On Sun, Sep 15, 2013 at 12:00 AM, <freesurfer-request@nmr.mgh.harvard.edu> wrote:

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

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

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

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

Today's Topics:

1. Re: Resolved, crash during longitudinal process when it run
mri_ca_register during CA reg. (Knut J Bjuland)
2. Re: Tracula and Qdec (Alan Francis)
3. Re: recon all question (Harms, Michael)
4. Re: Tracula and Qdec (Anastasia Yendiki)
5. Re: Tracula and Qdec (Alan Francis)
6. mapping extracted MNI152 ROIs to individual subjects (Paul Beach)
7. Getting around a design matrix with zero columns (ye tian)
8. Re: mapping extracted MNI152 ROIs to individual subjects
(Thomas Yeo)
9. Re: Interpretation of interaction effect in qdec (ye tian)

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

Message: 1
Date: Fri, 13 Sep 2013 19:11:28 +0200
From: Knut J Bjuland <knutjorgen@outlook.com>
Subject: Re: [Freesurfer] Resolved, crash during longitudinal process
when it run mri_ca_register during CA reg.
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <BLU0-SMTP155871B1490571BAB6BB181C33B0@phx.gbl>
Content-Type: text/plain; charset="iso-8859-1"

Closed, not bug in Freesurfer.

On 09/12/2013 10:31 PM, Knut J Bjuland wrote:
> When I run recon-all -base 1_template -tp 1_first -tp 1_secon -all
> -debug. It crash during CA Reg Thu Sep 12 19:59:01 CEST 2013. I can
> send the rest of the log.
> Knut J
>
>
>
>
> #--------------------------------------
> #@# CA Reg Thu Sep 12 19:59:01 CEST 2013
> /cluster/home/kjbjuland/freesurfer/long/NTNU_PRE_023_template/mri
>
> mri_ca_register -nobigventricles -T transforms/talairach.lta
> -align-after -mask
> brainmask.mgz norm.mgz
> /cluster/software/VERSIONS/freesurfer-5.3.0/average/RB_a
> ll_2008-03-26.gca transforms/talairach.m3z
>
> not handling expanded ventricles...
> using previously computed transform transforms/talairach.lta
> renormalizing sequences with structure alignment, equivalent to:
> -renormalize
> -regularize_mean 0.500
> -regularize 0.500
> using MR volume brainmask.mgz to mask input volume...
> reading 1 input volumes...
> logging results to talairach.log
>
>
> ======= NUMBER OF OPENMP THREADS = 1 =======
> reading input volume 'norm.mgz'...
> reading GCA
> '/cluster/software/VERSIONS/freesurfer-5.3.0/average/RB_all_2008-03-26.gca'...
> label assignment complete, 0 changed (0.00%)
> det(m_affine) = 1.55 (predicted orig area = 5.2)
> label assignment complete, 0 changed (0.00%)
> freeing gibbs priors...done.
> average std[0] = 5.0
> **************** pass 1 of 1 ************************
> setting smoothness coefficient to 0.039
> blurring input image with Gaussian with sigma=2.000...
> 0000: dt=0.000, rms=0.932, neg=0, invalid=96777
>
>
>
>
>
>
>
>
>
>
>
> On 09/12/2013 10:14 AM, Knut J Bjuland wrote:
>> Hi,
>> I have run recon-al longitudinal process on abel cluster with this
>> command recon-all -base @filename@_template -tp @filename@ -tp
>> @filename@v2 -all -debug. However, it crashed or is killed when it
>> ran mri_ca_register.
>> I have looked through the log, and I have not found a reason for it
>> being killed even tough I added -debug. The cluster is running sbatch
>> and CentOS release 6.4. Are there any debug options I can add or are
>> there any debugversion of mri_ca_register I can download? This happen
>> every time I run the program. I have asked for 8g ram when ran the
>> program.
>>
>> Best regards
>> Knut J?rgen Bjuland
>>
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom it is
>> addressed. If you believe this e-mail was sent to you in error and the e-mail
>> contains patient information, please contact the Partners Compliance HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you in error
>> but does not contain patient information, please contact the sender and properly
>> dispose of the e-mail.
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in error
> but does not contain patient information, please contact the sender and properly
> dispose of the e-mail.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20130913/e14719e3/attachment-0001.html

