Re: [Freesurfer] Co-registering different source data

[Bruce Fischl]

Hi Anna

freeview now checks (in the dev version I believe) if the label has been 
sampled onto the surface and won't crash, but you need to use 
mri_label2label to sample it onto the surface before loading it onto the 
inflated surface in freeview

cheers
Bruce


On Mon, 26 Sep 2016, Crawford, Anna wrote:

> Hi,
>
> i created a test ROI which saves as a label. Every time I try to load it as a 
> label on the surface (inflated), it crashed FreeView. I'm not sure why it 
> won't load there. I noticed this happens with some other ore-made labels as 
> well. What could be the cause of this?
>
> I also tried doing mri_label2vol (to then do vol2surf), but I am getting an 
> errorL option unknown. I did the following:
>
> mri_label2vol \  --label Testing.label \ --temp ../mri/brainmask.mgz
>
> among other similar variations. Am I just inputting it wrong or am I just 
> missing information?
>
> Thank you,
> Anna
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
> [fis...@nmr.mgh.harvard.edu]
> Sent: Monday, September 26, 2016 4:23 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Co-registering different source data
>
> Hi Anna
>
> scuba is very old and deprecated. Try using freeview instead
>
> cheers
> Bruce
> On Mon, 26 Sep
> 2016, Crawford, Anna wrote:
>
>> To create the volume ROI, I found something that said to use:
>>
>> scuba -v $filename
>>
>> to then make a new ROI.
>>
>> I got en error that I could not open scuba. Is this the correct way to go 
>> about this, or is there some other means that I should be doing not 'scuba'?
>>
>> Thank you,
>> Anna
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
>> [fis...@nmr.mgh.harvard.edu]
>> Sent: Monday, September 26, 2016 1:52 PM
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] Co-registering different source data
>>
>> yes, create a volume ROI and you can map it onto the surface using
>> mri_vol2surf
>>
>> cheers
>> Bruce
>> On Mon, 26 Sep 2016, Crawford, Anna wrote:
>>
>>> For now, I am just trying to get any arbitrary ROI that I define. (I'm new 
>>> to this and am just trying to figure out how to get the basic process 
>>> first.) Eventually, I will want it related to another signal such as the 
>>> EEG from an epilepsy subject for example. In that case, it would be the 
>>> active region that I want to capture and then map it to the surface. First, 
>>> I want to be sure that I can get an ROI that I can then project to the 
>>> surface (which I assume would be something like mri_vol2surf) if that makes 
>>> sense. So i first need to be able to create the volume or label.
>>>
>>> Thank you,
>>> Anna
>>> 
>>>
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
>>> [fis...@nmr.mgh.harvard.edu]
>>> Sent: Monday, September 26, 2016 1:16 PM
>>> To: Freesurfer support list
>>> Subject: Re: [Freesurfer] Co-registering different source data
>>>
>>> can you explain what the ROI is supposed to represent? If you can create
>>> it in the volume, you can use mri_vol2surf to map it onto the surface.
>>>
>>> cheers
>>> Bruce
>>>
>>>
>>> On Mon, 26 Sep 2016, Crawford, Anna wrote:
>>>
 Hi,

 I am having trouble figuring out how to create my own ROI. I can visualize 
 the anatomical ROI created automatically. How do I create a new ROI?

 Thanks,
 Anna
 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
 [fis...@nmr.mgh.harvard.edu]
 Sent: Monday, September 26, 2016 10:44 AM
 To: Freesurfer support list
 Subject: Re: [Freesurfer] Co-registering different source data

 Hi Anna

 I'm not exactly sure what you mean, but if you register EEG electrodes to
 the white or pial surface, then you can visualize them on the inflated
 surface trivially. That is, you can create your ROI on any surface of the
 same hemisphere/subject and visualize it on any other

 cheers
 Bruce


 On Mon, 26 Sep 2016, Crawford, Anna
 wrote:

> Hello,
>
> I am trying to create a new surface area on the inflated brain given by 
> freesurfer
> using recon-all. I make to create my own ROI that is co-registered onto 
> this surfer.
> Ultimately, I want to be able to take information from a different data 
> source such as
> EEG and have it co-registered onto the inflated surface. How do I go 
> about creating
> this new ROI surface?
>
> Thanks,
> Anna
>
> ===
>
> Please consider the environment before printing this e-mail
>
> 

Re: [Freesurfer] Co-registering different source data

[Crawford, Anna]

Hi,

i created a test ROI which saves as a label. Every time I try to load it as a 
label on the surface (inflated), it crashed FreeView. I'm not sure why it won't 
load there. I noticed this happens with some other ore-made labels as well. 
What could be the cause of this?

