> Data: 14-mar-2017 17.38
> > >> A: <freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>>
> > >> Ogg: Re: [Freesurfer] R: Re: Whole
> preprocessing with
> > >> FAST without to perform a seed based analysis
> > >>
> > >> You can't on either occasion just using
> preproc-sess.
> > >> You can create an analysis with those
> components, then
> > >> run selxavg3-sess with the -svres option.
> This will
> > >> create a folder called eres with volumes that
> have had
> > >> all the nuisance variables and low freqeuncies
> > regressed out
> > >>
> > >>
> > >> On 3/14/17 12:32 PM, stdp82@virgilio.it
> <mailto:stdp82@virgilio.it>
> > <mailto:stdp82@virgilio.it <mailto:stdp82@virgilio.it>> wrote:
> > >>> Thanks.
> > >>> 1- By using only preproc-sess, how can I
> perform "band
> > >>> pass filtering"?
> > >>> 2- And how can I take in account the nuisance
> > variables:
> > >>> the CSF from which the top 5 principle
> components, the
> > >>> white matter from which the top 5 principle
> > components,
> > >>> motion correction parameters (-mcextreg),
> 5th order
> > >>> polynomial. How can I eliminate the first 4 time
> > points?
> > >>> Regards
> > >>> Stefano
> > >>>
> > >>> ----Messaggio originale----
> > >>> Da: "Douglas Greve"
> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> > <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>>
> > >>> Data: 14-mar-2017 16.14
> > >>> A: <freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>>
> > >>> Ogg: Re: [Freesurfer] Whole
> preprocessing with
> > FAST
> > >>> without to perform a seed based analysis
> > >>>
> > >>> just use preproc-sess
> > >>>
> > >>>
> > >>> On 3/14/17 10:45 AM, stdp82@virgilio.it
> <mailto:stdp82@virgilio.it>
> > <mailto:stdp82@virgilio.it <mailto:stdp82@virgilio.it>> wrote:
> > >>>> Hi list,
> > >>>> in FS-FAST, on rs-fMRI data, is
> possible to run
> > >>>> selxavg3-sess without -a option?
> > >>>> I would use whole the FS-FAST to
> preprocess my
> > >>>> data. I would include the mkanalysis-sess
> > step but
> > >>>> I would not perform a seed-based analysis.
> > >>>> Thanks
> > >>>> Stefano
> > >>>>
> > >>>>
> > >>>> _______________________________________________
> > >>>> Freesurfer mailing list
> > >>>> Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > >>>>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
> > >>>
> > >>>
> > >>>
> > >>>
> > >>>
> > >>> _______________________________________________
> > >>> Freesurfer mailing list
> > >>> Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > >>>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
> > >>
> > >>
> > >>
> > >>
> > >>
> > >>
> > >>
> > >> _______________________________________________
> > >> Freesurfer mailing list
> > >> Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > >>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
> > >
> > >
> > >
> > >
> > >
> > > _______________________________________________
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > >
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>
> > Phone Number: 617-724-2358 <tel:%28617%29%20724-2358>
> > Fax: 617-726-7422 <tel:%28617%29%20726-7422>
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>
> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> <https://gate.nmr.mgh.harvard.edu/filedrop2>
> > <https://gate.nmr.mgh.harvard.edu/filedrop2
> <https://gate.nmr.mgh.harvard.edu/filedrop2>>
> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>
> > Outgoing:
> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>
> >
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>>
> >
> >
> >
> > ------------------------------
> >
> > Message: 26
> > Date: Thu, 6 Apr 2017 22:01:08 +0000
> > From: "Limachia, Gaurang (NIH/NINDS) [F]"
> > <gaurang.limachia@nih.gov <mailto:gaurang.limachia@nih.gov>
> <mailto:gaurang.limachia@nih.gov <mailto:gaurang.limachia@nih.gov>>>
> > Subject: [Freesurfer] QDEC-Cortical Thickness
> > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>>
> > Message-ID: <64A12700-9AC2-4072-A4AC-675A7621FB45@nih.gov
> <mailto:64A12700-9AC2-4072-A4AC-675A7621FB45@nih.gov>
> > <mailto:64A12700-9AC2-4072-A4AC-675A7621FB45@nih.gov
> <mailto:64A12700-9AC2-4072-A4AC-675A7621FB45@nih.gov>>>
> > Content-Type: text/plain; charset="utf-8"
> >
> > Hello Freesurfer Experts,
> >
> > I want to compare the cortical thickness between the groups
> (HC &
> > Patients), and wanted to know where qdec shows this information.
> > Once the design tab is loaded, I am seeing the question in the
> > analysis results ? does the correlation between thickness
> and Age
> > differ from zero? Do I need to a run the command for GLM in
> > order to see if there is a cortical difference between the two
> > populations? I would greatly appreciate your help.
> >
> > Thanks,
> >
> > Gaurang
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
> > URL:
> >
> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170406/221be21e/attachment-0001.html
> <http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170406/221be21e/attachment-0001.html>
> >
> <http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170406/221be21e/attachment-0001.html
> <http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170406/221be21e/attachment-0001.html>>
> >
> > ------------------------------
> >
> > Message: 27
> > Date: Thu, 06 Apr 2017 22:11:47 +0000
> > From: Linda Zhang <lzhang87@gmail.com
> <mailto:lzhang87@gmail.com> <mailto:lzhang87@gmail.com
> <mailto:lzhang87@gmail.com>>>
> > Subject: Re: [Freesurfer] Custom registration template
> > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>>
> > Message-ID:
> >
> >
> <CABCBU0VuY8Lf_tnQPkFuKUk7P9DvXBo4Nc7E=29NRaZU2aykoQ@mail.gmail.com
> <mailto:29NRaZU2aykoQ@mail.gmail.com>
> > <mailto:29NRaZU2aykoQ@mail.gmail.com
> <mailto:29NRaZU2aykoQ@mail.gmail.com>>>
> > Content-Type: text/plain; charset="utf-8"
> >
> > Hi Douglas,
> >
> > Thanks, good to know! That was the full terminal output
> after I ran
> > mris_preproc, though.
> >
> > Cheers,
> > Linda
> >
> >
> > On Thu, 6 Apr 2017 at 22:07 Douglas N Greve
> > <greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>
> > wrote:
> >
> > > 1. The "..." means to include the other options needed for the
> > command
> > > to run. Looks like you figured it out. Using -f as you have is
> > correct.
> > >
> > > 2. can you send the full terminal output?
> > >
> > >
> > > On 04/06/2017 08:55 AM, Linda Zhang wrote:
> > > > Dear all,
> > > >
> > > > I've been following the instructions for building a custom
> > > > registration template as written here
> > > >
> >
> (http://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates
> <http://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates>
> >
> <http://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates
> <http://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates>>)
> and
> > > > here
> > > > (
> > >
> >
> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-May/018345.html
> <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-May/018345.html>
> >
> <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-May/018345.html
> <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-May/018345.html>>
> > > ).
> > > >
> > > >
> > > > I'm now at the mris_preproc stage and according to the
> > instructions,
> > > > the command should be:
> > > >
> > > > # Get thickness values in the newtemplate space for GLM
> analysis
> > > > mris_preproc --surfreg sphere.reg.newtemplate --s subj1 --s
> > subj2 --s
> > > > subj3 ...
> > > >
> > > > I put my subject list into a text file and replaced --s
> with --f
> > > > [subjlist] but kept everything else the same. I got two
> errors
> > for no
> > > > source hemi specified and no output specified, so I added
> > --hemi lh
> > > > and --out lh.surfreg.newtemplate.thick --meas
> thickness. Am I
> > > > supposed to do this, and will the output file be used
> for anything
> > > > else down the line, i.e., should it be named something more
> > specific?
> > > > I see that the next step is to rerun the
> make_average_subject,
> > but I
> > > > don't see where the output from the mris_preproc step would
> > figure in.
> > > >
