[Freesurfer] DTI Paramters

[Peter J. Molfese]

Hello,

We're gearing up for a new study and planning to collect DTI data along with 
both functional and anatomical data.  Is there a particular protocol that 
Freesurfer (and Tracula) will work best with?  I found the suggested sequences 
for anatomical reconstruction, but didn't see any for DTI specifically.  

Also, any idea when version 5.1 will be out of beta?

Thanks,

Peter J. Molfese, Ph.D.
Postdoctoral Associate
Haskins Laboratories
300 George Street, Suite 900
New Haven, CT 06511
peter.molf...@yale.edu



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Re: [Freesurfer] No inflated brain...

[jim kroger]

Great idea, I didn't try this on the tutorial data set. Will let you know.
Jim



--
Cell: 575-571-8274
Email:  jkk...@gmail.com


On Wed, Apr 27, 2011 at 5:38 PM, Bruce Fischl wrote:

> so tksurfer has never worked for you on any dataset? Have you tried it on
> one of the ones that we distribute? If it hasn't worked, we'll need to know
> about your environment (what OS, what video card, are you running in a
> virtual box, etc...)
>
> cheers
> Bruce
>
>
> On Wed, 27 Apr 2011, jim kroger wrote:
>
>  No, I don't see anything, just black.
>> Thanks,
>> Jim
>>
>>
>>
>> --
>> Cell: 575-571-8274
>> Email:  jkk...@gmail.com
>>
>>
>>
>>
>>
>> On Wed, Apr 27, 2011 at 4:52 PM, Bruce Fischl > >wrote:
>>
>>  and do you see a hemisphere properly rendered or not?
>>>
>>>
>>> On Wed, 27 Apr 2011, jim kroger wrote:
>>>
>>>  Hi Bruce, this is my first attempt to see something in tksurfer. It's a
>>>
 step
 in the making edits to white matter. I will go through the tksurfer
 tutorial, but I noticed that when I start tksurfer, there may be an
 error.
 Here's the output, think this might be it? (I am using red hat on a 32
 gig
 Ram pretty fast machine, the drivers should be updated regularly along
 with
 all other updates)

 tksurfer heinrick rh inflated
 subject is heinrick
 hemiis rh
 surface is inflated
 surfer: current subjects dir: /usr/local/freesurfer/subjects/
 surfer: not in "scripts" dir ==> using cwd for session root
 surfer: session root data dir ($session) set to:
 surfer: /usr/local/freesurfer/subjects
 Reading image info (/usr/local/freesurfer/subjects//heinrick)
 Reading /usr/local/freesurfer/subjects//heinrick/mri/orig.mgz
 surfer: Reading header info from
 /usr/local/freesurfer/subjects//heinrick/mri/orig.mgz
 surfer: vertices=159373, faces=318742


 mrisReadTriangleFile(/usr/local/freesurfer/subjects//heinrick/surf/rh.sphere.reg):
 surface doesn't match
 /usr/local/freesurfer/subjects//heinrick/surf/rh.inflated

 mrisReadTriangleFile failed.

 surfer: single buffered window
 surfer: tkoInitWindow(heinrick)
 surfer: using interface /usr/local/freesurfer/lib/tcl/tksurfer.tcl
 Reading /usr/local/freesurfer/lib/tcl/tkm_common.tcl
 Reading /usr/local/freesurfer/lib/tcl/tkm_wrappers.tcl
 Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl
 Reading /usr/local/freesurfer/lib/tcl/tkUtils.tcl
 Successfully parsed tksurfer.tcl
 reading white matter vertex locations...


 --
 Cell: 575-571-8274
 Email:  jkk...@gmail.com



 On Mon, Apr 25, 2011 at 12:03 PM, Bruce Fischl
 wrote:

  is this in tksurfer? There have been issues with video card drivers, so

> make sure your's are up to date. Have you been able to view any
> surfaces
> in
> tksurfer?
>
>
> On Mon, 25 Apr 2011, jim kroger wrote:
>
>  HI Bruce, thanks so much for the reply. All of the surfaces we have
> needed
>
>  to view to fix the Talairach (was OK), white matter, etc., have been
>> there.
>> It's only when I tried to look at the inflated brain during the
>> WhiteMatterEdits
>> step that something seemed to be missing. I will look at tkmedit and
>> tkregister2 documentation to see if there are different ways to look
>> for
>> the
>> inflated brain, but if anybody has suggestions on why I'm seeing only
>> a
>> tiny
>> fraction it would be great. It sort of seems like a thresholding
>> issue,
>> but
>> I have no idea why on little 2 square inch or so section of cortex is
>> there
>> and the rest is not, or I can't see it. The edges of what I see are
>> very
>> sharp and defined.
>>
>> Jim
>>
>>
>>
>> On Sat, Apr 23, 2011 at 9:16 PM, Bruce Fischl <
>> fis...@nmr.mgh.harvard.edu
>>
>>  wrote:
>>>
>>>
>>  Hi Jim
>>
>>  Have you been able to view other surfaces in tksurfer? The situation
>>> you
>>> describe sounds normal except for the display issue (e.g. The
>>> thalamus
>>> should be interior to the white surface)
>>> Cheers
>>> Bruce
>>>
>>>
>>>
>>> On Apr 22, 2011, at 12:28 PM, jim kroger  wrote:
>>>
>>> Hello, I am following the sequence in the "FreeSurfer Troubleshooting
>>> Reconstruction Work Flow" instructions, and am at step 8,
>>> FsTutorial/WhiteMatterEdits. It looks like the thalamus and corpus
>>> callosum
>>> are included as white matter, and the pial surface surrounds some
>>> subcortical structures. Assuming this is not correct, I decided to
>>> look
>>> at
>>> the inflated surface as suggested in the referenced page " Making
>>> Edits
>>> to
>>> the White Matter." Unfortunately when I issue:
>>>
>>> tksurfer wm1_edits_before rh inflated
>>>
>>> I onl

Re: [Freesurfer] No inflated brain...