I also tried doing mri_label2vol (to then do vol2surf), but I am getting an 
errorL option unknown. I did the following:

mri_label2vol \  --label Testing.label \ --temp ../mri/brainmask.mgz 

among other similar variations. Am I just inputting it wrong or am I just 
missing information?

Thank you,
Anna

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Sent: Monday, September 26, 2016 4:23 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Co-registering different source data

Hi Anna

scuba is very old and deprecated. Try using freeview instead

cheers
Bruce
On Mon, 26 Sep
2016, Crawford, Anna wrote:

> To create the volume ROI, I found something that said to use:
>
> scuba -v $filename
>
> to then make a new ROI.
>
> I got en error that I could not open scuba. Is this the correct way to go 
> about this, or is there some other means that I should be doing not 'scuba'?
>
> Thank you,
> Anna
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
> [fis...@nmr.mgh.harvard.edu]
> Sent: Monday, September 26, 2016 1:52 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Co-registering different source data
>
> yes, create a volume ROI and you can map it onto the surface using
> mri_vol2surf
>
> cheers
> Bruce
> On Mon, 26 Sep 2016, Crawford, Anna wrote:
>
>> For now, I am just trying to get any arbitrary ROI that I define. (I'm new 
>> to this and am just trying to figure out how to get the basic process 
>> first.) Eventually, I will want it related to another signal such as the EEG 
>> from an epilepsy subject for example. In that case, it would be the active 
>> region that I want to capture and then map it to the surface. First, I want 
>> to be sure that I can get an ROI that I can then project to the surface 
>> (which I assume would be something like mri_vol2surf) if that makes sense. 
>> So i first need to be able to create the volume or label.
>>
>> Thank you,
>> Anna
>> 
>>
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
>> [fis...@nmr.mgh.harvard.edu]
>> Sent: Monday, September 26, 2016 1:16 PM
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] Co-registering different source data
>>
>> can you explain what the ROI is supposed to represent? If you can create
>> it in the volume, you can use mri_vol2surf to map it onto the surface.
>>
>> cheers
>> Bruce
>>
>>
>> On Mon, 26 Sep 2016, Crawford, Anna wrote:
>>
>>> Hi,
>>>
>>> I am having trouble figuring out how to create my own ROI. I can visualize 
>>> the anatomical ROI created automatically. How do I create a new ROI?
>>>
>>> Thanks,
>>> Anna
>>> 
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
>>> [fis...@nmr.mgh.harvard.edu]
>>> Sent: Monday, September 26, 2016 10:44 AM
>>> To: Freesurfer support list
>>> Subject: Re: [Freesurfer] Co-registering different source data
>>>
>>> Hi Anna
>>>
>>> I'm not exactly sure what you mean, but if you register EEG electrodes to
>>> the white or pial surface, then you can visualize them on the inflated
>>> surface trivially. That is, you can create your ROI on any surface of the
>>> same hemisphere/subject and visualize it on any other
>>>
>>> cheers
>>> Bruce
>>>
>>>
>>> On Mon, 26 Sep 2016, Crawford, Anna
>>> wrote:
>>>
 Hello,

 I am trying to create a new surface area on the inflated brain given by 
 freesurfer
 using recon-all. I make to create my own ROI that is co-registered onto 
 this surfer.
 Ultimately, I want to be able to take information from a different data 
 source such as
 EEG and have it co-registered onto the inflated surface. How do I go about 
 creating
 this new ROI surface?

 Thanks,
 Anna

 ===

 Please consider the environment before printing this e-mail

 Cleveland Clinic is ranked as one of the top hospitals in America by 
 U.S.News & World
 Report (2015). Visit us online at http://www.clevelandclinic.org for a 
 complete listing
 of our services, staff and locations. Confidentiality Note: This message 
 is intended
 for use only by the individual or entity to which it is addressed and may 
 contain
 information that is privileged, confidential, and exempt from disclosure 
 under
 

Re: [Freesurfer] Re Re: Question regarding mri_convert

[Bruce Fischl]

what was different? And can you send us the rawavg.mgz for the two cases?

On Mon, 26 Sep 2016, Tamara Tavares wrote:


Thank you Bruce!

Theoretically, I should get the same results if I pass my nii file through
the recon-all command if I converted my dicom/IMA file into a nii using
Slicer4 or the mri convert command? I did this and I got different volumes.

