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. GLM contrast vector for continuous variable interaction
      (Bronwyn Overs)
   2. Bus error when trying to launch tksurfer (Claire Morley)
   3. Re: Bus error when trying to launch tksurfer (J?rgen H?nggi)
   4. Re: Bus error when trying to launch tksurfer (Bruce Fischl)
   5. Do not have 'recon edit' button! Please help! (Smaragdi A.)
   6. Re: Do not have 'recon edit' button! Please help! (Bruce Fischl)
   7. Re: Do not have 'recon edit' button! Please help! (Smaragdi A.)
   8. unpacksdcmdir (Alshikho, Mohamad J.)
   9. Re: unpacksdcmdir (Shantanu Ghosh)
  10. Re: unpacksdcmdir (Douglas N Greve)
  11. Re: GLM contrast vector for continuous variable   interaction
      (Douglas N Greve)


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

Message: 1
Date: Mon, 20 Oct 2014 09:33:13 +1100
From: Bronwyn Overs <b.overs@neura.edu.au>
Subject: [Freesurfer] GLM contrast vector for continuous variable
        interaction
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <54443C29.9000309@neura.edu.au>
Content-Type: text/plain; charset="iso-8859-1"

Dear Freesurfer Mailing List,

I am running a GLM in freesurfer 2 categorical variables (2 levels), and
three continuous variables (age, prs, & sles). My fsgd file looks like this:

GroupDescriptorFile 1
Title GLM_sles-group-gender-age
Class genderMale-groupControl
Class genderFemale-groupControl
Class genderMale-groupAtRisk
Class genderFemale-groupAtRisk
Variables age prs sles
Input ID_001 genderFemale-groupAtRisk 20 21 96
Input ID_002 genderFemale-groupControl 21 13 79
...

I want to test for an interaction between prs and sles, while
controlling for age, gender, and group. Can you tell me if the following
contrast vector will correctly test for this interaction:

0    0    0    0    0    0    0    0    0       0 0       0       0.5
0.5    0.5    0.5
0    0    0    0    0    0    0    0    0.5    0.5    0.5    0.5 0
0       0       0

--

Kind regards,

Bronwyn Overs
Research Assistant

Neuroscience Research Australia

Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
*M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265

neura.edu.au <http://neura.edu.au>

Follow @neuraustralia on twitter
<https://twitter.com/neuraustralia>Follow NeuRA on facebook
<https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to the
NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20141020/131aa22d/attachment-0001.html
-------------- next part --------------
A non-text attachment was scrubbed...
Name: not available
Type: image/png
Size: 13292 bytes
Desc: not available
Url : http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20141020/131aa22d/attachment-0004.png
-------------- next part --------------
A non-text attachment was scrubbed...
Name: not available
Type: image/png
Size: 1233 bytes
Desc: not available
Url : http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20141020/131aa22d/attachment-0005.png
-------------- next part --------------
A non-text attachment was scrubbed...
Name: not available
Type: image/png
Size: 834 bytes
Desc: not available
Url : http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20141020/131aa22d/attachment-0006.png
-------------- next part --------------
A non-text attachment was scrubbed...
Name: not available
Type: image/png
Size: 3983 bytes
Desc: not available
Url : http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20141020/131aa22d/attachment-0007.png

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

Message: 2
Date: Mon, 20 Oct 2014 09:56:41 +0200
From: Claire Morley <clairemorley2014@u.northwestern.edu>
Subject: [Freesurfer] Bus error when trying to launch tksurfer
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
        <CACxfM7pPmQNQks_guW+=-U4QJ8MP6dDJsShfQJzvJNw+HJSxzQ@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Good Morning,
I have now been able to get the testing command: tksurfer bert rh pial to
run, but it stops midway and issues a bus error. Please see the following
script:

DBM-Users-MacBook-Pro-4:~ dbmuser$ tksurfer bert rh pial
subject is bert
hemi    is rh
surface is pial
surfer: current subjects dir: /Applications/freesurfer/subjects
surfer: not in "scripts" dir ==> using cwd for session root
surfer: session root data dir ($session) set to:
surfer:     /Users/dbmuser
checking for nofix files in 'pial'
Reading image info (/Applications/freesurfer/subjects/bert)
Reading /Applications/freesurfer/subjects/bert/mri/orig.mgz
surfer: Reading header info from
/Applications/freesurfer/subjects/bert/mri/orig.mgz
surfer: vertices=133299, faces=266594
surfer: single buffered window
surfer: tkoInitWindow(bert)
Bus error

Any idea what might be going wrong? I really need to use tksurfer to look
at cortical thickness in gyrification in ROIs. (Oh and before I did this, I
did set the environment as normal).