[Bruce Fischl]

so tksurfer has never worked for you on any dataset? Have you tried it on 
one of the ones that we distribute? If it hasn't worked, we'll need to know 
about your environment (what OS, what video card, are you running in a 
virtual box, etc...)

cheers
Bruce

On Wed, 27 Apr 2011, jim kroger wrote:

> No, I don't see anything, just black.
> Thanks,
> Jim
>
>
>
> --
> Cell: 575-571-8274
> Email:  jkk...@gmail.com
>
>
>
>
>
> On Wed, Apr 27, 2011 at 4:52 PM, Bruce Fischl 
> wrote:
>
>> and do you see a hemisphere properly rendered or not?
>>
>>
>> On Wed, 27 Apr 2011, jim kroger wrote:
>>
>>  Hi Bruce, this is my first attempt to see something in tksurfer. It's a
>>> step
>>> in the making edits to white matter. I will go through the tksurfer
>>> tutorial, but I noticed that when I start tksurfer, there may be an error.
>>> Here's the output, think this might be it? (I am using red hat on a 32 gig
>>> Ram pretty fast machine, the drivers should be updated regularly along
>>> with
>>> all other updates)
>>>
>>> tksurfer heinrick rh inflated
>>> subject is heinrick
>>> hemiis rh
>>> surface is inflated
>>> surfer: current subjects dir: /usr/local/freesurfer/subjects/
>>> surfer: not in "scripts" dir ==> using cwd for session root
>>> surfer: session root data dir ($session) set to:
>>> surfer: /usr/local/freesurfer/subjects
>>> Reading image info (/usr/local/freesurfer/subjects//heinrick)
>>> Reading /usr/local/freesurfer/subjects//heinrick/mri/orig.mgz
>>> surfer: Reading header info from
>>> /usr/local/freesurfer/subjects//heinrick/mri/orig.mgz
>>> surfer: vertices=159373, faces=318742
>>>
>>> mrisReadTriangleFile(/usr/local/freesurfer/subjects//heinrick/surf/rh.sphere.reg):
>>> surface doesn't match
>>> /usr/local/freesurfer/subjects//heinrick/surf/rh.inflated
>>>
>>> mrisReadTriangleFile failed.
>>>
>>> surfer: single buffered window
>>> surfer: tkoInitWindow(heinrick)
>>> surfer: using interface /usr/local/freesurfer/lib/tcl/tksurfer.tcl
>>> Reading /usr/local/freesurfer/lib/tcl/tkm_common.tcl
>>> Reading /usr/local/freesurfer/lib/tcl/tkm_wrappers.tcl
>>> Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl
>>> Reading /usr/local/freesurfer/lib/tcl/tkUtils.tcl
>>> Successfully parsed tksurfer.tcl
>>> reading white matter vertex locations...
>>>
>>>
>>> --
>>> Cell: 575-571-8274
>>> Email:  jkk...@gmail.com
>>>
>>>
>>>
>>> On Mon, Apr 25, 2011 at 12:03 PM, Bruce Fischl
>>> wrote:
>>>
>>>  is this in tksurfer? There have been issues with video card drivers, so
 make sure your's are up to date. Have you been able to view any surfaces
 in
 tksurfer?


 On Mon, 25 Apr 2011, jim kroger wrote:

  HI Bruce, thanks so much for the reply. All of the surfaces we have
 needed

> to view to fix the Talairach (was OK), white matter, etc., have been
> there.
> It's only when I tried to look at the inflated brain during the
> WhiteMatterEdits
> step that something seemed to be missing. I will look at tkmedit and
> tkregister2 documentation to see if there are different ways to look for
> the
> inflated brain, but if anybody has suggestions on why I'm seeing only a
> tiny
> fraction it would be great. It sort of seems like a thresholding issue,
> but
> I have no idea why on little 2 square inch or so section of cortex is
> there
> and the rest is not, or I can't see it. The edges of what I see are very
> sharp and defined.
>
> Jim
>
>
>
> On Sat, Apr 23, 2011 at 9:16 PM, Bruce Fischl <
> fis...@nmr.mgh.harvard.edu
>
>> wrote:
>>
>
>  Hi Jim
>
>> Have you been able to view other surfaces in tksurfer? The situation
>> you
>> describe sounds normal except for the display issue (e.g. The thalamus
>> should be interior to the white surface)
>> Cheers
>> Bruce
>>
>>
>>
>> On Apr 22, 2011, at 12:28 PM, jim kroger  wrote:
>>
>> Hello, I am following the sequence in the "FreeSurfer Troubleshooting
>> Reconstruction Work Flow" instructions, and am at step 8,
>> FsTutorial/WhiteMatterEdits. It looks like the thalamus and corpus
>> callosum
>> are included as white matter, and the pial surface surrounds some
>> subcortical structures. Assuming this is not correct, I decided to look
>> at
>> the inflated surface as suggested in the referenced page " Making Edits
>> to
>> the White Matter." Unfortunately when I issue:
>>
>> tksurfer wm1_edits_before rh inflated
>>
>> I only see what looks like a very small fraction of an egg shell for
>> the
>> rh, and nothing for lh. Can I check somehow to see why I have almost no
>> inflated brain?
>>
>> Thanks,
>> Jim
>>
>>
>> --
>> Cell: 575-571-8274
>> Email:  jkk...@gmail.com
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@n

Re: [Freesurfer] No inflated brain...

[jim kroger]

No, I don't see anything, just black.
Thanks,
Jim



--
Cell: 575-571-8274
Email:  jkk...@gmail.com





On Wed, Apr 27, 2011 at 4:52 PM, Bruce Fischl wrote:

> and do you see a hemisphere properly rendered or not?
>
>
> On Wed, 27 Apr 2011, jim kroger wrote:
>
>  Hi Bruce, this is my first attempt to see something in tksurfer. It's a
>> step
>> in the making edits to white matter. I will go through the tksurfer
>> tutorial, but I noticed that when I start tksurfer, there may be an error.
>> Here's the output, think this might be it? (I am using red hat on a 32 gig
>> Ram pretty fast machine, the drivers should be updated regularly along
>> with
>> all other updates)
>>
>> tksurfer heinrick rh inflated
>> subject is heinrick
>> hemiis rh
>> surface is inflated
>> surfer: current subjects dir: /usr/local/freesurfer/subjects/
>> surfer: not in "scripts" dir ==> using cwd for session root
>> surfer: session root data dir ($session) set to:
>> surfer: /usr/local/freesurfer/subjects
>> Reading image info (/usr/local/freesurfer/subjects//heinrick)
>> Reading /usr/local/freesurfer/subjects//heinrick/mri/orig.mgz
>> surfer: Reading header info from
>> /usr/local/freesurfer/subjects//heinrick/mri/orig.mgz
>> surfer: vertices=159373, faces=318742
>>
>> mrisReadTriangleFile(/usr/local/freesurfer/subjects//heinrick/surf/rh.sphere.reg):
>> surface doesn't match
>> /usr/local/freesurfer/subjects//heinrick/surf/rh.inflated
>>
>> mrisReadTriangleFile failed.
>>
>> surfer: single buffered window
>> surfer: tkoInitWindow(heinrick)
>> surfer: using interface /usr/local/freesurfer/lib/tcl/tksurfer.tcl
>> Reading /usr/local/freesurfer/lib/tcl/tkm_common.tcl
>> Reading /usr/local/freesurfer/lib/tcl/tkm_wrappers.tcl
>> Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl
>> Reading /usr/local/freesurfer/lib/tcl/tkUtils.tcl
>> Successfully parsed tksurfer.tcl
>> reading white matter vertex locations...
>>
>>
>> --
>> Cell: 575-571-8274
>> Email:  jkk...@gmail.com
>>
>>
>>
>> On Mon, Apr 25, 2011 at 12:03 PM, Bruce Fischl
>> wrote:
>>
>>  is this in tksurfer? There have been issues with video card drivers, so
>>> make sure your's are up to date. Have you been able to view any surfaces
>>> in
>>> tksurfer?
>>>
>>>
>>> On Mon, 25 Apr 2011, jim kroger wrote:
>>>
>>>  HI Bruce, thanks so much for the reply. All of the surfaces we have
>>> needed
>>>
 to view to fix the Talairach (was OK), white matter, etc., have been
 there.
 It's only when I tried to look at the inflated brain during the
 WhiteMatterEdits
 step that something seemed to be missing. I will look at tkmedit and
 tkregister2 documentation to see if there are different ways to look for
 the
 inflated brain, but if anybody has suggestions on why I'm seeing only a
 tiny
 fraction it would be great. It sort of seems like a thresholding issue,
 but
 I have no idea why on little 2 square inch or so section of cortex is
 there
 and the rest is not, or I can't see it. The edges of what I see are very
 sharp and defined.

 Jim



 On Sat, Apr 23, 2011 at 9:16 PM, Bruce Fischl <
 fis...@nmr.mgh.harvard.edu

> wrote:
>

  Hi Jim

> Have you been able to view other surfaces in tksurfer? The situation
> you
> describe sounds normal except for the display issue (e.g. The thalamus
> should be interior to the white surface)
> Cheers
> Bruce
>
>
>
> On Apr 22, 2011, at 12:28 PM, jim kroger  wrote:
>
> Hello, I am following the sequence in the "FreeSurfer Troubleshooting
> Reconstruction Work Flow" instructions, and am at step 8,
> FsTutorial/WhiteMatterEdits. It looks like the thalamus and corpus
> callosum
> are included as white matter, and the pial surface surrounds some
> subcortical structures. Assuming this is not correct, I decided to look
> at
> the inflated surface as suggested in the referenced page " Making Edits
> to
> the White Matter." Unfortunately when I issue:
>
> tksurfer wm1_edits_before rh inflated
>
> I only see what looks like a very small fraction of an egg shell for
> the
> rh, and nothing for lh. Can I check somehow to see why I have almost no
> inflated brain?
>
> Thanks,
> Jim
>
>
> --
> Cell: 575-571-8274
> Email:  jkk...@gmail.com
>
>
>
> ___
> 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
>>

Re: [Freesurfer] No inflated brain...

[Bruce Fischl]

and do you see a hemisphere properly rendered or not?

On Wed, 27 Apr 2011, jim kroger wrote:

> Hi Bruce, this is my first attempt to see something in tksurfer. It's a step
> in the making edits to white matter. I will go through the tksurfer
> tutorial, but I noticed that when I start tksurfer, there may be an error.
> Here's the output, think this might be it? (I am using red hat on a 32 gig
> Ram pretty fast machine, the drivers should be updated regularly along with
> all other updates)
>
> tksurfer heinrick rh inflated
> subject is heinrick
> hemiis rh
> surface is inflated
> surfer: current subjects dir: /usr/local/freesurfer/subjects/
> surfer: not in "scripts" dir ==> using cwd for session root
> surfer: session root data dir ($session) set to:
> surfer: /usr/local/freesurfer/subjects
> Reading image info (/usr/local/freesurfer/subjects//heinrick)
> Reading /usr/local/freesurfer/subjects//heinrick/mri/orig.mgz
> surfer: Reading header info from
> /usr/local/freesurfer/subjects//heinrick/mri/orig.mgz
> surfer: vertices=159373, faces=318742
> mrisReadTriangleFile(/usr/local/freesurfer/subjects//heinrick/surf/rh.sphere.reg):
> surface doesn't match
> /usr/local/freesurfer/subjects//heinrick/surf/rh.inflated
>
> mrisReadTriangleFile failed.
>
> surfer: single buffered window
> surfer: tkoInitWindow(heinrick)
> surfer: using interface /usr/local/freesurfer/lib/tcl/tksurfer.tcl
> Reading /usr/local/freesurfer/lib/tcl/tkm_common.tcl
> Reading /usr/local/freesurfer/lib/tcl/tkm_wrappers.tcl
> Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl
> Reading /usr/local/freesurfer/lib/tcl/tkUtils.tcl
> Successfully parsed tksurfer.tcl
> reading white matter vertex locations...
>
>
> --
> Cell: 575-571-8274
> Email:  jkk...@gmail.com
>
>
>
> On Mon, Apr 25, 2011 at 12:03 PM, Bruce Fischl
> wrote:
>
>> is this in tksurfer? There have been issues with video card drivers, so
>> make sure your's are up to date. Have you been able to view any surfaces in
>> tksurfer?
>>
>>
>> On Mon, 25 Apr 2011, jim kroger wrote:
>>
>>  HI Bruce, thanks so much for the reply. All of the surfaces we have needed
>>> to view to fix the Talairach (was OK), white matter, etc., have been
>>> there.
>>> It's only when I tried to look at the inflated brain during the
>>> WhiteMatterEdits
>>> step that something seemed to be missing. I will look at tkmedit and
>>> tkregister2 documentation to see if there are different ways to look for
>>> the
>>> inflated brain, but if anybody has suggestions on why I'm seeing only a
>>> tiny
>>> fraction it would be great. It sort of seems like a thresholding issue,
>>> but
>>> I have no idea why on little 2 square inch or so section of cortex is
>>> there
>>> and the rest is not, or I can't see it. The edges of what I see are very
>>> sharp and defined.
>>>
>>> Jim
>>>
>>>
>>>
>>> On Sat, Apr 23, 2011 at 9:16 PM, Bruce Fischl >>> wrote:
>>>
>>>  Hi Jim
 Have you been able to view other surfaces in tksurfer? The situation you
 describe sounds normal except for the display issue (e.g. The thalamus
 should be interior to the white surface)
 Cheers
 Bruce