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

Message: 2
Date: Fri, 13 Sep 2013 13:20:22 -0400
From: Alan Francis <alandarkenergy@gmail.com>
Subject: Re: [Freesurfer] Tracula and Qdec
To: Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu>
Cc: Freesurfer <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CADa7OD2Sa7W4jJ3qj61ss9=xWuYjV1_3t51E8DdYs0XNV9=o7g@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Hi Anastasia:

Yes I generated the left CST on a single subject using the Freeview -tv
option. But my boss wanted to know if it was possible to do a voxelwise
group analysis and show mean differences on a single inflated brain.

thanks,

Alan

On Fri, Sep 13, 2013 at 11:43 AM, Anastasia Yendiki <
ayendiki@nmr.mgh.harvard.edu> wrote:

>
> I see, then it's an ROI analysis, where the tract is the ROI. Isn't it
> sufficient for you to visualize the tracts in an example subject with the
> -tv option in freeview? What would you like to do beyond that?
>
>
> On Fri, 13 Sep 2013, Alan Francis wrote:
>
> Hi Anastasia:
>>
>> I am looking at Average AD in these tracts.
>>
>> thanks,
>>
>> Alan
>>
>>
>> On Fri, Sep 13, 2013 at 11:37 AM, Anastasia Yendiki
>> <ayendiki@nmr.mgh.harvard.edu> wrote:
>>
>> Hi Alan - Are you looking at average AD over the whole tract, or
>> AD along the tract?
>>
>> a.y
>>
>> On Fri, 13 Sep 2013, Alan Francis wrote:
>>
>> Hi Anastasia:
>>
>> Thanks for your quick reply. We would like to look
>> at the left and right
>> Cortico-spinal tract AD between the groups. Also
>> left and right ATR AD if
>> possible.
>>
>> thanks again,
>>
>> Alan
>>
>>
>> On Fri, Sep 13, 2013 at 10:53 AM, Anastasia Yendiki
>> <ayendiki@nmr.mgh.harvard.edu> wrote:
>>
>> Hi Alan - Glad to hear that you have an
>> interesting finding! Can
>> you describe what type of thing you want to
>> visualize a bit
>> more? If it's not on the surface, freeview
>> will more likely do
>> the trick rather than qdec.
>>
>> a.y
>>
>> On Fri, 13 Sep 2013, Alan Francis wrote:
>>
>> Hi Anastasia and FreeSurfers:
>>
>> Is it possible to model Tracula data on
>> Qdec? I have
>> some interesting
>> findings in FA and AD between two groups
>> that I am
>> hoping to visually
>> represent on a single brain.
>>
>> Any advice would be deeply appreciated.
>>
>> thank you,
>>
>> Alan
>>
>>
>>
>>
>> The information in this e-mail is intended only for
>> the person to whom
>> it is
>> addressed. If you believe this e-mail was sent to
>> you in error and the
>> e-mail
>> contains patient information, please contact the
>> Partners Compliance
>> HelpLine at
>> http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. If the
>> e-mail was sent to you
>> in error
>> but does not contain patient information, please
>> contact the sender
>> and properly
>> dispose of the e-mail.
>>
>>
>>
>>
>>
>>
>>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20130913/15b3969f/attachment-0001.html

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

Message: 3
Date: Fri, 13 Sep 2013 17:23:19 +0000
From: "Harms, Michael" <mharms@wustl.edu>
Subject: Re: [Freesurfer] recon all question
To: Rashmi Singh <rsingh@laureateinstitute.org>, Bruce Fischl
<fischl@nmr.mgh.harvard.edu>
Cc: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <CE58B405.1FEDF%harmsm@psychiatry.wustl.edu>
Content-Type: text/plain; charset="us-ascii"

Hi,
A reasonable definition of TBV would be TotalGrayVol +
CorticalWhiteMatterVol from the aseg.stats file.

cheers,
-MH

--
Michael Harms, Ph.D.