> > > > On a (maybe) separate issue, when I finally ran my
> command line:
> > > >
> > > > mris_preproc --surfreg sphere.reg.newtemplate --f subjlist
> > --hemi lh
> > > > --out lh.surfreg.newtemplate.thick --meas thickness
> > > >
> > > > I got the following error:
> > > >
> > > > nsubjects=100
> > > > tmpdir is ./tmp.mris_preproc.25619
> > > > /home/fsuser/data
> > > > set: Variable name must contain alphanumeric characters.
> > > >
> > > > I'm not sure where the problem might be here. I'm running
> > FreeSurfer
> > > > v.5.3 in Virtualbox, and I haven't had any problems
> while running
> > > > recon-all on the subjects previously.
> > > >
> > > > Any insight would be greatly appreciated, thank you!
> > > >
> > > > Cheers,
> > > > Linda
> > > >
> > > >
> > > >
> > > > _______________________________________________
> > > > Freesurfer mailing list
> > > > Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > > >
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
> > >
> > > --
> > > Douglas N. Greve, Ph.D.
> > > MGH-NMR Center
> > > greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>
> > > Phone Number: 617-724-2358 <tel:%28617%29%20724-2358>
> > > Fax: 617-726-7422 <tel:%28617%29%20726-7422>
> > >
> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>
> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> <https://gate.nmr.mgh.harvard.edu/filedrop2>
> > <https://gate.nmr.mgh.harvard.edu/filedrop2
> <https://gate.nmr.mgh.harvard.edu/filedrop2>>
> > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>
> > > Outgoing:
> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>
> >
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>>
> > >
> > > _______________________________________________
> > > Freesurfer mailing list
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> >
> > ------------------------------
> >
> > Message: 28
> > Date: Thu, 6 Apr 2017 17:28:21 -0500
> > From: "Gullickson, James" <jgullickson02@hamline.edu
> <mailto:jgullickson02@hamline.edu>
> > <mailto:jgullickson02@hamline.edu
> <mailto:jgullickson02@hamline.edu>>>
> > Subject: Re: [Freesurfer] Ventricle-to-Brain Ratio
> > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>>
> > Message-ID:
> >
> >
> <CAELhUFOrKPp7WrhDF0LhtXTkC2F2V+AyfoKvB58XZ3teMwXsVQ@mail.gmail.com
> <mailto:CAELhUFOrKPp7WrhDF0LhtXTkC2F2V%2BAyfoKvB58XZ3teMwXsVQ@mail.gmail.com>
> >
> <mailto:CAELhUFOrKPp7WrhDF0LhtXTkC2F2V%2BAyfoKvB58XZ3teMwXsVQ@mail.gmail.com
> <mailto:CAELhUFOrKPp7WrhDF0LhtXTkC2F2V%252BAyfoKvB58XZ3teMwXsVQ@mail.gmail.com>>>
> > Content-Type: text/plain; charset="utf-8"
> >
> > Doug,
> >
> > Thanks for your reply.
> >
> > Difference between the two TVV methods ranges between 1-6%
> > Difference between the two TBV methods ranges between 2-4%
> >
> > Basically, my question is two-fold:
> >
> > a) what is the most accurate representation of total ventricular
> > volume
> > b) what is the most accurate representation of total brain
> volume (all
> > parenchyma)
> >
> > Best,
> >
> > James
> >
> > On Thu, Apr 6, 2017 at 3:17 PM, Douglas N Greve
> > <greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>
> > wrote:
> >
> > > that looks right. how different are the values?
> > >
> > >
> > > On 04/05/2017 10:58 AM, Gullickson, James wrote:
> > > > Hello all,
> > > >
> > > > I want to calculate a Ventricle-to-Brain ratio (VBR) as a
> > measure of
> > > > parenchymal atrophy using Freesurfer version 5.3.0. I have
> > tried to go
> > > > about this using the aseg.stats output (using
> > asegstats2table), but am
> > > > running into inconsistencies.
> > > >
> > > > The basic calculation for VBR is:
> > > >
> > > > (Total Ventricular Volume/Total Brain Volume) * 100
> > > >
> > > > i.e. Bigler, E. D. (2013). Traumatic brain injury,
> > neuroimaging, and
> > > > neurodegeneration. /Frontiers in human neuroscience/,
> /7/, 395.
> > > >
> > > >
> > > > What is the best way to get Total Ventricular Volume
> (TVV) and
> > Total
> > > > Brain Volume (TBV) for this calculation? I have tried
> several
> > ways,
> > > > which lead to different values:
> > > >
> > > > TVV = left lateral ventricle + left inf lateral
> ventricle + right
> > > > lateral ventricle + right inf lateral ventricle + 3rd
> > ventricle + 4th
> > > > ventricle + 5th ventricle + choroid plexus
> > > >
> > > > which gives me a different result than
> > > >
> > > > TVV = BrainSegVol - BrainSegVolNotVent
> > > >
> > > >
> > > > and for TBV
> > > >
> > > > TBV = TotalGrayVol + CorticalWhiteMatterVol
> > > >
> > > > which differs from
> > > >
> > > > TBV = BrainSegVolNotVent
> > > >
> > > >
> > > > Thank you for your help,
> > > >
> > > > James Gullickson
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > _______________________________________________
> > > > Freesurfer mailing list
> > > > Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > > >
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
> > >
> > > --
> > > Douglas N. Greve, Ph.D.
> > > MGH-NMR Center
> > > greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>
> > > Phone Number: 617-724-2358 <tel:%28617%29%20724-2358>
> > > Fax: 617-726-7422 <tel:%28617%29%20726-7422>
> > >
> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>
> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> <https://gate.nmr.mgh.harvard.edu/filedrop2>
> > <https://gate.nmr.mgh.harvard.edu/filedrop2
> <https://gate.nmr.mgh.harvard.edu/filedrop2>>
> > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>
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> > >
> > > _______________________________________________
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> > >
> > >
> > > The information in this e-mail is intended only for the person
> > to whom it
> > > is
> > > addressed. If you believe this e-mail was sent to you in error
> > and the
> > > e-mail
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> >
> > ------------------------------
> >
> > Message: 29
> > Date: Thu, 6 Apr 2017 23:28:02 +0000
> > From: Ilaria Sani <isani01@mail.rockefeller.edu
> <mailto:isani01@mail.rockefeller.edu>
> > <mailto:isani01@mail.rockefeller.edu
> <mailto:isani01@mail.rockefeller.edu>>>
> > Subject: Re: [Freesurfer] MRIread (load_nifti)- Out of memory
> > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>>
> > Message-ID:
> > <cdf628175a004b51adf2bc86f4a0cc5a@RUMBX12.rockefeller.edu
> <mailto:cdf628175a004b51adf2bc86f4a0cc5a@RUMBX12.rockefeller.edu>
> >
> <mailto:cdf628175a004b51adf2bc86f4a0cc5a@RUMBX12.rockefeller.edu
> <mailto:cdf628175a004b51adf2bc86f4a0cc5a@RUMBX12.rockefeller.edu>>>
> > Content-Type: text/plain; charset="iso-8859-7"
> >
> > Hi Doug,
> >
> > Thanks for the tip. I can load the volume now!
> >
> > I'm getting different types of errors when I proceed with my
> > analyses though.
> >
> > Can you help me to understand why it works when data are
> > decompressed and in what way data are different now.
> >
> >
> > Thanks a lot,
> > Ilaria
> >
> > -----Original Message-----
> > From: freesurfer-bounces@nmr.mgh.harvard.edu
> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>
> > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu
> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>>
> > [mailto:freesurfer-bounces@nmr.mgh.harvard.edu
> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>
> > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu
> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>>] On Behalf Of
> > Douglas N Greve
> > Sent: Thursday, April 6, 2017 3:43 PM
> > To: freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>
> > Subject: Re: [Freesurfer] MRIread (load_nifti)- Out of memory
> >
> > is it a compressed nifti (nii.gz)? If so, try uncompressing
> it first
> >
> >
> > On 04/06/2017 02:53 PM, Ilaria Sani wrote:
> > > Hi Bruce,
> > >
> > > Not sure this answer your question...
> > >
> > > In matlab workspace, I am able to load data in two halves:
> > >
> > > H1=MRIread(half1)
> > > H2=MRIread(half2)
> > >
> > > And then concatenate the volumes
> > > concatenate them var=cat(4,H1,H2).
> > >
> > > So, somehow matlab can handle...
> > >
> > > However, when those operations are embedded inside a function