 On Apr 22, 2011, at 12:28 PM, jim kroger  wrote:

 Hello, I am following the sequence in the "FreeSurfer Troubleshooting
 Reconstruction Work Flow" instructions, and am at step 8,
 FsTutorial/WhiteMatterEdits. It looks like the thalamus and corpus
 callosum
 are included as white matter, and the pial surface surrounds some
 subcortical structures. Assuming this is not correct, I decided to look
 at
 the inflated surface as suggested in the referenced page " Making Edits
 to
 the White Matter." Unfortunately when I issue:

 tksurfer wm1_edits_before rh inflated

 I only see what looks like a very small fraction of an egg shell for the
 rh, and nothing for lh. Can I check somehow to see why I have almost no
 inflated brain?

 Thanks,
 Jim


 --
 Cell: 575-571-8274
 Email:  jkk...@gmail.com



 ___
 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

Re: [Freesurfer] No inflated brain...

[jim kroger]

Hi Bruce, this is my first attempt to see something in tksurfer. It's a step
in the making edits to white matter. I will go through the tksurfer
tutorial, but I noticed that when I start tksurfer, there may be an error.
Here's the output, think this might be it? (I am using red hat on a 32 gig
Ram pretty fast machine, the drivers should be updated regularly along with
all other updates)

 tksurfer heinrick rh inflated
subject is heinrick
hemiis rh
surface is inflated
surfer: current subjects dir: /usr/local/freesurfer/subjects/
surfer: not in "scripts" dir ==> using cwd for session root
surfer: session root data dir ($session) set to:
surfer: /usr/local/freesurfer/subjects
Reading image info (/usr/local/freesurfer/subjects//heinrick)
Reading /usr/local/freesurfer/subjects//heinrick/mri/orig.mgz
surfer: Reading header info from
/usr/local/freesurfer/subjects//heinrick/mri/orig.mgz
surfer: vertices=159373, faces=318742
mrisReadTriangleFile(/usr/local/freesurfer/subjects//heinrick/surf/rh.sphere.reg):
surface doesn't match
/usr/local/freesurfer/subjects//heinrick/surf/rh.inflated

mrisReadTriangleFile failed.

surfer: single buffered window
surfer: tkoInitWindow(heinrick)
surfer: using interface /usr/local/freesurfer/lib/tcl/tksurfer.tcl
Reading /usr/local/freesurfer/lib/tcl/tkm_common.tcl
Reading /usr/local/freesurfer/lib/tcl/tkm_wrappers.tcl
Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl
Reading /usr/local/freesurfer/lib/tcl/tkUtils.tcl
Successfully parsed tksurfer.tcl
reading white matter vertex locations...


--
Cell: 575-571-8274
Email:  jkk...@gmail.com



On Mon, Apr 25, 2011 at 12:03 PM, Bruce Fischl
wrote:

> is this in tksurfer? There have been issues with video card drivers, so
> make sure your's are up to date. Have you been able to view any surfaces in
> tksurfer?
>
>
> On Mon, 25 Apr 2011, jim kroger wrote:
>
>  HI Bruce, thanks so much for the reply. All of the surfaces we have needed
>> to view to fix the Talairach (was OK), white matter, etc., have been
>> there.
>> It's only when I tried to look at the inflated brain during the
>> WhiteMatterEdits
>> step that something seemed to be missing. I will look at tkmedit and
>> tkregister2 documentation to see if there are different ways to look for
>> the
>> inflated brain, but if anybody has suggestions on why I'm seeing only a
>> tiny
>> fraction it would be great. It sort of seems like a thresholding issue,
>> but
>> I have no idea why on little 2 square inch or so section of cortex is
>> there
>> and the rest is not, or I can't see it. The edges of what I see are very
>> sharp and defined.
>>
>> Jim
>>
>>
>>
>> On Sat, Apr 23, 2011 at 9:16 PM, Bruce Fischl > >wrote:
>>
>>  Hi Jim
>>> Have you been able to view other surfaces in tksurfer? The situation you
>>> describe sounds normal except for the display issue (e.g. The thalamus
>>> should be interior to the white surface)
>>> Cheers
>>> Bruce
>>>
>>>
>>>
>>> On Apr 22, 2011, at 12:28 PM, jim kroger  wrote:
>>>
>>> Hello, I am following the sequence in the "FreeSurfer Troubleshooting
>>> Reconstruction Work Flow" instructions, and am at step 8,
>>> FsTutorial/WhiteMatterEdits. It looks like the thalamus and corpus
>>> callosum
>>> are included as white matter, and the pial surface surrounds some
>>> subcortical structures. Assuming this is not correct, I decided to look
>>> at
>>> the inflated surface as suggested in the referenced page " Making Edits
>>> to
>>> the White Matter." Unfortunately when I issue:
>>>
>>> tksurfer wm1_edits_before rh inflated
>>>
>>> I only see what looks like a very small fraction of an egg shell for the
>>> rh, and nothing for lh. Can I check somehow to see why I have almost no
>>> inflated brain?
>>>
>>> Thanks,
>>> Jim
>>>
>>>
>>> --
>>> Cell: 575-571-8274
>>> Email:  jkk...@gmail.com
>>>
>>>
>>>
>>> ___
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>>> is
>>> addressed. If you believe this e-mail was sent to you in error and the
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>>> contains patient information, please contact the Partners Compliance
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Re: [Freesurfer] Unknown label in Parcellation

[Christophe Destrieux]

that's right

-- 
Christophe Destrieux, 

Directeur du Département Communication et Multimedia 
http://med.univ-tours.fr/M0S01/0/fiche___defaultstructureksup/&RH=1200651159612 

Unité « Imagerie et Cerveau » UMRS INSERM U930, CNRS ERL 3106, Université 
François Rabelais de Tours 
http://www.u930.tours.inserm.fr/ 

Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé 
37032 Tours - France 
tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07 