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

On 9/13/13 9:18 AM, "Rashmi Singh" <rsingh@laureateinstitute.org> wrote:

> I am doing volumetric studies where instead of using ICV, I use total
>brain volume as a co-variate. This is why I need total brain volume
>measurements. Do you suggest that its not a good idea to use mri-binarize
>of brain.mgz for calculating it?
>Earlier freesurfer experts had suggeted me to use this option.
>Rashmi
>_______________________
>________________________________________
>From: Bruce Fischl [fischl@nmr.mgh.harvard.edu]
>Sent: Friday, September 13, 2013 9:09 AM
>To: Rashmi Singh
>Cc: freesurfer@nmr.mgh.harvard.edu
>Subject: RE: [Freesurfer] recon all question
>
>what do you want to do with the brain volume? Are you really after
>ICV/TIV? We use the det. of the jacobian of the tal xform as per Randy
>Buckner, and for it we have compared to actual ICV volumes derived from T2
>volumes and manual stripping
>
>For the FLAIR, we usually get a T2-space based FLAIR that is also 1mm
>isotropic. Once you are done with recon-all, you run it again with the
>switch -FLAIRpial <path to flair volume> and it will do a post-hoc surface
>deformation to avoid dura.
>
>cheers
>Bruce
>
>On Fri, 13 Sep 2013, Rashmi Singh wrote:
>
>> Thank you Bruce !
>> mri_binarize was suggested to me by the freesurfer group, so now I am a
>little concerned when you say that this has not been assessed for
>accuracy.
>May you suggest how otherwise do you get the total brain volume ( which
>you
>suggest is more accurate), as this measurement is not present in the
>freesurfer output stat files.
>>
>> May you please elaborate a little more the steps of using T2-FlAIR for
>recon all or suggest me where I can find the detail information ( may be
>on
>the website). While scanning we do collect T2-FLAIR that is linked with
>T1
>for each subject. Is that what you mean by get a T2-FLAIR? Also, what is a
>-T2Flair swicht?
>> Sorry, with a background of molecular biology and being a novice in
>>image
>analysis, it really takes me time and lots of effort to understand
>imaging
>and its analysis. Your guidance is appreciated.
>> Thanks,
>>
>> Rashmi
>> ________________________________________
>> From: Bruce Fischl [fischl@nmr.mgh.harvard.edu]
>> Sent: Friday, September 13, 2013 8:46 AM
>> To: Rashmi Singh
>> Cc: freesurfer@nmr.mgh.harvard.edu
>> Subject: RE: [Freesurfer] recon all question
>>
>> 1. I don't think I know anyone who has done this, and we haven't
>>assessed