Thanks so much for your help!
Claire

--

*We shall not cease from exploration. And the end of all our exploring will
be to arrive where we started and know the place for the first time- T.S.
Eliot*
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20141020/31619a03/attachment-0001.html

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

Message: 3
Date: Mon, 20 Oct 2014 10:13:51 +0200
From: J?rgen H?nggi     <j.haenggi@psychologie.uzh.ch>
Subject: Re: [Freesurfer] Bus error when trying to launch tksurfer
To: Freesurfer Mailinglist <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <D06A906B.2DC75%j.haenggi@psychologie.uzh.ch>
Content-Type: text/plain; charset="iso-8859-1"

Daer Claire

The bus error might be related to Xquartz. Installing Xquartz again solved
the issue on most Intel-based Macs.

Cheers
J?rgen

----------------------------------------------------------------------------
J?rgen H?nggi, Ph.D.
Division Neuropsychology
Institute of Psychology
University of Zurich
Binzmuehlestrasse 14, PO Box 25
8050 Zurich, Switzerland
0041 44 635 73 97 (phone office)
0041 76 445 86 84 (phone mobile)
0041 44 635 74 09 (fax office)
BIN 4.D.04 (office room number)
j.haenggi[at]psychologie.uzh.ch (email)
http://www.psychologie.uzh.ch/neuropsy/ (website)
http://www.juergenhaenggi.ch (private website)

This e-mail (and any attachment/s) contains confidential and/or privileged
information. If you are not the intended recipient (or have received this
e-mail in error) please notify the sender immediately and destroy this
e-mail. Any unauthorised copying, disclosure or distribution of the
material in this e-mail is strictly forbidden.
----------------------------------------------------------------------------


Von:  Claire Morley <clairemorley2014@u.northwestern.edu>
Antworten an:  Freesurfer Mailinglist <freesurfer@nmr.mgh.harvard.edu>
Datum:  Montag, 20. Oktober 2014 09:56
An:  Freesurfer Mailinglist <freesurfer@nmr.mgh.harvard.edu>
Betreff:  [Freesurfer] Bus error when trying to launch tksurfer

Good Morning,
I have now been able to get the testing command: tksurfer bert rh pial to
run, but it stops midway and issues a bus error. Please see the following
script:

DBM-Users-MacBook-Pro-4:~ dbmuser$ tksurfer bert rh pial
subject is bert
hemi    is rh
surface is pial
surfer: current subjects dir: /Applications/freesurfer/subjects
surfer: not in "scripts" dir ==> using cwd for session root
surfer: session root data dir ($session) set to:
surfer:     /Users/dbmuser
checking for nofix files in 'pial'
Reading image info (/Applications/freesurfer/subjects/bert)
Reading /Applications/freesurfer/subjects/bert/mri/orig.mgz
surfer: Reading header info from
/Applications/freesurfer/subjects/bert/mri/orig.mgz
surfer: vertices=133299, faces=266594
surfer: single buffered window
surfer: tkoInitWindow(bert)
Bus error

Any idea what might be going wrong? I really need to use tksurfer to look at
cortical thickness in gyrification in ROIs. (Oh and before I did this, I did
set the environment as normal).

Thanks so much for your help!
Claire

--

We shall not cease from exploration. And the end of all our exploring will
be to arrive where we started and know the place for the first time- T.S.
Eliot


_______________________________________________ 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/20141020/8c361fa7/attachment-0001.html

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

Message: 4
Date: Mon, 20 Oct 2014 08:21:56 -0400 (EDT)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Bus error when trying to launch tksurfer
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <alpine.LRH.2.03.1410200821380.27072@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

Hi Claire

what version are you using? And what is your hardware and software
environment? RAM, OS version, etc....?
Bruce
On Mon, 20 Oct 2014, Claire Morley
wrote:

> Good Morning,
> I have now been able to get the testing command: tksurfer bert rh pial to
> run, but it stops midway and issues a bus error. Please see the following
> script:
>
> DBM-Users-MacBook-Pro-4:~ dbmuser$ tksurfer bert rh pial
> subject is bert
> hemi??? is rh
> surface is pial
> surfer: current subjects dir: /Applications/freesurfer/subjects
> surfer: not in "scripts" dir ==> using cwd for session root
> surfer: session root data dir ($session) set to:
> surfer:???? /Users/dbmuser
> checking for nofix files in 'pial'
> Reading image info (/Applications/freesurfer/subjects/bert)
> Reading /Applications/freesurfer/subjects/bert/mri/orig.mgz
> surfer: Reading header info from
> /Applications/freesurfer/subjects/bert/mri/orig.mgz
> surfer: vertices=133299, faces=266594
> surfer: single buffered window
> surfer: tkoInitWindow(bert)
> Bus error
>
> Any idea what might be going wrong? I really need to use tksurfer to look at
> cortical thickness in gyrification in ROIs. (Oh and before I did this, I did
> set the environment as normal).
>
> Thanks so much for your help!
> Claire
>
> --
>
> We shall not cease from exploration. And the end of all our exploring will
> be to arrive where we started and know the place for the first time- T.S.
> Eliot
>
>
>
>

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

Message: 5
Date: Mon, 20 Oct 2014 13:16:31 +0000
From: "Smaragdi A." <A.Smaragdi@soton.ac.uk>
Subject: [Freesurfer] Do not have 'recon edit' button! Please help!
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <D06AC9BE.416A%A.Smaragdi@soton.ac.uk>
Content-Type: text/plain; charset="us-ascii"

Dear mailing list,

I am really stuck here.. Please can someone tell me why I cannot find the recon edit button on freeview!

I am not sure if the version of Freesurfer I have downloaded is old, or I have
done something wrong, or I am just blind.. But I cannot find the 'recon edit'
button in freeview (see attached screenshot). What am I not doing right?

Many thanks,

Areti


-------------- next part --------------
A non-text attachment was scrubbed...
Name: Screen Shot 2014-10-14 at 13.22.42.png
Type: image/png
Size: 71321 bytes
Desc: Screen Shot 2014-10-14 at 13.22.42.png
Url : http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20141020/4dbc998f/attachment-0001.png

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

Message: 6
Date: Mon, 20 Oct 2014 09:24:42 -0400 (EDT)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Do not have 'recon edit' button! Please
        help!
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <alpine.LRH.2.03.1410200924350.27072@nmr.mgh.harvard.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed

Hi Areti

what version of freeview are you using?
Bruce
On Mon, 20 Oct 2014, Smaragdi A.
wrote:

> Dear mailing list,
>
> I am really stuck here.. Please can someone tell me why I cannot find the recon edit button on freeview!
>
> I am not sure if the version of Freesurfer I have downloaded is old, or I have
> done something wrong, or I am just blind.. But I cannot find the 'recon edit'
> button in freeview (see attached screenshot). What am I not doing right?
>
> Many thanks,
>
> Areti
>
>
>


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

Message: 7
Date: Mon, 20 Oct 2014 13:30:55 +0000
From: "Smaragdi A." <A.Smaragdi@soton.ac.uk>
Subject: Re: [Freesurfer] Do not have 'recon edit' button! Please
        help!
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <D06ACCCB.416E%A.Smaragdi@soton.ac.uk>
Content-Type: text/plain; charset="us-ascii"

Hi Bruce,

Thank you for getting back to me! Its the 1.0 version, downloaded from the
website.

Thanks,

Areti





On 20/10/2014 14:24, "Bruce Fischl" <fischl@nmr.mgh.harvard.edu> wrote:

>Hi Areti
>
>what version of freeview are you using?
>Bruce
>On Mon, 20 Oct 2014, Smaragdi A.
>wrote:
>
>> Dear mailing list,
>>
>> I am really stuck here.. Please can someone tell me why I cannot find
>>the recon edit button on freeview!
>>
>> I am not sure if the version of Freesurfer I have downloaded is old, or
>>I have
>> done something wrong, or I am just blind.. But I cannot find the 'recon
>>edit'
>> button in freeview (see attached screenshot). What am I not doing right?
>>
>> Many thanks,
>>
>> Areti
>>
>>
>>
>_______________________________________________
>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 --------------
A non-text attachment was scrubbed...
Name: Screen Shot 2014-10-20 at 14.30.33.png
Type: image/png
Size: 49832 bytes
Desc: Screen Shot 2014-10-20 at 14.30.33.png
Url : http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20141020/bfd7ae42/attachment-0001.png

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

Message: 8
Date: Mon, 20 Oct 2014 14:41:06 +0000
From: "Alshikho, Mohamad J." <MALSHIKHO@mgh.harvard.edu>
Subject: [Freesurfer] unpacksdcmdir
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <E2104E910166894E926B16BCD6DCF00B0F718852@PHSX10MB5.partners.org>
Content-Type: text/plain; charset="iso-8859-1"

Hi ,
The command <unpacksdcmdir> is only used to unpack Siemens DICOM files, How can I unpack the non Siemens DICOMs?