- Mail original -
> De: "Bruce Fischl" 
> À: "Pedro Paulo de Magalhães Oliveira Junior" 
> Cc: "Freesurfer Mailing List" 
> Envoyé: Mercredi 27 Avril 2011 21:57:01
> Objet: Re: [Freesurfer] Unknown label in Parcellation
> I think unknown is the medial wall area that is non-cortical, so
> should
> be ignored
> Bruce
> On Wed, 27 Apr 2011, Pedro Paulo de Magalhães Oliveira Junior
> wrote:
> 
> > lh.aparc.stats
> >
> > 2011/4/27 Bruce Fischl 
> >
> >> which parcellation are you using?
> >>
> >>
> >> On Wed, 27 Apr 2011, Pedro Paulo de Magalhães Oliveira Junior
> >> wrote:
> >>
> >>  In one study we are conducting we found significant difference in
> >>  cortical
> >>> thickness between the two groups in some areas. One of those areas
> >>> are
> >>> lh_unknown.
> >>>
> >>> Is this an error or it's a still unlabelled area?
> >>>
> >>> thanks
> >>>
> >>> Pedro Paulo Jr
> >>>
> >>>
> >>
> >> The information in this e-mail is intended only for the person to
> >> whom it
> >> is
> >> addressed. If you believe this e-mail was sent to you in error and
> >> the
> >> e-mail
> >> contains patient information, please contact the Partners
> >> Compliance
> >> HelpLine at
> >> http://www.partners.org/complianceline . If the e-mail was sent to
> >> you in
> >> error
> >> but does not contain patient information, please contact the sender
> >> and
> >> properly
> >> dispose of the e-mail.
> >>
> >
> ___
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> 
> 
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> it is
> addressed. If you believe this e-mail was sent to you in error and the
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Re: [Freesurfer] Unknown label in Parcellation

[Bruce Fischl]

I think unknown is the medial wall area that is non-cortical, so should 
be ignored

Bruce
On Wed, 27 Apr 2011, Pedro Paulo de Magalhães Oliveira Junior 
wrote:



lh.aparc.stats

2011/4/27 Bruce Fischl 


which parcellation are you using?


On Wed, 27 Apr 2011, Pedro Paulo de Magalhães Oliveira Junior wrote:

 In one study we are conducting we found significant difference in cortical

thickness between the two groups in some areas. One of those areas are
lh_unknown.

Is this an error or it's a still unlabelled area?

thanks

Pedro Paulo Jr




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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error
but does not contain patient information, please contact the sender and
properly
dispose of the e-mail.

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Re: [Freesurfer] Unknown label in Parcellation

[Pedro Paulo de Magalhães Oliveira Junior]

lh.aparc.stats

2011/4/27 Bruce Fischl 

> which parcellation are you using?
>
>
> On Wed, 27 Apr 2011, Pedro Paulo de Magalhães Oliveira Junior wrote:
>
>  In one study we are conducting we found significant difference in cortical
>> thickness between the two groups in some areas. One of those areas are
>> lh_unknown.
>>
>> Is this an error or it's a still unlabelled area?
>>
>> thanks
>>
>> Pedro Paulo Jr
>>
>>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
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Re: [Freesurfer] Unknown label in Parcellation

[Bruce Fischl]

which parcellation are you using?

On Wed, 27 Apr 2011, Pedro Paulo de Magalhães Oliveira 
Junior wrote:



In one study we are conducting we found significant difference in cortical
thickness between the two groups in some areas. One of those areas are
lh_unknown.

Is this an error or it's a still unlabelled area?

thanks

Pedro Paulo Jr
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[Freesurfer] Unknown label in Parcellation

[Pedro Paulo de Magalhães Oliveira Junior]

In one study we are conducting we found significant difference in cortical
thickness between the two groups in some areas. One of those areas are
lh_unknown.

Is this an error or it's a still unlabelled area?

thanks

Pedro Paulo Jr
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dispose of the e-mail.

Re: [Freesurfer] Interpreting results from Qdec

[Gallen, Courtney (NIH/NIDA) [F]]

Thanks Jesse. This does sound very similar to my issue.

How did you resolve the problem?

Thanks again!

From: jessebled...@gmail.com [mailto:jessebled...@gmail.com] On Behalf Of Jesse 
Bledsoe
Sent: Wednesday, April 27, 2011 1:19 PM
To: Gallen, Courtney (NIH/NIDA) [F]; Freesurfer Mailing List
Subject: Re: [Freesurfer] Interpreting results from Qdec

Hi Courtney,

I'm no expert but I recalled a post similar to yours awhile ago with the same 
question you ask. Doug and Nick offered an answer that may be of help:

http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15586.html

Jesse
On Wed, Apr 27, 2011 at 1:12 PM, Gallen, Courtney (NIH/NIDA) [F] 
mailto:galle...@nida.nih.gov>> wrote:
Hi Doug

Have a follow up question regarding significance levels in Qdec related to 
extracting means from ROIs, etc. I'm posting to the entire mailing list in case 
anyone else has ideas.

Basically, I extracted mean volumes (from my set of participants) of ROIs for 
which Qdec reports an interaction between two variables. I want to look at 
these mean volumes in something like SPSS to see what is driving the 
interaction/generate figures, etc.

I'm having an issue with one such ROI, in that when I extract the mean volumes 
and look for this interaction in SPSS, it is not significant (p ~ 0.5, so 
really not significant at all). Is there any way that an ROI could be 
significant in Qdec (p of 0.05, Monte Carlo sim), but not in SPSS when I 
extract means for each participant?

Let me know if this isn't clear. Any thoughts would be appreciated!
Courtney


Courtney Gallen
Post-baccalaureate IRTA
Neuroimaging Research Branch
National Institute on Drug Abuse (IRP)
251 Bayview Blvd
Suite 200
Baltimore, MD 21224
Tel: (443) 740-2631

-Original Message-
From: Douglas Greve 
[mailto:gr...@nmr.mgh.harvard.edu]
Sent: Tuesday, April 26, 2011 1:06 PM
To: Gallen, Courtney (NIH/NIDA) [F]
Subject: Re: [Freesurfer] Interpreting results from Qdec

Those are the values outside (first column) and inside (2nd col) the
ROI. You can add "--id 1" to only report the values inside the ROI.