Thank you,
Tamara 


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Re: [Freesurfer] Co-registering different source data

[Bruce Fischl]

Hi Anna

scuba is very old and deprecated. Try using freeview instead

cheers
Bruce
On Mon, 26 Sep 
2016, Crawford, Anna wrote:

> To create the volume ROI, I found something that said to use:
>
> scuba -v $filename
>
> to then make a new ROI.
>
> I got en error that I could not open scuba. Is this the correct way to go 
> about this, or is there some other means that I should be doing not 'scuba'?
>
> Thank you,
> Anna
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
> [fis...@nmr.mgh.harvard.edu]
> Sent: Monday, September 26, 2016 1:52 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Co-registering different source data
>
> yes, create a volume ROI and you can map it onto the surface using
> mri_vol2surf
>
> cheers
> Bruce
> On Mon, 26 Sep 2016, Crawford, Anna wrote:
>
>> For now, I am just trying to get any arbitrary ROI that I define. (I'm new 
>> to this and am just trying to figure out how to get the basic process 
>> first.) Eventually, I will want it related to another signal such as the EEG 
>> from an epilepsy subject for example. In that case, it would be the active 
>> region that I want to capture and then map it to the surface. First, I want 
>> to be sure that I can get an ROI that I can then project to the surface 
>> (which I assume would be something like mri_vol2surf) if that makes sense. 
>> So i first need to be able to create the volume or label.
>>
>> Thank you,
>> Anna
>> 
>>
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
>> [fis...@nmr.mgh.harvard.edu]
>> Sent: Monday, September 26, 2016 1:16 PM
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] Co-registering different source data
>>
>> can you explain what the ROI is supposed to represent? If you can create
>> it in the volume, you can use mri_vol2surf to map it onto the surface.
>>
>> cheers
>> Bruce
>>
>>
>> On Mon, 26 Sep 2016, Crawford, Anna wrote:
>>
>>> Hi,
>>>
>>> I am having trouble figuring out how to create my own ROI. I can visualize 
>>> the anatomical ROI created automatically. How do I create a new ROI?
>>>
>>> Thanks,
>>> Anna
>>> 
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
>>> [fis...@nmr.mgh.harvard.edu]
>>> Sent: Monday, September 26, 2016 10:44 AM
>>> To: Freesurfer support list
>>> Subject: Re: [Freesurfer] Co-registering different source data
>>>
>>> Hi Anna
>>>
>>> I'm not exactly sure what you mean, but if you register EEG electrodes to
>>> the white or pial surface, then you can visualize them on the inflated
>>> surface trivially. That is, you can create your ROI on any surface of the
>>> same hemisphere/subject and visualize it on any other
>>>
>>> cheers
>>> Bruce
>>>
>>>
>>> On Mon, 26 Sep 2016, Crawford, Anna
>>> wrote:
>>>
 Hello,

 I am trying to create a new surface area on the inflated brain given by 
 freesurfer
 using recon-all. I make to create my own ROI that is co-registered onto 
 this surfer.
 Ultimately, I want to be able to take information from a different data 
 source such as
 EEG and have it co-registered onto the inflated surface. How do I go about 
 creating
 this new ROI surface?

 Thanks,
 Anna

 ===

 Please consider the environment before printing this e-mail

 Cleveland Clinic is ranked as one of the top hospitals in America by 
 U.S.News & World
 Report (2015). Visit us online at http://www.clevelandclinic.org for a 
 complete listing
 of our services, staff and locations. Confidentiality Note: This message 
 is intended
 for use only by the individual or entity to which it is addressed and may 
 contain
 information that is privileged, confidential, and exempt from disclosure 
 under
 applicable law. If the reader of this message is not the intended 
 recipient or the
 employee or agent responsible for delivering the message to the intended 
 recipient, you
 are hereby notified that any dissemination, distribution or copying of this
 communication is strictly prohibited. If you have received this 
 communication in error,
 please contact the sender immediately and destroy the material in its 
 entirety, whether
 electronic or hard copy. Thank you.


>>> ___
>>> 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 

[Freesurfer] Regional White Matter Hypointensity Volumes

[Bharadwaj, Pradyumna - (prad)]

Hello Freesurfers,


I am interested in obtaining the regional volumes of white matter 
hypointensities.


What volume would I use a reference for obtaining the 'regions' ? and what 
commands would I need to use to obtain these regional volumes ?