>> it for accuracy.
>>
>> 2. The best thing to do is get a T2-FLAIR and run it with the -T2Flair
>> switch after recon-all is done. This does a great job avoiding dura
>>
>> cheers
>> Bruce
>>
>>
>> On Fri, 13 Sep 2013, Rashmi Singh wrote:
>>
>>> Hey Bruce,
>>> I have two more questions.
>>> 1) I was suggested to use mri_binarize with brain.mgz to get the total
>brain volume. Is there any reference that I can cite regarding use of
>mri_binarize to calculate total brain volume.
>>>
>>> 2)I learnt that using T2 weighted image along with T1 weighted image
>from the same scanning session generates a good contrast and gives better
>segmentation/parcellation outputs using FreeSurfer.
>>> May the FreeSurfer experts guide me through this.
>>>
>>> Thanks,
>>> Rashmi
>>> ________________________________________
>>> From: Bruce Fischl [fischl@nmr.mgh.harvard.edu]
>>> Sent: Thursday, September 12, 2013 5:27 PM
>>> To: Rashmi Singh
>>> Cc: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] recon all question
>>>
>>> Hi Rashmi
>>>
>>> putting them in the orig folder with those numbers will get recon-all
>>>to
>>> do motion correction and averaging.
>>>
>>> cheers
>>> Bruce
>>> On Thu, 12 Sep 2013, Rashmi Singh wrote:
>>>
>>>>
>>>> Hello Freesurfer experts,
>>>> I am doing volumetrics study. During the scan we get 2-3 mprage per
>>>> scan for a subject.
>>>> While running the FreeSurfer, if I want to use the three mprages
>for
>>>> that subject as an input file, may I just keep the three mgz files
>>>> (001.mgz, 002 .mgz and 003.mgz) in the orig folder and run the simple
>>> recon
>>>> all command :=Recon-all -s (subject file name) -all or do I need to
>have
>>>> some additional l flags so that recon all command will use the three
>T1
>>>> images to get one output file?
>>>> Thanks,
>>>> Rashmi
>>>>
>>>>
>>>
>>>
>>> The information in this e-mail is intended only for the person to whom
>it
>>> is
>>> addressed. If you believe this e-mail was sent to you in error and the
>>> e-mail
>>> contains patient information, please contact the Partners Compliance
>>> HelpLine at
>>> http://www.partners.org/complianceline . If the e-mail was sent to you
>in
>>> error
>>> but does not contain patient information, please contact the sender and
>>> properly
>>> dispose of the e-mail.
>>>
>>>
>>>
>>>
>>>
>>
>>
>>
>
>
>
>_______________________________________________
>Freesurfer mailing list
>Freesurfer@nmr.mgh.harvard.edu
>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