> > (like in the case of load_nifti and MRIread) I get the error.
> > >
> > >
> > > Thanks,
> > > Ilaria
> > >
> > >
> > > -----Original Message-----
> > > From: freesurfer-bounces@nmr.mgh.harvard.edu
> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>
> > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu
> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>>
> > > [mailto:freesurfer-bounces@nmr.mgh.harvard.edu
> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>
> > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu
> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>>] On Behalf Of Bruce
> > > Fischl
> > > Sent: Thursday, April 6, 2017 1:36 PM
> > > To: Freesurfer support list
> <freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>>
> > > Subject: Re: [Freesurfer] MRIread (load_nifti)- Out of memory
> > >
> > > Hi Ilaria
> > >
> > > do you have any reason to believe that it isn't just out of
> > memory? If
> > > so, there's not much to do other than get more RAM or use a
> > different
> > > machine
> > >
> > > cheers
> > > Bruce
> > >
> > >
> > > On Thu,
> > > 6 Apr 2017, Ilaria Sani wrote:
> > >
> > >> Dear All,
> > >>
> > >>
> > >>
> > >> I?m trying to load a pretty big diffusion MRI dataset
> > (320x320x260x122).
> > >>
> > >> I?m running matlab 2015a 64bit on a linux machine.
> > >>
> > >>
> > >>
> > >> I?m using MRIread, which in turn calls load_nifti.
> > >>
> > >> I?m getting the following error:
> > >>
> > >>
> > >>
> > >> Error using +
> > >>
> > >> Out of memory. Type HELP MEMORY for your options.
> > >>
> > >>
> > >>
> > >> Error in load_nifti (line 158)
> > >>
> > >> hdr.vol = hdr.vol * hdr.scl_slope + hdr.scl_inter;
> > >>
> > >>
> > >>
> > >> Error in MRIread (line 158)
> > >>
> > >> hdr = load_nifti(fspec,headeronly);
> > >>
> > >>
> > >>
> > >> When I load half dataset (320x320x260x61) it works ok.
> > >>
> > >> I tried to increase the Maximum array size in Matalb (default
> > 1,000 - now 10,000), but I?m still getting the error.
> > >>
> > >> I tried to change machine (which runs matlab 2013a on linux)
> > and it worked fine.
> > >>
> > >>
> > >>
> > >> I think this is due to some matlab settings.
> > >>
> > >> Can anyone help?
> > >>
> > >>
> > >>
> > >> Thanks a lot,
> > >>
> > >> Ilaria
> > >>
> > >>
> > >>
> > >>
> > >>
> > >> -------------------------------------------
> > >> Ilaria Sani, PhD
> > >> Postdoctoral Fellow, Freiwald Lab
> > >> The Rockefeller University
> > >> 1230 York Ave., New York, NY 10065.
> > >> Phone: (212) 327 7699 <tel:%28212%29%20327-7699>
> > >> Fax: (212) 327 7698 <tel:%28212%29%20327-7698>
> > >> Email: isani01@rockefeller.edu
> <mailto:isani01@rockefeller.edu> <mailto:isani01@rockefeller.edu
> <mailto:isani01@rockefeller.edu>>
> > >>
> > >>
> > >>
> > >>
> > >>
> > > _______________________________________________
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > >
> >
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> >
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> > >
> > >
> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>
> > Phone Number: 617-724-2358 <tel:%28617%29%20724-2358>
> > Fax: 617-726-7422 <tel:%28617%29%20726-7422>
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
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> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>
> > FileDrop:
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> >
> > ------------------------------
> >
> > Message: 30
> > Date: Fri, 7 Apr 2017 00:44:29 +0000
> > From: Chris Adamson <chris.adamson@mcri.edu.au
> <mailto:chris.adamson@mcri.edu.au>
> > <mailto:chris.adamson@mcri.edu.au
> <mailto:chris.adamson@mcri.edu.au>>>
> > Subject: Re: [Freesurfer] long mri_ca_register error
> > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>>
> > Message-ID:
> >
> >
> <43A4603348D2AC409B1B958EFE5C8B94029B028E3C@MITSMXMBX02V.mcri.edu.au
> <mailto:43A4603348D2AC409B1B958EFE5C8B94029B028E3C@MITSMXMBX02V.mcri.edu.au>
> >
> <mailto:43A4603348D2AC409B1B958EFE5C8B94029B028E3C@MITSMXMBX02V.mcri.edu.au
> <mailto:43A4603348D2AC409B1B958EFE5C8B94029B028E3C@MITSMXMBX02V.mcri.edu.au>>>
> > Content-Type: text/plain; charset="iso-8859-7"
> >
> > Just the standard pipeline.
> >
> > recon-all -s cross1 -all -bigventricles
> > recon-all -base cross -tp cross1 ... -all -bigventricles
> > recon-all -long cross1 cross -all -bigventricles
> >
> > -----Original Message-----
> > From: freesurfer-bounces@nmr.mgh.harvard.edu
> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>
> > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu
> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>>
> > [mailto:freesurfer-bounces@nmr.mgh.harvard.edu
> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>
> > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu
> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>>] On Behalf Of
> > Bruce Fischl
> > Sent: Friday, 7 April 2017 3:37 AM
> > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>>
> > Subject: Re: [Freesurfer] long mri_ca_register error
> >
> > Hi Chris
> >
> > it's possible we never looked at -bigventricle in the long
> stage.
> > What was your recon-all command line?
> >
> > cheers
> > Bruce
> > On Thu, 6 Apr 2017, Chris Adamson wrote:
> >
> > >
> > > It happens when I use -bigventricles.
> > >
> > > ?
> > >
> > > From: freesurfer-bounces@nmr.mgh.harvard.edu
> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>
> > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu
> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>>
> > > [mailto:freesurfer-bounces@nmr.mgh.harvard.edu
> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>
> > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu
> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>>] On Behalf Of Chris
> > > Adamson
> > > Sent: Thursday, 6 April 2017 12:27 PM
> > > To: freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>
> > > Subject: [Freesurfer] long mri_ca_register error
> > >
> > > ?
> > >
> > > Freesurfer devs,
> > >
> > > ?
> > >
> > > In freesurfer 6 stable I?m having a problem at the careg stage
> > of the
> > > long. The relevant recon-all log is pasted below. Could you
> > point me to where to debug this problem?
> > >
> > > ?
> > >
> > > Cheers,
> > >
> > > ?
> > >
> > > Chris.
> > >
> > > ?
> > >
> > > mri_ca_register -rusage
> > >
> 136_S_0426_20070604.long.136_S_0426/touch/rusage.mri_ca_register.dat
> > > -bigventricles -smoothness 0.5 -levels 2 -A 1 -l
> > > *base*/transforms/talairach.m3z identity.nofile
> -align-after -mask
> > > brainmask.mgz norm.mgz
> > >
> /usr/local/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca
> > > transforms/talairach.m3z
> > >
> > > ?
> > >
> > > handling expanded ventricles...
> > >
> > > l_smoothness = 0.50
> > >
> > > levels = 2
> > >
> > > smoothing gradient with 1 averages...
> > >
> > > reading previously computed atlas xform
> > >
> >
> /isilon/data/addo/ADNI3T/freesurfer6/136_S_0426/mri/transforms/talaira
> > > ch.m3z and applying inverse registration identity.nofile
> > >
> > > renormalizing sequences with structure alignment,
> equivalent to:
> > >
> > > ??? -renormalize
> > >
> > > ??? -regularize_mean 0.500
> > >
> > > ??? -regularize 0.500
> > >
> > > using MR volume brainmask.mgz to mask input volume...
> > >
> > > ?
> > >
> > > == Number of threads available to mri_ca_register for
> OpenMP = 2 ==
> > >
> > > reading 1 input volumes...
> > >
> > > logging results to talairach.log
> > >
> > > reading input volume 'norm.mgz'...
> > >
> > > reading GCA
> >
> '/usr/local/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca'...
> > >
> > > label assignment complete, 0 changed (0.00%)
> > >
> > > TransformSample: gcam has not been inverted!
> > >
> > > freeing gibbs priors...done.
> > >
> > > average std[0] = 5.0
> > >
> > > setting orig areas to linear transform determinant scaled 8.40
> > >
> > > writing talairach.invalid.mgz
> > >
> > > writing talairach.status.mgz
> > >
> > > registering ventricular system...
> > >
> > > using threshold 45.0 from atlas ventricle (20.1 +- 5.0)
> and caudate
> > > (70.0 +- 5.0) distributions for initial ventricular estimate
> > >
> > > No such file or directory