?If there isn't an appropriate white matter volume that can be used as a 
reference, then is there a way to divide a subject's brain image or white 
matter volume image into say 8 equal quadrants, which can then be used as masks 
to obtain regional WMH volume in these quadrants?



Thanks,

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

[Freesurfer] Re Re: Question regarding mri_convert

[Tamara Tavares]

Thank you Bruce!

Theoretically, I should get the same results if I pass my nii file through
the recon-all command if I converted my dicom/IMA file into a nii using
Slicer4 or the mri convert command? I did this and I got different volumes.

Thank you,
Tamara
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Co-registering different source data

[Crawford, Anna]

To create the volume ROI, I found something that said to use:

scuba -v $filename

to then make a new ROI.

I got en error that I could not open scuba. Is this the correct way to go about 
this, or is there some other means that I should be doing not 'scuba'?

Thank you,
Anna 

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Sent: Monday, September 26, 2016 1:52 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Co-registering different source data

yes, create a volume ROI and you can map it onto the surface using
mri_vol2surf

cheers
Bruce
On Mon, 26 Sep 2016, Crawford, Anna wrote:

> For now, I am just trying to get any arbitrary ROI that I define. (I'm new to 
> this and am just trying to figure out how to get the basic process first.) 
> Eventually, I will want it related to another signal such as the EEG from an 
> epilepsy subject for example. In that case, it would be the active region 
> that I want to capture and then map it to the surface. First, I want to be 
> sure that I can get an ROI that I can then project to the surface (which I 
> assume would be something like mri_vol2surf) if that makes sense. So i first 
> need to be able to create the volume or label.
>
> Thank you,
> Anna
> 
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
> [fis...@nmr.mgh.harvard.edu]
> Sent: Monday, September 26, 2016 1:16 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Co-registering different source data
>
> can you explain what the ROI is supposed to represent? If you can create
> it in the volume, you can use mri_vol2surf to map it onto the surface.
>
> cheers
> Bruce
>
>
> On Mon, 26 Sep 2016, Crawford, Anna wrote:
>
>> Hi,
>>
>> I am having trouble figuring out how to create my own ROI. I can visualize 
>> the anatomical ROI created automatically. How do I create a new ROI?
>>
>> Thanks,
>> Anna
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
>> [fis...@nmr.mgh.harvard.edu]
>> Sent: Monday, September 26, 2016 10:44 AM
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] Co-registering different source data
>>
>> Hi Anna
>>
>> I'm not exactly sure what you mean, but if you register EEG electrodes to
>> the white or pial surface, then you can visualize them on the inflated
>> surface trivially. That is, you can create your ROI on any surface of the
>> same hemisphere/subject and visualize it on any other
>>
>> cheers
>> Bruce
>>
>>
>> On Mon, 26 Sep 2016, Crawford, Anna
>> wrote:
>>
>>> Hello,
>>>
>>> I am trying to create a new surface area on the inflated brain given by 
>>> freesurfer
>>> using recon-all. I make to create my own ROI that is co-registered onto 
>>> this surfer.
>>> Ultimately, I want to be able to take information from a different data 
>>> source such as
>>> EEG and have it co-registered onto the inflated surface. How do I go about 
>>> creating
>>> this new ROI surface?
>>>
>>> Thanks,
>>> Anna
>>>
>>> ===
>>>
>>> Please consider the environment before printing this e-mail
>>>
>>> Cleveland Clinic is ranked as one of the top hospitals in America by 
>>> U.S.News & World
>>> Report (2015). Visit us online at http://www.clevelandclinic.org for a 
>>> complete listing
>>> of our services, staff and locations. Confidentiality Note: This message is 
>>> intended
>>> for use only by the individual or entity to which it is addressed and may 
>>> contain
>>> information that is privileged, confidential, and exempt from disclosure 
>>> under
>>> applicable law. If the reader of this message is not the intended recipient 
>>> or the
>>> employee or agent responsible for delivering the message to the intended 
>>> recipient, you
>>> are hereby notified that any dissemination, distribution or copying of this
>>> communication is strictly prohibited. If you have received this 
>>> communication in error,
>>> please contact the sender immediately and destroy the material in its 
>>> entirety, whether
>>> electronic or hard copy. Thank you.
>>>
>>>
>> ___
>> 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.
>>
>>
>> 

Re: [Freesurfer] Sulcus depth

[Bruce Fischl]

1. It is the signed dot product of the movement vector with the outwards 
pointing surface normal of the white matter surface during inflation.