________________________________
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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

Message: 4
Date: Fri, 13 Sep 2013 13:37:23 -0400 (EDT)
From: Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Tracula and Qdec
To: Alan Francis <alandarkenergy@gmail.com>
Cc: Freesurfer <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <alpine.LRH.2.03.1309131336580.4838@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="iso-8859-1"

Hi Alan - Sorry, tracula doesn't do voxel-based analyses, only
tract-based.

a.y

On Fri, 13 Sep 2013, Alan Francis wrote:

> Hi Anastasia:
>
> Yes I generated the left CST on a single subject using the Freeview -tv
> option. But my boss wanted to know if it was possible to do a voxelwise
> group analysis and show mean differences on a single inflated brain.
>
> thanks,
>
> Alan
>
>
> On Fri, Sep 13, 2013 at 11:43 AM, Anastasia Yendiki
> <ayendiki@nmr.mgh.harvard.edu> wrote:
>
> I see, then it's an ROI analysis, where the tract is the ROI.
> Isn't it sufficient for you to visualize the tracts in an
> example subject with the -tv option in freeview? What would you
> like to do beyond that?
>
> On Fri, 13 Sep 2013, Alan Francis wrote:
>
> Hi Anastasia:
>
> I am looking at Average AD in these tracts.
>
> thanks,
>
> Alan
>
>
> On Fri, Sep 13, 2013 at 11:37 AM, Anastasia Yendiki
> <ayendiki@nmr.mgh.harvard.edu> wrote:
>
> ? ? ? Hi Alan - Are you looking at average AD over
> the whole tract, or
> ? ? ? AD along the tract?
>
> ? ? ? a.y
>
> ? ? ? On Fri, 13 Sep 2013, Alan Francis wrote:
>
> ? ? ? ? ? ? Hi Anastasia:
>
> ? ? ? ? ? ? Thanks for your quick reply. We would
> like to look
> ? ? ? ? ? ? at the left and right
> ? ? ? ? ? ? Cortico-spinal tract AD between the
> groups. Also
> ? ? ? ? ? ? left and right ATR AD if
> ? ? ? ? ? ? possible.
>
> ? ? ? ? ? ? thanks again,
>
> ? ? ? ? ? ? Alan
>
>
> ? ? ? ? ? ? On Fri, Sep 13, 2013 at 10:53 AM,
> Anastasia Yendiki
> ? ? ? ? ? ? <ayendiki@nmr.mgh.harvard.edu> wrote:
>
> ? ? ? ? ? ? ? ? ? Hi Alan - Glad to hear that you
> have an
> ? ? ? ? ? ? interesting finding! Can
> ? ? ? ? ? ? ? ? ? you describe what type of thing
> you want to
> ? ? ? ? ? ? visualize a bit
> ? ? ? ? ? ? ? ? ? more? If it's not on the surface,
> freeview
> ? ? ? ? ? ? will more likely do
> ? ? ? ? ? ? ? ? ? the trick rather than qdec.
>
> ? ? ? ? ? ? ? ? ? a.y
>
> ? ? ? ? ? ? ? ? ? On Fri, 13 Sep 2013, Alan Francis
> wrote:
>
> ? ? ? ? ? ? ? ? ? ? ? ? Hi Anastasia and
> FreeSurfers:
>
> ? ? ? ? ? ? ? ? ? ? ? ? Is it possible to model
> Tracula data on
> ? ? ? ? ? ? Qdec? I have
> ? ? ? ? ? ? ? ? ? ? ? ? some interesting
> ? ? ? ? ? ? ? ? ? ? ? ? findings in FA and AD
> between two groups
> ? ? ? ? ? ? that I am
> ? ? ? ? ? ? ? ? ? ? ? ? hoping to visually
> ? ? ? ? ? ? ? ? ? ? ? ? represent on a single brain.
>
> ? ? ? ? ? ? ? ? ? ? ? ? Any advice would be deeply
> appreciated.
>
> ? ? ? ? ? ? ? ? ? ? ? ? thank you,
>
> ? ? ? ? ? ? ? ? ? ? ? ? Alan
>
>
>
>
> ? ? ? ? ? ? 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.
>
>
>
>
>
>
>
>
>

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

Message: 5
Date: Fri, 13 Sep 2013 14:02:22 -0400
From: Alan Francis <alandarkenergy@gmail.com>
Subject: Re: [Freesurfer] Tracula and Qdec
To: Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu>
Cc: Freesurfer <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CADa7OD20gzbiQaAoYKrwNdp_abcoLTwHZE_tmTOL0FjqE0oioQ@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Thanks Anastasia.

On Fri, Sep 13, 2013 at 1:37 PM, Anastasia Yendiki <
ayendiki@nmr.mgh.harvard.edu> wrote:

>
> Hi Alan - Sorry, tracula doesn't do voxel-based analyses, only tract-based.
>
>
> a.y
>
> On Fri, 13 Sep 2013, Alan Francis wrote:
>
> Hi Anastasia:
>>
>> Yes I generated the left CST on a single subject using the Freeview -tv
>> option. But my boss wanted to know if it was possible to do a voxelwise
>> group analysis and show mean differences on a single inflated brain.
>>
>> thanks,
>>
>> Alan
>>
>>
>> On Fri, Sep 13, 2013 at 11:43 AM, Anastasia Yendiki
>> <ayendiki@nmr.mgh.harvard.edu> wrote:
>>
>> I see, then it's an ROI analysis, where the tract is the ROI.
>> Isn't it sufficient for you to visualize the tracts in an
>> example subject with the -tv option in freeview? What would you
>> like to do beyond that?
>>
>> On Fri, 13 Sep 2013, Alan Francis wrote:
>>
>> Hi Anastasia:
>>
>> I am looking at Average AD in these tracts.
>>
>> thanks,
>>
>> Alan
>>
>>
>> On Fri, Sep 13, 2013 at 11:37 AM, Anastasia Yendiki
>> <ayendiki@nmr.mgh.harvard.edu> wrote:
>>
>> Hi Alan - Are you looking at average AD over
>> the whole tract, or
>> AD along the tract?
>>
>> a.y
>>
>> On Fri, 13 Sep 2013, Alan Francis wrote:
>>
>> Hi Anastasia:
>>
>> Thanks for your quick reply. We would
>> like to look
>> at the left and right
>> Cortico-spinal tract AD between the
>> groups. Also
>> left and right ATR AD if
>> possible.
>>
>> thanks again,
>>
>> Alan
>>
>>
>> On Fri, Sep 13, 2013 at 10:53 AM,
>> Anastasia Yendiki
>> <ayendiki@nmr.mgh.harvard.edu> wrote:
>>
>> Hi Alan - Glad to hear that you
>> have an
>> interesting finding! Can
>> you describe what type of thing
>> you want to
>> visualize a bit
>> more? If it's not on the surface,
>> freeview
>> will more likely do
>> the trick rather than qdec.
>>
>> a.y
>>
>> On Fri, 13 Sep 2013, Alan Francis
>> wrote:
>>
>> Hi Anastasia and
>> FreeSurfers:
>>
>> Is it possible to model
>> Tracula data on
>> Qdec? I have
>> some interesting
>> findings in FA and AD
>> between two groups
>> that I am
>> hoping to visually
>> represent on a single brain.
>>
>> Any advice would be deeply
>> appreciated.
>>
>> thank you,
>>
>> Alan
>>
>>
>>
>>
>> The information in this e-mail is
>> intended only for
>> the person to whom
>> it is
>> addressed. If you believe this e-mail
>> was sent to
>> you in error and the
>> e-mail
>> contains patient information, please
>> contact the
>> Partners Compliance
>> HelpLine at
>> http://www.partners.org/**complianceline<http://www.partners.org/complianceline>.
>> If the
>> e-mail was sent to you
>> in error
>> but does not contain patient
>> information, please
>> contact the sender
>> and properly
>> dispose of the e-mail.
>>
>>
>>
>>
>>
>>
>>
>>
>>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20130913/9b134f52/attachment-0001.html

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

Message: 6
Date: Fri, 13 Sep 2013 16:19:21 -0400
From: Paul Beach <pabeach1@gmail.com>
Subject: [Freesurfer] mapping extracted MNI152 ROIs to individual
subjects
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CAPhC-1xnfw2dPAFfhyFT6YFpnHOMAzAGM=Ex=Xz=rnUdO5wwDw@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Hello Freesurfer experts,

I am currently trying to take extracted cortical networks from the
Yeo_JNeurophysiol11_MNI152
package<https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011>and
translate them to individual subjects to perform functional
connectivity analyses - based on the individual networks, themselves.
Currently the extracted ROIs are in '.nii.gz' format.

My question is: How do I take the extracted ROIs and map them on to
individual subjects? My thought was that mri_vol2vol could perhaps
accomplish this, but I cannot find a help file for this command that would
guide me in developing the line of code to write.

Thanks!
--
Paul Beach
DO/PhD candidate - Year VI
Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
- Bozoki Lab: Neurology/Radiology
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20130913/1511a750/attachment-0001.html

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

Message: 7
Date: Fri, 13 Sep 2013 15:21:29 -0500
From: ye tian <tianye730@gmail.com>
Subject: [Freesurfer] Getting around a design matrix with zero columns
To: Freesurfer <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CAGsOs9DKCTgHpCpMDN5hgQKmBTH4H3bs-M3S8sMPx_kBeeAkkA@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Dear Freesurfers,

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

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

Any suggestion is highly appreciated.