> > >
> > > TransformSample: gcam has not been inverted!
> > >
> > > No such file or directory
> > >
> > > TransformSample: gcam has not been inverted!
> > >
> > > No such file or directory
> > >
> > > TransformSample: gcam has not been inverted!
> > >
> > > No such file or directory
> > >
> > > TransformSample: gcam has not been inverted!
> > >
> > > No such file or directory
> > >
> > > TransformSample: gcam has not been inverted!
> > >
> > > No such file or directory
> > >
> > > TransformSample: gcam has not been inverted!
> > >
> > > No such file or directory
> > >
> > > TransformSample: gcam has not been inverted!
> > >
> > > No such file or directory
> > >
> > > TransformSample: gcam has not been inverted!
> > >
> > > No such file or directory
> > >
> > > TransformSample: gcam has not been inverted!
> > >
> > > No such file or directory
> > >
> > > TransformSample: gcam has not been inverted!
> > >
> > > No such file or directory
> > >
> > > TransformSample: gcam has not been inverted!
> > >
> > > No such file or directory
> > >
> > > ?
> > >
> > > Dr Chris Adamson
> > >
> > > Senior Research Officer
> > >
> > > Developmental Imaging, Clinical Sciences
> > >
> > > ?
> > >
> > > Murdoch Childrens Research Institute
> > >
> > > The Royal Children?s Hospital
> > >
> > > Flemington Road, Parkville, VIC 3052 Australia
> > >
> > > E?chris.adamson@mcri.edu.au
> <mailto:chris.adamson@mcri.edu.au>
> <mailto:chris.adamson@mcri.edu.au <mailto:chris.adamson@mcri.edu.au>>
> > >
> > > www.mcri.edu.au <http://www.mcri.edu.au>
> <http://www.mcri.edu.au>
> > >
> > > ?
> > >
> > > ?
> > >
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> >
> > ------------------------------
> >
> > Message: 31
> > Date: Fri, 7 Apr 2017 10:23:03 +0530
> > From: Dilip Puri <dilippuripuri@gmail.com
> <mailto:dilippuripuri@gmail.com>
> > <mailto:dilippuripuri@gmail.com
> <mailto:dilippuripuri@gmail.com>>>
> > Subject: Re: [Freesurfer] help
> > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>>
> > Message-ID:
> >
> >
> <CAHLUP+B3v_roRUCZjA+OJM+4krJNfVQO3HcVXgq9bY-R0Mq_zg@mail.gmail.com
> <mailto:CAHLUP%2BB3v_roRUCZjA%2BOJM%2B4krJNfVQO3HcVXgq9bY-R0Mq_zg@mail.gmail.com>
> >
> <mailto:CAHLUP%2BB3v_roRUCZjA%2BOJM%2B4krJNfVQO3HcVXgq9bY-R0Mq_zg@mail.gmail.com
> <mailto:CAHLUP%252BB3v_roRUCZjA%252BOJM%252B4krJNfVQO3HcVXgq9bY-R0Mq_zg@mail.gmail.com>>>
> > Content-Type: text/plain; charset="utf-8"
> >
> > Hi everyone,
> >
> > when I used following command:
> >
> > mri_binarize --i myfile.img --match 17 --binval -1 --o
> > your.lefthippo.nii.gz
> >
> > then I got output your.lefthippo.nii.gz file when I read
> this file
> > using
> > FREEVIEW then it completly different from original mask.
> >
> >
> >
> > Thanks
> >
> > Dilip?
> >
> > On Thu, Apr 6, 2017 at 11:08 PM, Bruce Fischl
> > <fischl@nmr.mgh.harvard.edu
> <mailto:fischl@nmr.mgh.harvard.edu>
> <mailto:fischl@nmr.mgh.harvard.edu
> <mailto:fischl@nmr.mgh.harvard.edu>>>
> > wrote:
> >
> > > Hi Dilip
> > >
> > > yes, freesurfer will do this for you, although the labels will
> > be 17 for
> > > left hippocampus and 53 for right.
> > >
> > > cheers
> > > Bruce
> > > On Thu, 6 Apr 2017, Dilip Puri wrote:
> > >
> > > > Hi everyone,
> > > >
> > > > I am working on Hippocampus segmentation using Neural
> Networks
> > for that
> > > I need labeled images of Hippocampus corresponding to original
> > images.
> > > >
> > > > I am using OASIS Dataset for this. I want to generate
> labeled
> > images
> > > using FREESURFER. Is there any way to label each 3D
> co-ordinate
> > > > HippoCampus -1
> > > > Otherwise - 0
> > > >
> > > > Here are sample files link
> > > >
> > > > Kindly help me!
> > > >
> > > >
> > > > Dilip Puri
> > > > IIIT Vadodara
> > > >
> > > >
> > > _______________________________________________
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
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> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > >
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> > >
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> >
> <http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170407/69d56ed1/attachment-0001.png
> <http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170407/69d56ed1/attachment-0001.png>>
> >
> > ------------------------------
> >
> > Message: 32
> > Date: Fri, 7 Apr 2017 09:52:53 +0100
> > From: Shane S <shane.schofield@yahoo.com
> <mailto:shane.schofield@yahoo.com>
> > <mailto:shane.schofield@yahoo.com
> <mailto:shane.schofield@yahoo.com>>>
> > Subject: [Freesurfer] How to segment subnuclei of thalamus?
> > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>>
> > Message-ID: <etPan.58e75365.225461f5.17c60@yahoo.com
> <mailto:etPan.58e75365.225461f5.17c60@yahoo.com>
> > <mailto:etPan.58e75365.225461f5.17c60@yahoo.com
> <mailto:etPan.58e75365.225461f5.17c60@yahoo.com>>>
> > Content-Type: text/plain; charset="utf-8"
> >
> > Hello Experts,
> >
> > I am interested to do a segmentation of the thalamus subnuclei
> > based on T1 data. Is there any atlas that I could use for this??
> >
> > Best Wishes,
> > S
> >
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
> > URL:
> >
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> >
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> <http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170407/03cd331f/attachment-0001.html>>
> >
> > ------------------------------
> >
> > Message: 33
> > Date: Fri, 07 Apr 2017 18:41:48 +0900
> > From: kjunji@med.kanazawa-u.ac.jp
> <mailto:kjunji@med.kanazawa-u.ac.jp>
> <mailto:kjunji@med.kanazawa-u.ac.jp
> <mailto:kjunji@med.kanazawa-u.ac.jp>>
> > Subject: [Freesurfer] withdrawing from the mailing list.
> > To: Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > Message-ID:
> <3a1b2370509f7f0adb8d1b5ff38a7154@med.kanazawa-u.ac.jp
> <mailto:3a1b2370509f7f0adb8d1b5ff38a7154@med.kanazawa-u.ac.jp>
> >
> <mailto:3a1b2370509f7f0adb8d1b5ff38a7154@med.kanazawa-u.ac.jp
> <mailto:3a1b2370509f7f0adb8d1b5ff38a7154@med.kanazawa-u.ac.jp>>>
> > Content-Type: text/plain; charset=US-ASCII; format=flowed
> >
> > Dear Secretariat of Freesurfer mailing list
> >
> > I want to stop receiving emails from the Freesurfer mailing
> list.
> > Please teach me to withdraw from the mailing list.
> >
> > Sincerely yours.
> >
> > Junji Komatsu in Kanazawa university hospital.
> >
> >
> >
> >
> > ------------------------------
> >
> > Message: 34
> > Date: Fri, 7 Apr 2017 12:48:36 +0200
> > From: Yong Li <yongli86@gmail.com
> <mailto:yongli86@gmail.com> <mailto:yongli86@gmail.com
> <mailto:yongli86@gmail.com>>>
> > Subject: Re: [Freesurfer] QA Tools v1.2 and future release
> > To: freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>
> > Message-ID:
> >
> >
> <CAKmw9f=zG4G-DDuRpuochiyn91w9YAx8e1L-r5+=_a9heyTUmQ@mail.gmail.com
> <mailto:a9heyTUmQ@mail.gmail.com>
> > <mailto:a9heyTUmQ@mail.gmail.com
> <mailto:a9heyTUmQ@mail.gmail.com>>>
> > Content-Type: text/plain; charset="utf-8"
> >
> > Dear Freesurfer Experts,
> >
> > Please excuse my long email yesterday.
> >
> > Now, I finished code update of the outlier detection part for
> > brainstem
> > substructures (bs) and Hippocampal Subfields (hc) modules. Code
> > updated in
> > the similar way as my last email except that I combined the
> output
> > of both
> > modules to simplify the process. The following log files might
> > show some
> > clue of my exploration:
> >
> > YongbshcLUT (like asegLUT_112511):
> >
> > Medulla 0.287988 +/- 0.0304379
> > Pons 0.864817 +/- 0.128019
> > SCP 0.0161611 +/- 0.0030778
> > Midbrain 0.388938 +/- 0.038842
> > Whole_brainstem 1.8246 +/- 0.184472
> > Left-Hippocampal_tail 0.0291617 +/- 0.00437039
> > Left-subiculum 0.0237801 +/- 0.0044348
> > Left-CA1 0.0387709 +/- 0.00612168
> > Left-hippocampal-fissure 0.00944849 +/- 0.00188347
> > Left-presubiculum 0.0177329 +/- 0.00272706
> > Left-parasubiculum 0.00372024 +/- 0.000876862
> > Left-molecular_layer_HP 0.0320802 +/- 0.00806223
> > Left-GC-ML-DG 0.0186971 +/- 0.00308382
> > Left-CA3 0.0120106 +/- 0.00198279
> > Left-CA4 0.0132618 +/- 0.00261687
> > Left-fimbria 0.00371701 +/- 0.00166146
> > Left-HATA 0.0031189 +/- 0.000692806