doug

On 4/26/11 1:02 PM, Gallen, Courtney (NIH/NIDA) [F] wrote:
> It worked!
> Now, last question. The txt file has two separate values (?averages). What do 
> they each represent?
>
> -Original Message-
> From: Douglas Greve 
> [mailto:gr...@nmr.mgh.harvard.edu]
> Sent: Tuesday, April 26, 2011 12:53 PM
> To: Gallen, Courtney (NIH/NIDA) [F]
> Subject: Re: [Freesurfer] Interpreting results from Qdec
>
> try "--slabel fsaverage lh ROI-drawn-on-QDEC-brain.label"
>
>
> On 4/26/11 12:52 PM, Gallen, Courtney (NIH/NIDA) [F] wrote:
>> Actually, I hope I'm wrong about what I thought below. If I specify 
>> individual subject's label and run:
>>
>> mri_segstats --in 
>> /prot/Mprot/CTQ/freesurferDone/8579/surf/lh.volume.fwhm10.fsaverage.mgh 
>> --slabel 8579 lh 
>> /prot/Mprot/CTQ/freesurferDone/8579/label/lh.SupTemp_CTQxBDNFctrls.label 
>> --avgwf lhSupTempctrls.txt
>>
>> I still get the same error about dimension mismatch
>>
>>
>> -Original Message-
>> From: Gallen, Courtney (NIH/NIDA) [F]
>> Sent: Tuesday, April 26, 2011 12:43 PM
>> To: 'Douglas Greve'
>> Subject: RE: [Freesurfer] Interpreting results from Qdec
>>
>> Ah I think I see the problem now.
>>
>> The label I originally specified is the general label created from the ROI 
>> drawing in Qdec. Instead, I should use the individual subject's label (from 
>> 'Map Label to Subjects') instead, right?
>>
>> Thank you!
>>
>> -Original Message-
>> From: Douglas Greve 
>> [mailto:gr...@nmr.mgh.harvard.edu]
>> Sent: Tuesday, April 26, 2011 12:38 PM
>> To: Gallen, Courtney (NIH/NIDA) [F]
>> Subject: Re: [Freesurfer] Interpreting results from Qdec
>>
>> You have to use the subject that matches the input, fsaverage in this
>> case. How did you define your label? If you defined it on subject 123,
>> you can transfer it to fsaverage using mri_label2label.
>> doug
>>
>> On 4/26/11 12:28 PM, Gallen, Courtney (NIH/NIDA) [F] wrote:
>>> Not a problem at all!
>>>
>>> If I use --in, I get an error saying that there is a dimension mismatch 
>>> between input volume and seg.
>>>
>>> Any other thoughts? Thanks again!
>>>
>>> -Original Message-
>>> From: Douglas Greve 
>>> [mailto:gr...@nmr.mgh.harvard.edu]
>>> Sent: Tuesday, April 26, 2011 11:40 AM
>>> To: Gallen, Courtney (NIH/NIDA) [F]
>>> Subject: Re: [Freesurfer] Interpreting results from Qdec
>>>
>>>
>>> Hi Courtney, sorry for the delay. If more than a few days go by without
>>> a response, feel free to repost -- I promise not to get annoyed!
>>> Sometimes, things get pushed up and out of my mail browser window, and I
>>> often don't get back to them. Sorry!
>>>
>>> To answer your question, try using --in where you have --seg. The
>>> "segmentation" is actually already specified because you've specifie

Re: [Freesurfer] Interpreting results from Qdec

[Jesse Bledsoe]

Hi Courtney,

I'm no expert but I recalled a post similar to yours awhile ago with the
same question you ask. Doug and Nick offered an answer that may be of help:

http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15586.html

Jesse

On Wed, Apr 27, 2011 at 1:12 PM, Gallen, Courtney (NIH/NIDA) [F] <
galle...@nida.nih.gov> wrote:

> Hi Doug
>
> Have a follow up question regarding significance levels in Qdec related to
> extracting means from ROIs, etc. I'm posting to the entire mailing list in
> case anyone else has ideas.
>
> Basically, I extracted mean volumes (from my set of participants) of ROIs
> for which Qdec reports an interaction between two variables. I want to look
> at these mean volumes in something like SPSS to see what is driving the
> interaction/generate figures, etc.
>
> I'm having an issue with one such ROI, in that when I extract the mean
> volumes and look for this interaction in SPSS, it is not significant (p ~
> 0.5, so really not significant at all). Is there any way that an ROI could
> be significant in Qdec (p of 0.05, Monte Carlo sim), but not in SPSS when I
> extract means for each participant?
>
> Let me know if this isn't clear. Any thoughts would be appreciated!
> Courtney
>
>
> Courtney Gallen
> Post-baccalaureate IRTA
> Neuroimaging Research Branch
> National Institute on Drug Abuse (IRP)
> 251 Bayview Blvd
> Suite 200
> Baltimore, MD 21224
> Tel: (443) 740-2631
>
> -Original Message-
> From: Douglas Greve [mailto:gr...@nmr.mgh.harvard.edu]
> Sent: Tuesday, April 26, 2011 1:06 PM
> To: Gallen, Courtney (NIH/NIDA) [F]
> Subject: Re: [Freesurfer] Interpreting results from Qdec
>
> Those are the values outside (first column) and inside (2nd col) the
> ROI. You can add "--id 1" to only report the values inside the ROI.
>
> doug
>
> On 4/26/11 1:02 PM, Gallen, Courtney (NIH/NIDA) [F] wrote:
> > It worked!
> > Now, last question. The txt file has two separate values (?averages).
> What do they each represent?
> >
> > -Original Message-
> > From: Douglas Greve [mailto:gr...@nmr.mgh.harvard.edu]
> > Sent: Tuesday, April 26, 2011 12:53 PM
> > To: Gallen, Courtney (NIH/NIDA) [F]
> > Subject: Re: [Freesurfer] Interpreting results from Qdec
> >
> > try "--slabel fsaverage lh ROI-drawn-on-QDEC-brain.label"
> >
> >
> > On 4/26/11 12:52 PM, Gallen, Courtney (NIH/NIDA) [F] wrote:
> >> Actually, I hope I'm wrong about what I thought below. If I specify
> individual subject's label and run:
> >>
> >> mri_segstats --in
> /prot/Mprot/CTQ/freesurferDone/8579/surf/lh.volume.fwhm10.fsaverage.mgh
> --slabel 8579 lh
> /prot/Mprot/CTQ/freesurferDone/8579/label/lh.SupTemp_CTQxBDNFctrls.label
> --avgwf lhSupTempctrls.txt
> >>
> >> I still get the same error about dimension mismatch
> >>
> >>
> >> -Original Message-
> >> From: Gallen, Courtney (NIH/NIDA) [F]
> >> Sent: Tuesday, April 26, 2011 12:43 PM
> >> To: 'Douglas Greve'
> >> Subject: RE: [Freesurfer] Interpreting results from Qdec
> >>
> >> Ah I think I see the problem now.
> >>
> >> The label I originally specified is the general label created from the
> ROI drawing in Qdec. Instead, I should use the individual subject's label
> (from 'Map Label to Subjects') instead, right?
> >>
> >> Thank you!
> >>
> >> -Original Message-
> >> From: Douglas Greve [mailto:gr...@nmr.mgh.harvard.edu]
> >> Sent: Tuesday, April 26, 2011 12:38 PM
> >> To: Gallen, Courtney (NIH/NIDA) [F]
> >> Subject: Re: [Freesurfer] Interpreting results from Qdec
> >>
> >> You have to use the subject that matches the input, fsaverage in this
> >> case. How did you define your label? If you defined it on subject 123,
> >> you can transfer it to fsaverage using mri_label2label.
> >> doug
> >>
> >> On 4/26/11 12:28 PM, Gallen, Courtney (NIH/NIDA) [F] wrote:
> >>> Not a problem at all!
> >>>
> >>> If I use --in, I get an error saying that there is a dimension mismatch
> between input volume and seg.
> >>>
> >>> Any other thoughts? Thanks again!
> >>>
> >>> -Original Message-
> >>> From: Douglas Greve [mailto:gr...@nmr.mgh.harvard.edu]
> >>> Sent: Tuesday, April 26, 2011 11:40 AM
> >>> To: Gallen, Courtney (NIH/NIDA) [F]
> >>> Subject: Re: [Freesurfer] Interpreting results from Qdec
> >>>
> >>>
> >>> Hi Courtney, sorry for the delay. If more than a few days go by without
> >>> a response, feel free to repost -- I promise not to get annoyed!
> >>> Sometimes, things get pushed up and out of my mail browser window, and
> I
> >>> often don't get back to them. Sorry!
> >>>
> >>> To answer your question, try using --in where you have --seg. The
> >>> "segmentation" is actually already specified because you've specified a
> >>> label.
> >>>
> >>> doug
> >>>
> >>> On 4/26/11 11:03 AM, Gallen, Courtney (NIH/NIDA) [F] wrote:
>  Hi Doug,
>  Sorry to keep bugging you but any thoughts about my response to your
> e-mail from 2 weeks ago? I've given the exact command line I'm using with
> mri_segstats.
>  Thanks again for all your help
> >>