2. Yes, because moving inwards for gyri the dot product is negative.

3. Yes, I think so, although I'm not sure I understand.

4. mris_anatomical_stats can do this if you specify sulc as the "thickness"
file

 On 
Mon, 26 Sep 2016, Hanbyul Cho wrote:



Dear FreeSurfer Team,

I have questions about the sulcal depth.

1) I heard that the output/surf/?h.sulc is showing the sulcal depth.
  Is it correct that the sulcal depth measure unit is normalized z-score, mm? 
And is
it correct that the (-) values of sulcal depth mean gyral region (green), and 
(+)
values mean sulcal region (red)?

2) I wonder if ?h.sulc is based on white matter surface or pial matter surface.

3) I analyzed the sulcal depth by vertex-level. if the results include the sulc 
(-)
values region, Is it meaning that the gyral height?

4) I wonder the method/commands for extracting the sulc value by label-level.

5) Could you let me know the recommended smoothing option if it possible?  (e.g.
--fwhm-trg [N])

I appreciate your help.

Thank you.

Han Byul Cho

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addressed. If you believe this e-mail was sent to you in error and the e-mail
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Sulcus depth

[Hanbyul Cho]

Dear FreeSurfer Team,

I have questions about the sulcal depth.

1) I heard that the output/surf/?h.sulc is showing the sulcal depth.
  Is it correct that the sulcal depth measure unit is normalized z-score,
mm? And is it correct that the (-) values of sulcal depth mean gyral region
(green), and (+) values mean sulcal region (red)?

2) I wonder if ?h.sulc is based on white matter surface or pial matter
surface.

3) I analyzed the sulcal depth by vertex-level. if the results include the
sulc (-) values region, Is it meaning that the gyral height?

4) I wonder the method/commands for extracting the sulc value by
label-level.

5) Could you let me know the recommended smoothing option if it possible?
 (e.g. --fwhm-trg [N])

I appreciate your help.

Thank you.

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

Re: [Freesurfer] Co-registering different source data

[Bruce Fischl]

yes, create a volume ROI and you can map it onto the surface using 
mri_vol2surf

cheers
Bruce
On Mon, 26 Sep 2016, Crawford, Anna wrote:

> For now, I am just trying to get any arbitrary ROI that I define. (I'm new to 
> this and am just trying to figure out how to get the basic process first.) 
> Eventually, I will want it related to another signal such as the EEG from an 
> epilepsy subject for example. In that case, it would be the active region 
> that I want to capture and then map it to the surface. First, I want to be 
> sure that I can get an ROI that I can then project to the surface (which I 
> assume would be something like mri_vol2surf) if that makes sense. So i first 
> need to be able to create the volume or label.
>
> Thank you,
> Anna
> 
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
> [fis...@nmr.mgh.harvard.edu]
> Sent: Monday, September 26, 2016 1:16 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Co-registering different source data
>
> can you explain what the ROI is supposed to represent? If you can create
> it in the volume, you can use mri_vol2surf to map it onto the surface.
>
> cheers
> Bruce
>
>
> On Mon, 26 Sep 2016, Crawford, Anna wrote:
>
>> Hi,
>>
>> I am having trouble figuring out how to create my own ROI. I can visualize 
>> the anatomical ROI created automatically. How do I create a new ROI?
>>
>> Thanks,
>> Anna
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
>> [fis...@nmr.mgh.harvard.edu]
>> Sent: Monday, September 26, 2016 10:44 AM
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] Co-registering different source data
>>
>> Hi Anna
>>
>> I'm not exactly sure what you mean, but if you register EEG electrodes to
>> the white or pial surface, then you can visualize them on the inflated
>> surface trivially. That is, you can create your ROI on any surface of the
>> same hemisphere/subject and visualize it on any other
>>
>> cheers
>> Bruce
>>
>>
>> On Mon, 26 Sep 2016, Crawford, Anna
>> wrote:
>>
>>> Hello,
>>>
>>> I am trying to create a new surface area on the inflated brain given by 
>>> freesurfer
>>> using recon-all. I make to create my own ROI that is co-registered onto 
>>> this surfer.
>>> Ultimately, I want to be able to take information from a different data 
>>> source such as
>>> EEG and have it co-registered onto the inflated surface. How do I go about 
>>> creating
>>> this new ROI surface?
>>>
>>> Thanks,
>>> Anna
>>>
>>> ===
>>>
>>> Please consider the environment before printing this e-mail
>>>
>>> Cleveland Clinic is ranked as one of the top hospitals in America by 
>>> U.S.News & World
>>> Report (2015). Visit us online at http://www.clevelandclinic.org for a 
>>> complete listing
>>> of our services, staff and locations. Confidentiality Note: This message is 
>>> intended
>>> for use only by the individual or entity to which it is addressed and may 
>>> contain
>>> information that is privileged, confidential, and exempt from disclosure 
>>> under
>>> applicable law. If the reader of this message is not the intended recipient 
>>> or the
>>> employee or agent responsible for delivering the message to the intended 
>>> recipient, you
>>> are hereby notified that any dissemination, distribution or copying of this
>>> communication is strictly prohibited. If you have received this 
>>> communication in error,
>>> please contact the sender immediately and destroy the material in its 
>>> entirety, whether
>>> electronic or hard copy. Thank you.
>>>
>>>
>> ___
>> 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.
>>
>>
>> ===
>>
>>
>> Please consider the environment before printing this e-mail
>>
>> Cleveland Clinic is ranked as one of the top hospitals in America by 
>> U.S.News & World Report (2015).
>> Visit us online at http://www.clevelandclinic.org for a complete listing of 
>> our services, staff and locations.
>>
>>
>> Confidentiality Note:  This message is intended for use only by the 
>> individual or entity to which it is addressed and may contain information 
>> that is privileged, confidential, and exempt from disclosure under 
>> applicable law.  If the reader of this 