> > Left-Whole_hippocampus 0.190022 +/- 0.0246413
> > Right-Hippocampal_tail 0.030817 +/- 0.00496078
> > Right-subiculum 0.0248689 +/- 0.00427691
> > Right-CA1 0.0370719 +/- 0.00873442
> > Right-hippocampal-fissure 0.0103329 +/- 0.00187117
> > Right-presubiculum 0.0178487 +/- 0.00260947
> > Right-parasubiculum 0.00380418 +/- 0.000861778
> > Right-molecular_layer_HP 0.032938 +/- 0.00448073
> > Right-GC-ML-DG 0.0168729 +/- 0.00304788
> > Right-CA3 0.0130893 +/- 0.00239818
> > Right-CA4 0.0143492 +/- 0.00281808
> > Right-fimbria 0.00438099 +/- 0.00176098
> > Right-HATA 0.00338842 +/- 0.0006037
> > Right-Whole_hippocampus 0.198797 +/- 0.0243668
> >
> > an example subject's bshc.stats (like aseg.stats):
> >
> > Medulla 4288.386728
> > Pons 12836.783824
> > SCP 194.446727
> > Midbrain 8306.988464
> > Whole_brainstem 22293.878740
> > Left-Hippocampal_tail 462.086606
> > Left-subiculum 307.970217
> > Left-CA1 816.878818
> > Left-hippocampal-fissure 118.986208
> > Left-presubiculum 227.392060
> > Left-parasubiculum 84.381831
> > Left-molecular_layer_HP 841.496111
> > Left-GC-ML-DG 238.308049
> > Left-CA3 183.383724
> > Left-CA4 196.098618
> > Left-fimbria 73.990998
> > Left-HATA 36.237082
> > Left-Whole_hippocampus 2838.187477
> > Right-Hippocampal_tail 408.832729
> > Right-subiculum 388.667888
> > Right-CA1 801.601831
> > Right-hippocampal-fissure 132.071091
> > Right-presubiculum 242.179137
> > Right-parasubiculum 43.414171
> > Right-molecular_layer_HP 487.298072
> > Right-GC-ML-DG 246.283617
> > Right-CA3 164.849646
> > Right-CA4 209.108368
> > Right-fimbria 90.291400
> > Right-HATA 42.073898
> > Right-Whole_hippocampus 2791.300419
> >
> > icv.txt (actually eITV instead of ICV):
> >
> > 1420463.178113
> >
> > bshc_outliers.log:
> >
> > Subject 008 Right-HATA value .002080900 is an outlier ...
> >
> > Note: all data here are kind of simulation results because
> of data
> > safety
> > reason and these logs only serve as signs of correct code
> update.
> >
> > I guess that both the only output of bs and hc (bshc.stats)
> is segment
> > volume, not the 'normMean normStdDev ...' in aseg.stats.
> > So is it senseful to include those 'norm*' measures in the
> bs & hc
> > modules
> > in the future?
> > BTW, is there an advantage to use normMax / eITV rather than
> > normMean /
> > eITV in outlier detection in theory?
> >
> > Thank you very much again!
> >
> > I wish all of you a nice weekend!
> >
> > Best regards,
> >
> > Yong
> > _________________________
> > Yong Li, PhD
> > Department of Neurology,
> > Klinikum rechts der Isar,
> > Technische Universit?t M?nchen,
> > Munich, Germany
> >
> > On Thu, Apr 6, 2017 at 11:36 AM, Yong Li <yongli86@gmail.com
> <mailto:yongli86@gmail.com>
> > <mailto:yongli86@gmail.com <mailto:yongli86@gmail.com>>> wrote:
> >
> > > Dear Freesurfer Experts,
> > >
> > > As one of the new freesurfers, I really appreciate the
> excellent
> > work of
> > > authors as well as great support of users' forum.
> > >
> > > A good guess of mine is that authors, e.g., Vasanth or Louis
> > etc., are
> > > busy updating QA tools after the FSv6 release since the QA
> Tools
> > v1.2 was
> > > written for FSv5.3. If so, is it possible to provide an
> > estimated release
> > > date please so as to adjust my plan? Thanks for understanding!
> > >
> > > In case, it might take a while to release the next QA
> Tool, may
> > I dare to
> > > provide my attempts of code updating of some functions in QA
> > Tools? The
> > > following are the brief list of code adapting steps:
> > > 1. modified codes for generating file order list in
> recon_checker;
> > > 2. modified codes for matching segment names for instance from
> > > DefaultAsegMeans.txt in gparcmean_from_table;
> > > 3. adapted default_FOF and default_status_log for FSv6.
> > >
> > > After these adaptation, QA Tools ran through and I only
> > encountered some
> > > 'syntax error' in terminal for 2 segments, 5th-Ventricle and
> > > WM-hypointensities, that I have to ask the experts to guide me
> > through this
> > > point if it's of your interests. To ensure the QA Tools
> > functioning well, I
> > > tested 116 elderly patients and detected reasonable
> outliers per
> > patient.
> > > Therefore, I would like to double that my code updating
> based on
> > my general
> > > understanding of QA Tool still fit to the basic purpose of
> > authors by
> > > asking the following theoretical questions:
> > >
> > > 1. SNR and segments outliers detection are measures of quality
> > assessment
> > > in QA Tools. Have other factors such as subject's motion,
> image
> > bias,
> > > resolution etc. been considered in QA Tools or future release?
> > The default
> > > SNR threshold is 16 based on any reference? The max SNR of my
> > patients so
> > > far is 32. Any idea of scores of healthy elderly controls?
> > >
> > > 2. The QA Tools v1.2 analyzes aseg.stats output. Is it
> possible
> > to include
> > > output of brainstem substructures and HippocampalSubfields of
> > FSv6? If yes,
> > > I would like to adapt the codes and provide you some
> feedback if
> > you think
> > > that I can help bit.
> > >
> > > 3. Future directions mentioned in QA Tools wiki site are
> > interesting and
> > > thoughtful. Are other features like 'Detect outliers in aparc
> > and aparc2009
> > > volumes' on the way?
> > >
> > > 4. Is there a function to summarize all QA measures to csv
> > files, like the
> > > quantifyBrainstemStructures.sh in brainstem substructures?
> > >
> > > Thank you in advance!
> > >
> > > Kind regards,
> > >
> > > Yong Li, PhD
> > > _________________________
> > > Department of Neurology,
> > > Klinikum rechts der Isar,
> > > Technische Universit?t M?nchen,
> > > Munich, Germany
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
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> >
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> <http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170407/1fc2312c/attachment-0001.html>
> >
> <http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170407/1fc2312c/attachment-0001.html
> <http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170407/1fc2312c/attachment-0001.html>>
> >
> > ------------------------------
> >
> > Message: 35
> > Date: Fri, 7 Apr 2017 11:17:20 +0000
> > From: Nina Jacobsen <njacob12@student.aau.dk
> <mailto:njacob12@student.aau.dk>
> > <mailto:njacob12@student.aau.dk
> <mailto:njacob12@student.aau.dk>>>
> > Subject: [Freesurfer] Hippocampal subfield segmentation,
> file content
> > To: "freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>"
> > <freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>>
> > Message-ID:
> >
> >
> <C81DC33B38A91045AE898B7F15429E970125EC8B5B@AD-EXCHMBX4-1.aau.dk
> <mailto:C81DC33B38A91045AE898B7F15429E970125EC8B5B@AD-EXCHMBX4-1.aau.dk>
> >
> <mailto:C81DC33B38A91045AE898B7F15429E970125EC8B5B@AD-EXCHMBX4-1.aau.dk
> <mailto:C81DC33B38A91045AE898B7F15429E970125EC8B5B@AD-EXCHMBX4-1.aau.dk>>>
> > Content-Type: text/plain; charset="iso-8859-1"
> >
> > Hi All,
> >
> > I have made a hippocampal subfield segmentation using FreeSurfer
> > version 6.0 with multispectral segmentation settings, and have
> > both labels for the right and left hippocampus. The
> segmentations
> > look very nice when viewed with freeview, so all good.
> >
> > Now, my problem is the file content. I would like a segmentation
> > file, which labels all subfields with a single value (all voxels
> > in CA1 would for example be with value 1, all voxels in CA2
> would
> > be with value 2 and so on). Does anyone know how i can gain this
> > file? Is it in some way possible to convert the label files
> > (lh.hippoSfLabel.v10.mgz) into such a "simple" segmentation
> file?
> > Currently, the content of the label files
> > (lh.hippoSfLabel.v10.mgz) is values in the range 0-226, which I
> > guess origin from the RGB encoding - I opened the file with
> matlab.
> >
> > Hope my question is clear.
> >
> > Thanks,
> > Nina Jacobsen.
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
> > URL:
> >
> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170407/62c48bf9/attachment-0001.html