Re: [Freesurfer] Interpreting results from Qdec

[Gallen, Courtney (NIH/NIDA) [F]]

Hi Doug

Have a follow up question regarding significance levels in Qdec related to 
extracting means from ROIs, etc. I'm posting to the entire mailing list in case 
anyone else has ideas.

Basically, I extracted mean volumes (from my set of participants) of ROIs for 
which Qdec reports an interaction between two variables. I want to look at 
these mean volumes in something like SPSS to see what is driving the 
interaction/generate figures, etc.

I'm having an issue with one such ROI, in that when I extract the mean volumes 
and look for this interaction in SPSS, it is not significant (p ~ 0.5, so 
really not significant at all). Is there any way that an ROI could be 
significant in Qdec (p of 0.05, Monte Carlo sim), but not in SPSS when I 
extract means for each participant?

Let me know if this isn't clear. Any thoughts would be appreciated!
Courtney


Courtney Gallen
Post-baccalaureate IRTA
Neuroimaging Research Branch
National Institute on Drug Abuse (IRP)
251 Bayview Blvd
Suite 200
Baltimore, MD 21224
Tel: (443) 740-2631

-Original Message-
From: Douglas Greve [mailto:gr...@nmr.mgh.harvard.edu]
Sent: Tuesday, April 26, 2011 1:06 PM
To: Gallen, Courtney (NIH/NIDA) [F]
Subject: Re: [Freesurfer] Interpreting results from Qdec

Those are the values outside (first column) and inside (2nd col) the
ROI. You can add "--id 1" to only report the values inside the ROI.

doug

On 4/26/11 1:02 PM, Gallen, Courtney (NIH/NIDA) [F] wrote:
> It worked!
> Now, last question. The txt file has two separate values (?averages). What do 
> they each represent?
>
> -Original Message-
> From: Douglas Greve [mailto:gr...@nmr.mgh.harvard.edu]
> Sent: Tuesday, April 26, 2011 12:53 PM
> To: Gallen, Courtney (NIH/NIDA) [F]
> Subject: Re: [Freesurfer] Interpreting results from Qdec
>
> try "--slabel fsaverage lh ROI-drawn-on-QDEC-brain.label"
>
>
> On 4/26/11 12:52 PM, Gallen, Courtney (NIH/NIDA) [F] wrote:
>> Actually, I hope I'm wrong about what I thought below. If I specify 
>> individual subject's label and run:
>>
>> mri_segstats --in 
>> /prot/Mprot/CTQ/freesurferDone/8579/surf/lh.volume.fwhm10.fsaverage.mgh 
>> --slabel 8579 lh 
>> /prot/Mprot/CTQ/freesurferDone/8579/label/lh.SupTemp_CTQxBDNFctrls.label 
>> --avgwf lhSupTempctrls.txt
>>
>> I still get the same error about dimension mismatch
>>
>>
>> -Original Message-
>> From: Gallen, Courtney (NIH/NIDA) [F]
>> Sent: Tuesday, April 26, 2011 12:43 PM
>> To: 'Douglas Greve'
>> Subject: RE: [Freesurfer] Interpreting results from Qdec
>>
>> Ah I think I see the problem now.
>>
>> The label I originally specified is the general label created from the ROI 
>> drawing in Qdec. Instead, I should use the individual subject's label (from 
>> 'Map Label to Subjects') instead, right?
>>
>> Thank you!
>>
>> -Original Message-
>> From: Douglas Greve [mailto:gr...@nmr.mgh.harvard.edu]
>> Sent: Tuesday, April 26, 2011 12:38 PM
>> To: Gallen, Courtney (NIH/NIDA) [F]
>> Subject: Re: [Freesurfer] Interpreting results from Qdec
>>
>> You have to use the subject that matches the input, fsaverage in this
>> case. How did you define your label? If you defined it on subject 123,
>> you can transfer it to fsaverage using mri_label2label.
>> doug
>>
>> On 4/26/11 12:28 PM, Gallen, Courtney (NIH/NIDA) [F] wrote:
>>> Not a problem at all!
>>>
>>> If I use --in, I get an error saying that there is a dimension mismatch 
>>> between input volume and seg.
>>>
>>> Any other thoughts? Thanks again!
>>>
>>> -Original Message-
>>> From: Douglas Greve [mailto:gr...@nmr.mgh.harvard.edu]
>>> Sent: Tuesday, April 26, 2011 11:40 AM
>>> To: Gallen, Courtney (NIH/NIDA) [F]
>>> Subject: Re: [Freesurfer] Interpreting results from Qdec
>>>
>>>
>>> Hi Courtney, sorry for the delay. If more than a few days go by without
>>> a response, feel free to repost -- I promise not to get annoyed!
>>> Sometimes, things get pushed up and out of my mail browser window, and I
>>> often don't get back to them. Sorry!
>>>
>>> To answer your question, try using --in where you have --seg. The
>>> "segmentation" is actually already specified because you've specified a
>>> label.
>>>
>>> doug
>>>
>>> On 4/26/11 11:03 AM, Gallen, Courtney (NIH/NIDA) [F] wrote:
 Hi Doug,
 Sorry to keep bugging you but any thoughts about my response to your 
 e-mail from 2 weeks ago? I've given the exact command line I'm using with 
 mri_segstats.
 Thanks again for all your help
 Courtney