Re: [Freesurfer] Co-registering different source data

[Crawford, Anna]

For now, I am just trying to get any arbitrary ROI that I define. (I'm new to 
this and am just trying to figure out how to get the basic process first.) 
Eventually, I will want it related to another signal such as the EEG from an 
epilepsy subject for example. In that case, it would be the active region that 
I want to capture and then map it to the surface. First, I want to be sure that 
I can get an ROI that I can then project to the surface (which I assume would 
be something like mri_vol2surf) if that makes sense. So i first need to be able 
to create the volume or label.

Thank you,
Anna


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Sent: Monday, September 26, 2016 1:16 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Co-registering different source data

can you explain what the ROI is supposed to represent? If you can create
it in the volume, you can use mri_vol2surf to map it onto the surface.

cheers
Bruce


On Mon, 26 Sep 2016, Crawford, Anna wrote:

> Hi,
>
> I am having trouble figuring out how to create my own ROI. I can visualize 
> the anatomical ROI created automatically. How do I create a new ROI?
>
> Thanks,
> Anna
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
> [fis...@nmr.mgh.harvard.edu]
> Sent: Monday, September 26, 2016 10:44 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Co-registering different source data
>
> Hi Anna
>
> I'm not exactly sure what you mean, but if you register EEG electrodes to
> the white or pial surface, then you can visualize them on the inflated
> surface trivially. That is, you can create your ROI on any surface of the
> same hemisphere/subject and visualize it on any other
>
> cheers
> Bruce
>
>
> On Mon, 26 Sep 2016, Crawford, Anna
> wrote:
>
>> Hello,
>>
>> I am trying to create a new surface area on the inflated brain given by 
>> freesurfer
>> using recon-all. I make to create my own ROI that is co-registered onto this 
>> surfer.
>> Ultimately, I want to be able to take information from a different data 
>> source such as
>> EEG and have it co-registered onto the inflated surface. How do I go about 
>> creating
>> this new ROI surface?
>>
>> Thanks,
>> Anna
>>
>> ===
>>
>> Please consider the environment before printing this e-mail
>>
>> Cleveland Clinic is ranked as one of the top hospitals in America by 
>> U.S.News & World
>> Report (2015). Visit us online at http://www.clevelandclinic.org for a 
>> complete listing
>> of our services, staff and locations. Confidentiality Note: This message is 
>> intended
>> for use only by the individual or entity to which it is addressed and may 
>> contain
>> information that is privileged, confidential, and exempt from disclosure 
>> under
>> applicable law. If the reader of this message is not the intended recipient 
>> or the
>> employee or agent responsible for delivering the message to the intended 
>> recipient, you
>> are hereby notified that any dissemination, distribution or copying of this
>> communication is strictly prohibited. If you have received this 
>> communication in error,
>> please contact the sender immediately and destroy the material in its 
>> entirety, whether
>> electronic or hard copy. Thank you.
>>
>>
> ___
> 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.
>
>
> ===
>
>
> Please consider the environment before printing this e-mail
>
> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News 
> & World Report (2015).
> Visit us online at http://www.clevelandclinic.org for a complete listing of 
> our services, staff and locations.
>
>
> Confidentiality Note:  This message is intended for use only by the 
> individual or entity to which it is addressed and may contain information 
> that is privileged, confidential, and exempt from disclosure under applicable 
> law.  If the reader of this message is not the intended recipient or the 
> employee or agent responsible for delivering the message to the intended 
> recipient, you are hereby notified that any dissemination, distribution or 
> copying of this communication is strictly prohibited.  If you have received 
> this 