> <http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170407/62c48bf9/attachment-0001.html>
> >
> <http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170407/62c48bf9/attachment-0001.html
> <http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170407/62c48bf9/attachment-0001.html>>
> >
> > ------------------------------
> >
> > Message: 36
> > Date: Fri, 7 Apr 2017 11:29:14 +0000 (UTC)
> > From: teodora petrova <teddi_petrova@yahoo.com
> <mailto:teddi_petrova@yahoo.com>
> > <mailto:teddi_petrova@yahoo.com
> <mailto:teddi_petrova@yahoo.com>>>
> > Subject: Re: [Freesurfer] Multiple Comparisons Correction
> thresh error
> > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>>
> > Message-ID: <1890557955.1725598.1491564554325@mail.yahoo.com
> <mailto:1890557955.1725598.1491564554325@mail.yahoo.com>
> > <mailto:1890557955.1725598.1491564554325@mail.yahoo.com
> <mailto:1890557955.1725598.1491564554325@mail.yahoo.com>>>
> > Content-Type: text/plain; charset="utf-8"
> >
> > Hi,
> > We managed to avoid getting the error by typing the following in
> > the terminal before the command:
> > export LC_NUMERIC="en_US.UTF-8"
> > Best,Teodora
> > On Thursday, April 6, 2017, 5:59:05 PM GMT+2, Douglas Greve
> > <greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>> wrote:
> > I think this is a "language" problem in that it is
> converting the
> > "1.3" into "1,3" and then getting confused. I'm not sure how to
> > fix it, but I think it has to do with the LOCAL setting.
> >
> >
> > On 4/6/17 5:07 AM, teodora petrova wrote:
> >
> > Hello,
> > I would like to correct my glm_fit results for multiple
> > comparisons.? I am using the following commands, similar to the
> > one in the group analysis tutorial:
> > mri_glmfit-sim? --glmdir lh.index.glmdir? --cache 1.3 abs?
> --cwp
> > 0.05? --2spaces mri_glmfit-sim? --glmdir lh.index.glmdir?
> --cache
> > 2.0 pos? --cwp 0.05? --2spaces
> > And receive the following errors:
> > ERROR:thresh=1,3, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0
> > ERROR:thresh=2,0, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0
> > I am sure I am typing a point, but it is read as a comma. Any
> > ideas why?
> > Freesurfer version:
> > freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
> > Platform: Ubuntu MATE 16.04 Thank you very much!
> > Regards, Teodora
> >
> >
> >
> >
> >
> >
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <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>
> > <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.
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
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> >
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> <http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170407/5fe3d2e2/attachment-0001.html>
> >
> <http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170407/5fe3d2e2/attachment-0001.html
> <http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170407/5fe3d2e2/attachment-0001.html>>
> >
> > ------------------------------
> >
> > Message: 37
> > Date: Fri, 7 Apr 2017 12:34:37 +0100
> > From: Arman Eshaghi <arman.eshaghi@gmail.com
> <mailto:arman.eshaghi@gmail.com>
> > <mailto:arman.eshaghi@gmail.com
> <mailto:arman.eshaghi@gmail.com>>>
> > Subject: [Freesurfer] Longitudinal Pipeline
> > To: Freesurfer support list <Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>>
> > Message-ID:
> >
> >
> <CAKy1A=HxDhEY92goc3-UsLGABx9k0=AY4hCV_2+QsQV3goXCGA@mail.gmail.com
> <mailto:AY4hCV_2%2BQsQV3goXCGA@mail.gmail.com>
> > <mailto:AY4hCV_2%2BQsQV3goXCGA@mail.gmail.com
> <mailto:AY4hCV_2%252BQsQV3goXCGA@mail.gmail.com>>>
> > Content-Type: text/plain; charset="utf-8"
> >
> > Hi,
> >
> > I wonder if there is a way for mri_robust_template to perform
> > iterative
> > registration with 9 DOF rather than 6-7 default. The rational is
> > to allow
> > for a bit of scaling to adjust for potential scanner drifts in a
> > longitudinal study over years.
> >
> > Thanks,
> > Arman
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
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> >
> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170407/ae625622/attachment-0001.html
> <http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170407/ae625622/attachment-0001.html>
> >
> <http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170407/ae625622/attachment-0001.html
> <http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170407/ae625622/attachment-0001.html>>
> >
> > ------------------------------
> >
> > Message: 38
> > Date: Fri, 7 Apr 2017 12:42:34 +0000
> > From: "Iglesias Gonzalez, Eugenio" <e.iglesias@ucl.ac.uk
> <mailto:e.iglesias@ucl.ac.uk>
> > <mailto:e.iglesias@ucl.ac.uk <mailto:e.iglesias@ucl.ac.uk>>>
> > Subject: Re: [Freesurfer] Hippocampal subfield segmentation,
> file
> > content
> > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>>
> > Message-ID: <B9A34CC0-D6BB-4AEE-9428-7E715598727E@ucl.ac.uk
> <mailto:B9A34CC0-D6BB-4AEE-9428-7E715598727E@ucl.ac.uk>
> > <mailto:B9A34CC0-D6BB-4AEE-9428-7E715598727E@ucl.ac.uk
> <mailto:B9A34CC0-D6BB-4AEE-9428-7E715598727E@ucl.ac.uk>>>
> > Content-Type: text/plain; charset="utf-8"
> >
> > Hi Nina,
> > I?m very glad to hear that the segmentations look
> satisfactory :-)
> > The ?h.hippoSfLabel.v10.mgz files already have that information;
> > they are label volumes (FreeView assigns colors to the
> labels for
> > visualization). The lookup table can be found in
> > $FREESURFER_HOME/FreeSurferColorLUT.txt (you?re interested in
> > the range 200-226).
> > Cheers,
> > /Eugenio
> >
> > Juan Eugenio Iglesias
> > ERC Senior Research Fellow
> > Translational Imaging Group
> > University College London
> > http://www.jeiglesias.com
> > http://cmictig.cs.ucl.ac.uk/
> >
> >
> > On 7 Apr 2017, at 12:17, Nina Jacobsen
> <njacob12@student.aau.dk <mailto:njacob12@student.aau.dk>
> > <mailto:njacob12@student.aau.dk
> <mailto:njacob12@student.aau.dk>><mailto:njacob12@student.aau.dk
> <mailto:njacob12@student.aau.dk>
> > <mailto:njacob12@student.aau.dk
> <mailto:njacob12@student.aau.dk>>>> wrote:
> >
> > Hi All,
> >
> > I have made a hippocampal subfield segmentation using FreeSurfer
> > version 6.0 with multispectral segmentation settings, and have
> > both labels for the right and left hippocampus. The
> segmentations
> > look very nice when viewed with freeview, so all good.
> >
> > Now, my problem is the file content. I would like a segmentation
> > file, which labels all subfields with a single value (all voxels
> > in CA1 would for example be with value 1, all voxels in CA2
> would
> > be with value 2 and so on). Does anyone know how i can gain this
> > file? Is it in some way possible to convert the label files
> > (lh.hippoSfLabel.v10.mgz) into such a "simple" segmentation
> file?
> > Currently, the content of the label files
> > (lh.hippoSfLabel.v10.mgz) is values in the range 0-226, which I
> > guess origin from the RGB encoding - I opened the file with
> matlab.
> >
> > Hope my question is clear.
> >
> > Thanks,
> > Nina Jacobsen.
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>><mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <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>
> > <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.
> >
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> >
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> <http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170407/a5c3e0ea/attachment-0001.html>>
> >
> > ------------------------------
> >
> > Message: 39
> > Date: Fri, 7 Apr 2017 10:27:57 -0400 (EDT)
> > From: Bruce Fischl <fischl@nmr.mgh.harvard.edu
> <mailto:fischl@nmr.mgh.harvard.edu>
> > <mailto:fischl@nmr.mgh.harvard.edu
> <mailto:fischl@nmr.mgh.harvard.edu>>>
> > Subject: Re: [Freesurfer] How to segment subnuclei of thalamus?
> > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>>
> > Message-ID:
> >
> >
> <alpine.LRH.2.20.1704071027520.23501@door.nmr.mgh.harvard.edu
> <mailto:alpine.LRH.2.20.1704071027520.23501@door.nmr.mgh.harvard.edu>
> >
> <mailto:alpine.LRH.2.20.1704071027520.23501@door.nmr.mgh.harvard.edu
> <mailto:alpine.LRH.2.20.1704071027520.23501@door.nmr.mgh.harvard.edu>>>