Thank you very much!
Sincerely,
Ye
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20130913/c44e4b79/attachment-0001.html

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

Message: 8
Date: Sat, 14 Sep 2013 11:57:09 +0800
From: Thomas Yeo <ythomas@csail.mit.edu>
Subject: Re: [Freesurfer] mapping extracted MNI152 ROIs to individual
subjects
To: Paul Beach <pabeach1@gmail.com>
Cc: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CANZVnTZwTqzkKSBECAhWq1RP6Patfn7q6sgzBrF8-JLjh0v2RA@mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Hi Paul,

What we typically do is to either (1) Transform the subjects' fMRI
data to MNI152 space and then use the MNI ROIs to perform the
functional connectivity analysis OR (2) Transform the subjects' fMRI
data to fsaverage surface space and then use the surface-based
fsaverage ROIs to perform the functional connectivity analysis. The
second approach is definitely more accurate because the ROIs were
originally generated in fsaverage space and then projected to MNI152
space and because working on the surface respects the cerebral
cortex's 2D topology.

If for some reason, you really want to perform the analysis in the
subjects' native space, I would suggest resampling the surface-based
fsaverage ROIs (instead of the MNI152 ROIs) to your subject's native
space . Assuming you have run your subject's anatomical through
recon-all, I believe (and someone please correct me if I am wrong) you
can use mri_label2vol to do the resampling.

--Thomas

On Sat, Sep 14, 2013 at 4:19 AM, Paul Beach <pabeach1@gmail.com> wrote:
> Hello Freesurfer experts,
>
> I am currently trying to take extracted cortical networks from the
> Yeo_JNeurophysiol11_MNI152 package and translate them to individual subjects
> to perform functional connectivity analyses - based on the individual
> networks, themselves. Currently the extracted ROIs are in '.nii.gz' format.
>
> My question is: How do I take the extracted ROIs and map them on to
> individual subjects? My thought was that mri_vol2vol could perhaps
> accomplish this, but I cannot find a help file for this command that would
> guide me in developing the line of code to write.
>
>
> Thanks!
> --
> Paul Beach
> DO/PhD candidate - Year VI
> Michigan State University
> - College of Osteopathic Medicine
> - Neuroscience Program
> - Bozoki Lab: Neurology/Radiology
>
> _______________________________________________
> 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.
>

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

Message: 9
Date: Sat, 14 Sep 2013 01:01:05 -0500
From: ye tian <tianye730@gmail.com>
Subject: Re: [Freesurfer] Interpretation of interaction effect in qdec
To: Douglas Greve <greve@nmr.mgh.harvard.edu>
Cc: Freesurfer <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CAGsOs9DoKv+iQzVTeRUF3UG7Tak81f_KiwJ1YPJopRvhxLid1A@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Dear Freesurfers,

If I understand correctly, the red (positive) means design*contrast>0; blue
(negative) means design*contrast<0. Is this correct?

How should I interpret the color scales (signs) when my contrast has more
than one rows?
For example, I have one discrete factor with three levels, control, drug1
and drug2; and my test hypothesis is "Is there a group effect", with the
following contrast
1 -1 0
1 0 -1

In this case, what does the color scale mean?

Thank you very much!
Sincerely,
Ye

On Fri, Sep 6, 2013 at 9:16 PM, Douglas Greve <greve@nmr.mgh.harvard.edu>wrote:

> yes, that is correct
> doug
>
>
> On 9/6/13 5:48 PM, Yang, Daniel wrote:
>
> Hi FreeSurfer experts,
>
> Let's say I have two class variables:
>
> Sex (female, male)
> Dx (patient, control)
>
> I see that the analysis results show the following:
>
> Does the average thickness, accounting for Dx, diff between female and
> male? Red means: female > male
> Does the average thickness, accounting for Sex, diff between patient and
> control? Red means: patient > control
> Is there a Sex-Dx interaction in the mean thickness? Red means either
> (a) the female > male effect is stronger in patient (vs. control); or (b)
> the patient > control effect is stronger in female (vs. male)
>
> Is my interpretation correct?
>
> Thanks!
> Daniel
>
> --
> Yung-Jui "Daniel" Yang, PhD
> Postdoctoral Researcher
> Yale Child Study Center
> New Haven, CT
> (203) 737-5454
>
>
> _______________________________________________
> Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20130914/c115917e/attachment-0001.html

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

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

End of Freesurfer Digest, Vol 115, Issue 20
*******************************************