Re: [Freesurfer] Co-registering different source data

[Bruce Fischl]

can you explain what the ROI is supposed to represent? If you can create 
it in the volume, you can use mri_vol2surf to map it onto the surface.

cheers
Bruce


On Mon, 26 Sep 2016, Crawford, Anna wrote:

> Hi,
>
> I am having trouble figuring out how to create my own ROI. I can visualize 
> the anatomical ROI created automatically. How do I create a new ROI?
>
> Thanks,
> Anna
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
> [fis...@nmr.mgh.harvard.edu]
> Sent: Monday, September 26, 2016 10:44 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Co-registering different source data
>
> Hi Anna
>
> I'm not exactly sure what you mean, but if you register EEG electrodes to
> the white or pial surface, then you can visualize them on the inflated
> surface trivially. That is, you can create your ROI on any surface of the
> same hemisphere/subject and visualize it on any other
>
> cheers
> Bruce
>
>
> On Mon, 26 Sep 2016, Crawford, Anna
> wrote:
>
>> Hello,
>>
>> I am trying to create a new surface area on the inflated brain given by 
>> freesurfer
>> using recon-all. I make to create my own ROI that is co-registered onto this 
>> surfer.
>> Ultimately, I want to be able to take information from a different data 
>> source such as
>> EEG and have it co-registered onto the inflated surface. How do I go about 
>> creating
>> this new ROI surface?
>>
>> Thanks,
>> Anna
>>
>> ===
>>
>> Please consider the environment before printing this e-mail
>>
>> Cleveland Clinic is ranked as one of the top hospitals in America by 
>> U.S.News & World
>> Report (2015). Visit us online at http://www.clevelandclinic.org for a 
>> complete listing
>> of our services, staff and locations. Confidentiality Note: This message is 
>> intended
>> for use only by the individual or entity to which it is addressed and may 
>> contain
>> information that is privileged, confidential, and exempt from disclosure 
>> under
>> applicable law. If the reader of this message is not the intended recipient 
>> or the
>> employee or agent responsible for delivering the message to the intended 
>> recipient, you
>> are hereby notified that any dissemination, distribution or copying of this
>> communication is strictly prohibited. If you have received this 
>> communication in error,
>> please contact the sender immediately and destroy the material in its 
>> entirety, whether
>> electronic or hard copy. Thank you.
>>
>>
> ___
> 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.
>
>
> ===
>
>
> Please consider the environment before printing this e-mail
>
> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News 
> & World Report (2015).
> Visit us online at http://www.clevelandclinic.org for a complete listing of 
> our services, staff and locations.
>
>
> Confidentiality Note:  This message is intended for use only by the 
> individual or entity to which it is addressed and may contain information 
> that is privileged, confidential, and exempt from disclosure under applicable 
> law.  If the reader of this message is not the intended recipient or the 
> employee or agent responsible for delivering the message to the intended 
> recipient, you are hereby notified that any dissemination, distribution or 
> copying of this communication is strictly prohibited.  If you have received 
> this communication in error,  please contact the sender immediately and 
> destroy the material in its entirety, whether electronic or hard copy.
>
> Thank you.
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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Re: [Freesurfer] Freesurfer Digest, Vol 151, Issue 30

[KALEY E ELLIS]

Hi Ruopeng,


When I try to open it, this is part of the error message that appears:

freeview -v 2000_2/mri/T1.mgz 2000_2/mri/brainmask.mgz:colormap=heat:opacity=0.4

libGL error: No matching fbConfigs or visuals found

libGL error: failed to load driver: swrast

X Error: BadValue (integer parameter out of range for operation) 2

  Extension:150 (Uknown extension)

  Minor opcode: 3 (Unknown request)

  Resource id:  0x0

X Error: GLXBadContext 160

  Extension:150 (Uknown extension)

  Minor opcode: 5 (Unknown request)

  Resource id:  0x6000ba

X Error: 0 0

  Extension:150 (Uknown extension)

  Minor opcode: 26 (Unknown request)

  Resource id:  0x0

X Error: GLXBadContext 160

  Extension:150 (Uknown extension)