Thanks,
Moahmad
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20141020/3a65f36c/attachment-0001.html

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

Message: 9
Date: Mon, 20 Oct 2014 11:21:36 -0400 (EDT)
From: "Shantanu Ghosh" <shantanu@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] unpacksdcmdir
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Cc: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <49253.128.103.186.182.1413818496.squirrel@mail.nmr.mgh.harvard.edu>
Content-Type: text/plain;charset=iso-8859-1

Hi Mohamad

You could convert the Dicoms in other s/w to .nii and then read them.
Maybe Bruce and Doug have more elegant solutions

Hth
Shantanu


On Mon, October 20, 2014 10:41 am, Alshikho, Mohamad J. wrote:
> Hi ,
> The command <unpacksdcmdir> is only used to unpack Siemens DICOM files,
> How can I unpack the non Siemens DICOMs?
>
> Thanks,
> Moahmad
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


--
Shantanu Ghosh, Ph.D.
Harvard Medical School & Massachusetts General Hospital
Martinos Center for Biomedical Imaging
--
Not only is the universe stranger than we think, it is stranger than we
can think. -Werner Heisenberg



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

Message: 10
Date: Mon, 20 Oct 2014 11:35:03 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] unpacksdcmdir
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <54452BA7.2050601@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

dcmunpack will unpack any dicoms

On 10/20/2014 11:21 AM, Shantanu Ghosh wrote:
> Hi Mohamad
>
> You could convert the Dicoms in other s/w to .nii and then read them.
> Maybe Bruce and Doug have more elegant solutions
>
> Hth
> Shantanu
>
>
> On Mon, October 20, 2014 10:41 am, Alshikho, Mohamad J. wrote:
>> Hi ,
>> The command <unpacksdcmdir> is only used to unpack Siemens DICOM files,
>> How can I unpack the non Siemens DICOMs?
>>
>> Thanks,
>> Moahmad
>> _______________________________________________
>> 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: 11
Date: Mon, 20 Oct 2014 11:37:09 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] GLM contrast vector for continuous variable
        interaction
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <54452C25.9000501@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed


I think this is the contrast you need

0    0    0    0    0    0    0    0 0.5    0.5    0.5    0.5  - 0.5
-0.5    -0.5    -0.5

On 10/19/2014 06:33 PM, Bronwyn Overs wrote:
> Dear Freesurfer Mailing List,
>
> I am running a GLM in freesurfer 2 categorical variables (2 levels),
> and three continuous variables (age, prs, & sles). My fsgd file looks
> like this:
>
> GroupDescriptorFile 1
> Title GLM_sles-group-gender-age
> Class genderMale-groupControl
> Class genderFemale-groupControl
> Class genderMale-groupAtRisk
> Class genderFemale-groupAtRisk
> Variables age prs sles
> Input ID_001 genderFemale-groupAtRisk 20 21 96
> Input ID_002 genderFemale-groupControl 21 13 79
> ...
>
> I want to test for an interaction between prs and sles, while
> controlling for age, gender, and group. Can you tell me if the
> following contrast vector will correctly test for this interaction:
>
> 0    0    0    0    0    0    0    0    0       0 0       0
> 0.5    0.5    0.5    0.5
> 0    0    0    0    0    0    0    0    0.5    0.5    0.5 0.5
> 0       0       0       0
>
> --
>
> Kind regards,
>
> Bronwyn Overs
> Research Assistant
>
> Neuroscience Research Australia
>
> Neuroscience Research Australia
> Margarete Ainsworth Building
> Barker Street Randwick Sydney NSW 2031 Australia
> *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265
>
> neura.edu.au <http://neura.edu.au>
>
> Follow @neuraustralia on twitter
> <https://twitter.com/neuraustralia>Follow NeuRA on facebook
> <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to
> the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe>
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/



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

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

End of Freesurfer Digest, Vol 128, Issue 26
*******************************************