> > Content-Type: text/plain; charset="utf-8"
> >
> > sorry, not yet. We are working on it
> > Bruce
> > On Fri, 7 Apr 2017, Shane S wrote:
> >
> > > Hello Experts,
> > >
> > > I am interested to do a segmentation of the thalamus subnuclei
> > based on T1
> > > data. Is there any atlas that I could use for this??
> > >
> > > Best Wishes,
> > > S
> > >
> > >
> > >
> >
> > ------------------------------
> >
> > Message: 40
> > Date: Fri, 7 Apr 2017 11:11:46 -0400
> > From: Marissa Pifer <marissapifer@gmail.com
> <mailto:marissapifer@gmail.com>
> > <mailto:marissapifer@gmail.com <mailto:marissapifer@gmail.com>>>
> > Subject: [Freesurfer] Analyzing xhemi results
> > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>>
> > Message-ID:
> >
> >
> <CAEHKf7bbt_mF0rH3Zynp+B25FA=7n6YnYr-_6uyO3iUA+bw=6A@mail.gmail.com
> <mailto:6A@mail.gmail.com>
> > <mailto:6A@mail.gmail.com <mailto:6A@mail.gmail.com>>>
> > Content-Type: text/plain; charset="utf-8"
> >
> > Hi free surfers,
> >
> > I have run the xhemi process on the subjects for my study. The
> > study is on
> > stroke patients and their lesions are a mix of left and right
> > hemispheres.
> > In analyzing the results, we want to look at correlations
> between fmri
> > activation in M1 and the cortical thickness of M1
> ipsilesional and
> > contralesional. To do so, I followed instructions written out in
> > response
> > to a question about xhemi on the mailing list:
> >
> >
> https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-December/026823.html
> <https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-December/026823.html>
> >
> <https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-December/026823.html
> <https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-December/026823.html>>
> >
> > My question, is there a way when running the analysis step:
> >
> > *# Analyze
> > *>* mri_glmfit --y lh.lh-rh.thickness.sm05.mgh --glmdir
> > *>* glm.lh.lh-rh.thickness.sm05 \
> > *>* --osgm --surf fsaverage_sym lh
> > *>
> >
> > Can I modify this command line to include my fmri data and
> run that
> > correlation also?
> >
> > Thank you,
> >
> > Marissa
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
> > URL:
> >
> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170407/be12d8d8/attachment-0001.html
> <http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170407/be12d8d8/attachment-0001.html>
> >
> <http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170407/be12d8d8/attachment-0001.html
> <http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170407/be12d8d8/attachment-0001.html>>
> >
> > ------------------------------
> >
> > Message: 41
> > Date: Fri, 7 Apr 2017 11:47:56 -0400
> > From: Arnaud Bor? <arnaud.bore@gmail.com
> <mailto:arnaud.bore@gmail.com>
> > <mailto:arnaud.bore@gmail.com <mailto:arnaud.bore@gmail.com>>>
> > Subject: Re: [Freesurfer] QDEC and ROI drawing
> > To: freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>,
> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> > <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>
> > Message-ID:
> >
> >
> <CAPA8YjZCsVwy0nfueXpObz45HkyCBkoaoRB8jOwXcycCyuA5AA@mail.gmail.com
> <mailto:CAPA8YjZCsVwy0nfueXpObz45HkyCBkoaoRB8jOwXcycCyuA5AA@mail.gmail.com>
> >
> <mailto:CAPA8YjZCsVwy0nfueXpObz45HkyCBkoaoRB8jOwXcycCyuA5AA@mail.gmail.com
> <mailto:CAPA8YjZCsVwy0nfueXpObz45HkyCBkoaoRB8jOwXcycCyuA5AA@mail.gmail.com>>>
> > Content-Type: text/plain; charset="utf-8"
> >
> > I used this command line: mri_label2label --srclabel
> rh.M1_v4.label
> > --srcsubject fsaverage --trgsubject O_Nap_04MB --trglabel
> > rh.M1_v4.label
> > --regmethod surface --hemi rh
> > The output label overlaps the surface using freeview but using
> > qdec it is
> > shifted.
> > Thank you for your help.
> > Arnaud
> >
> > 2017-04-07 10:23 GMT-04:00 basile pinsard
> > <basile.pinsard@gmail.com <mailto:basile.pinsard@gmail.com>
> <mailto:basile.pinsard@gmail.com <mailto:basile.pinsard@gmail.com>>>:
> >
> > >
> > > ---------- Forwarded message ----------
> > > From: Douglas N Greve <greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>
> > <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>>
> > > Date: Thu, Apr 6, 2017 at 4:53 PM
> > > Subject: Re: [Freesurfer] QDEC and ROI drawing
> > > To: freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>
> > >
> > >
> > > what is your label2label command line?
> > >
> > >
> > >
> > > On 04/06/2017 04:52 PM, Arnaud Bor? wrote:
> > > > Dear Freesurfer's experts,
> > > > I draw a specific region on fsaverage using QDEC, then I
> > mapped this
> > > > label on each subject using mri_label2label. I looked at
> these
> > > > registered labels using freeview. Most of them are
> perfect but for
> > > > some of them I would like to correct the segmentation. I
> would
> > like to
> > > > modify it using QDEC but when I overlay this label on the
> > surface of
> > > > my subject it has been shifted. I think this shift is
> because
> > QDEC is
> > > > using fsaverage as the standard space. I try opening QDEC
> > using the
> > > > "average" option and use the subject I want but I still
> get this
> > > > shift. am I missing something ?
> > > > Thank you in advance for your help.
> > > > Arnaud Bore
> > > >
> > > >
> > > >
> > > > _______________________________________________
> > > > Freesurfer mailing list
> > > > Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > > >
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
> > >
> > > --
> > > Douglas N. Greve, Ph.D.
> > > MGH-NMR Center
> > > greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>
> > > Phone Number: 617-724-2358 <tel:%28617%29%20724-2358>
> > > Fax: 617-726-7422 <tel:%28617%29%20726-7422>
> > >
> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>
> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> <https://gate.nmr.mgh.harvard.edu/filedrop2>
> > <https://gate.nmr.mgh.harvard.edu/filedrop2
> <https://gate.nmr.mgh.harvard.edu/filedrop2>>
> > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>
> > > Outgoing:
> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>
> >
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>>
> > >
> > > _______________________________________________
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > >
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
> >
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <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>
> > <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.
> > >
> > >
> > >
> > >
> > > --
> > > Basile Pinsard
> > >
> > > *PhD candidate, *
> > > Laboratoire d'Imagerie Biom?dicale, UMR S 1146 / UMR 7371,
> Sorbonne
> > > Universit?s, UPMC, INSERM, CNRS
> > > *Brain-Cognition-Behaviour Doctoral School **, *ED3C*, *UPMC,
> > Sorbonne
> > > Universit?s
> > > Biomedical Sciences Doctoral School, Faculty of Medicine,
> > Universit? de
> > > Montr?al
> > > CRIUGM, Universit? de Montr?al
> > >
> >
> >
> >
> > --
> > Arnaud BORE
> > Research assistant
> > Cellulaire : (001) 514-647-8649 <tel:%28514%29%20647-8649>
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> >
> > ------------------------------
> >
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> > Freesurfer mailing list
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> >
> > End of Freesurfer Digest, Vol 158, Issue 12
> > *******************************************
> >
> >
> >
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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> Freesurfer mailing list
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> *******************************************
>
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>
>
> _______________________________________________
> Freesurfer mailing list
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> 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: 7
Date: Thu, 20 Apr 2017 15:41:00 +0000
From: "Jacobson, Aaron" <ajacobson@ucsd.edu>
Subject: Re: [Freesurfer] Using registration.dat to register a dataset
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <702DEC95-43A9-4203-8E0C-15685B654430@ucsd.edu>
Content-Type: text/plain; charset="utf-8"