 -Original Message-
 From: Gallen, Courtney (NIH/NIDA) [F]
 Sent: Tuesday, April 12, 2011 10:59 AM
 To: 'Douglas N Greve'
 Subject: RE: [Freesurfer] Interpreting results from Qdec

 That may be the problem. ${sub} is an actual person's directory

 E.g., sub# 123--command line would be:
 mri_segstats --seg 
 /prot/Mprot/CTQ/freesurferDone/123/surf/lh.volume.fwhm10.fsaverage.mgh 
 --slabel 123 lh \
 lh.SupTemp_CTQxBDNFctrls.label --avgwf lhSupTempctrl

Re: [Freesurfer] about mri_vol2surf

[greve]

>
> Hi Doug:
>
>  When you talk about zero out subcortical region, when does this zero
> out happen? it should happen after register vertex into functional
> space, right? Then it happens before functional space interpolation
> or after interpolation?

It happens after interpolation.

>
>  And one more question about the register.dat file used for this
> process. whose resolution info is used in register.dat file ? the low
> resolution functional image (moving image) or high resolution anatomy
> image?  Is the resolution of fsaverage is 2mm*2mm*0.15mm?

The low resolution (though those numbers are no longer used internally --
the resolution is obtained from the mov volume).

doug

>
> Thanks much!
>
> Jing
>
> Date: Tue, 26 Apr 2011 17:11:45 -0400
> From: gr...@nmr.mgh.harvard.edu
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] about mri_vol2surf
>
>
>
>
>
>
>
>
>
> Hi Jing, by default it does include all the non-cortical structures
> in the medial wall, including any subcortical structures. If you
> include --cortex in the command-line it zeros them out. The way it
> works is that it goes through each vertex on the surface, gets the
> RAS coordinate for that vertex, applies the registration matrix to
> map it into the function space, then samples the function value
> using nearest neighbor (can change to trilinear with --interp
> trilin).
>
>
>
> doug
>
>
>
> On 4/26/11 1:51 PM, Jing Ming wrote:
>
>
>   Hi Surfers:
>
>
>
> I am using mri_vol2surf to project fMRI result into the
>   fsaverage surface. And the fMRI result may contain some
>   subcortical regions, so, I wonder mri_vol2surf will automatically
>   get rid of the subcortical region and only map cortical area into
>   surface right? Is there any material about the mapping algorithm
>   of mri_vol2surf? Thanks much!
>
>
>
>   Jing
>
>
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>
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>
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> addressed. If you believe this e-mail was sent to you in error and the
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[Freesurfer] GroupAnaysis Tutorial question: GLM directory error

[Carl Anderson]

Dear Freesurfer,

My current subjects dir is:
/Applications/freesurfer/subjects/buckner_data/tutorial_subjs/group_analysis_tutorial

When I run the following (from the tutorial):

 mri_glmfit-sim --glmdir lh.gender_age.glmdir --sim mc-z 5 4 mc-z.negative
--sim-sign neg --overwrite

I get the following error:

ERROR: cannot find
/autofs/space/birn_045/users/BWH/buckner_data/tutorial_subjs/group_analysis_tutorial/glm

I tried the following:

mri_glmfit-sim --glmdir
/Applications/freesurfer/subjects/buckner_data/tutorial_subjs/group_analysis_tutorial/glm/lh.gender_age.glmdir
--sim mc-z 5 4 mc-z.negative --sim-sign neg --overwrite

With the same result.

Any suggestions?

Thanks!
-- 
<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>
Carl M. Anderson, Ph.D. (mail stop 204)
Assistant Professor of Psychiatry,
Harvard Medical School &
The Neuroimaging Center,
McLean Hospital 115 Mill St.  Belmont, MA 02478
Ph: 617-855-2972;  Fax: 617-855-2770
e-mail: remfr...@gmail.com; carl_ander...@hms.harvard.edu
<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>
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Re: [Freesurfer] wrong sagittal orientation

[Bruce Fischl]

that's normal. freeview will also display what it thinks the anatomical 
axes are, so in the nose direction you should see a little A for anterior 
(for example)
On Wed, 27 Apr 2011, Saad Ramadan wrote:

> Hi all,
>
> Upon creating my .nii file from my Siemens MPRAGE data using mri_convert,
> and opening nii file in freesurfer,
> I notice that the sagital view has the wrong orientation.
>
> What I mean is that on teh scanner I can see nose on left side of image, but
> on freesurfer I see nose on right.
> I am using mri-convert with no options.
>
> Is thsi normal or am doing anything wrong?
>
>
> Thanks in advance.
>
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Re: [Freesurfer] qdec analysis different scanner

[Pedro Paulo de Magalhães Oliveira Junior]

Yes it does. However you can maybe use the scanner as a covariate.


On Wed, Apr 27, 2011 at 09:24, John Fredy  wrote:

> Hello all,
>
> In voxel based morphometry is not recommended use images from different
> scanners. This recommendation also apply in the qdec analysis?
>
> Thanks in advance
>
> John Ochoa
> Universidad de Antioquia
> Instituto Neurológico de Antioquia
>
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[Freesurfer] qdec analysis different scanner

[John Fredy]

Hello all,

In voxel based morphometry is not recommended use images from different
scanners. This recommendation also apply in the qdec analysis?

Thanks in advance

John Ochoa
Universidad de Antioquia
Instituto Neurológico de Antioquia
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