Absolutely, thanks for looking into this.

I have 3 datasets:

1. T1 anatomical
2. DTI
3. Unusual dataset (derived from DTI) that does not have a contrast that bbregister can use to register the data

I want to register the unusual dataset (#3) to the T1 anatomical.

Since the unusual dataset cannot be read successfully by bbregister, I registered the DTI to the anatomical and I would like to use the registration parameters from that registration (DTI to t1) to register the unusual dataset to the T1.

Is this a possibility?

Aaron D. Jacobson
Technical Operations Manager
UCSD Center for Functional MRI
9500 Gilman Drive
La Jolla CA 92093-0677

On 4/20/17, 8:09 AM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of greve@nmr.mgh.harvard.edu> wrote:

I don't know what you are trying to do. Can you elaborate?

On 04/19/2017 07:26 PM, Jacobson, Aaron wrote:
> Hello,
>
> I am new to freesurfer. I have been looking for an answer to this
> issue for days.
>
> I ran bbregister to align a dti scan to a t1 struc.
>
> It worked beautifully.
>
> I am trying to register a very abnormal looking dataset to the t1
> using the registration parameters created during the first bbregister
> (dti to t1).
>
> I have been unable to figure this out, but it seems like it must be a
> common procedure. Any advice would be greatly appreciated.
>
>
> _______________________________________________
> 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/

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Message: 8
Date: Thu, 20 Apr 2017 11:42:51 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Using registration.dat to register a dataset
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <886e02f5-49a4-13f7-63b3-bf4d6176b558@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed

Yes, when using mri_vol2vol or mri_vol2surf, spec the unusual data set
as the --mov but pass the bbregister registration to the --reg flag.

On 04/20/2017 11:41 AM, Jacobson, Aaron wrote:
> Absolutely, thanks for looking into this.
>
> I have 3 datasets:
>
> 1. T1 anatomical
> 2. DTI
> 3. Unusual dataset (derived from DTI) that does not have a contrast that bbregister can use to register the data
>
> I want to register the unusual dataset (#3) to the T1 anatomical.
>
> Since the unusual dataset cannot be read successfully by bbregister, I registered the DTI to the anatomical and I would like to use the registration parameters from that registration (DTI to t1) to register the unusual dataset to the T1.
>
> Is this a possibility?
>
> Aaron D. Jacobson
> Technical Operations Manager
> UCSD Center for Functional MRI
> 9500 Gilman Drive
> La Jolla CA 92093-0677
>
>
>
> On 4/20/17, 8:09 AM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of greve@nmr.mgh.harvard.edu> wrote:
>
> I don't know what you are trying to do. Can you elaborate?
>
>
> On 04/19/2017 07:26 PM, Jacobson, Aaron wrote:
> > Hello,
> >
> > I am new to freesurfer. I have been looking for an answer to this
> > issue for days.
> >
> > I ran bbregister to align a dti scan to a t1 struc.
> >
> > It worked beautifully.
> >
> > I am trying to register a very abnormal looking dataset to the t1
> > using the registration parameters created during the first bbregister
> > (dti to t1).
> >
> > I have been unable to figure this out, but it seems like it must be a
> > common procedure. Any advice would be greatly appreciated.
> >
> >
> > _______________________________________________
> > 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
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in error
> but does not contain patient information, please contact the sender and properly
> dispose of the e-mail.
>
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
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/

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

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End of Freesurfer Digest, Vol 158, Issue 39
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