  Minor opcode: 5 (Unknown request)

  Resource id:  0x6000ba

X Error: 0 0

  Extension:150 (Uknown extension)

  Minor opcode: 26 (Unknown request)

  Resource id:  0x0

X Error: GLXBadContext 160

  Extension:150 (Uknown extension)

  Minor opcode: 5 (Unknown request)

  Resource id:  0x6000ba

X Error: 0 0

  Extension:150 (Uknown extension)

  Minor opcode: 26 (Unknown request)

  Resource id:  0x0

X Error: GLXBadContext 160

  Extension:150 (Uknown extension)

  Minor opcode: 5 (Unknown request)

  Resource id:  0x6000ba

X Error: 0 0

  Extension:150 (Uknown extension)

  Minor opcode: 26 (Unknown request)

  Resource id:  0x0

X Error: GLXBadContext 160

  Extension:150 (Uknown extension)

  Minor opcode: 5 (Unknown request)

  Resource id:  0x6000ba

X Error: 0 0

  Extension:150 (Uknown extension)

  Minor opcode: 26 (Unknown request)

  Resource id:  0x0

X Error: BadMatch (invalid parameter attributes) 8

  Extension:150 (Uknown extension)

  Minor opcode: 11 (Unknown request)

  Resource id:  0x6000b8


If I run glxgears, this appears:

[edwards@guero ~]$ glxgears

libGL error: No matching fbConfigs or visuals found

libGL error: failed to load driver: swrast

X Error of failed request:  BadValue (integer parameter out of range for 
operation)

  Major opcode of failed request:  150 (GLX)

  Minor opcode of failed request:  3 (X_GLXCreateContext)

  Value in failed request:  0x0

  Serial number of failed request:  28

  Current serial number in output stream:  30

[edwards@guero ~]$


Thank you!

Kaley


Message: 6
Date: Fri, 23 Sep 2016 18:53:45 -0400
From: Ruopeng Wang 
Subject: Re: [Freesurfer] freeview display problem
To: Freesurfer support list 
Message-ID: <732e27d8-179e-4b66-8762-7bf26c1df...@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

Is there any error message on the terminal? What happens if you run ?glxgears? 
command? Does it run?

Best,
Ruopeng

> On Sep 23, 2016, at 4:35 PM, KALEY E ELLIS  wrote:
>
> Hello FreeSurfer Developers,
>
> I am attempting to open freeview to view the brainmask on a subject in our 
> study. Everything looks normal, except there is no image displayed (see 
> attachment). Could you please let me know how I can fix this?
>
> Thank you,
> Kaley
>
> Associate Research Specialist
> Center for Healthy Minds
> Waisman Center for Brain Imaging and Behavior
> University of Wisconsin-Madison
>  PM.png>___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu 
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
> 
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Message: 7
Date: Sat, 24 Sep 2016 11:36:46 -0400
From: Satrajit Ghosh 
Subject: [Freesurfer] avoiding FSL when using T2pial
To: Freesurfer Mailing List 
Message-ID:

Content-Type: text/plain; charset="utf-8"

hi doug,

without hacking recon-all is there a way to avoid using FSL when using the
T2pial flag?

cheers,

satra

#@# Refine Pial Surfs w/ T2/FLAIR Sat Sep 24 08:42:34 UTC 2016

 bbregister --s sub-01 --mov /subjects/sub-01/mri/orig/T2raw.mgz --lta
/subjects/sub-01/mri/transforms/T2raw.lta --init-fsl --T2

Log file is /subjects/sub-01/mri/transforms/T2raw.dat.log
Sat Sep 24 08:42:35 UTC 2016

setenv SUBJECTS_DIR /subjects
cd /subjects/sub-01/scripts
/opt2/freesurfer/bin/bbregister --s sub-01 --mov
/subjects/sub-01/mri/orig/T2raw.mgz --lta
/subjects/sub-01/mri/transforms/T2raw.lta --init-fsl --T2

$Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $
Linux b62492e050ac 4.4.20-moby #1 SMP Thu Sep 8 21:27:34 UTC 2016 x86_64
GNU/Linux
FREESURFER_HOME /opt2/freesurfer
mri_convert /subjects/sub-01/mri/orig/T2raw.mgz
/subjects/sub-01/mri/transforms/tmp.bbregister.4836/template.nii
mri_convert 

Re: [Freesurfer] Software License for Industry

[zkaufman]

The FreeSurfer Software License Agreement does not contain any language
explicitly or implicitly preventing commercial usage, however I will
highlight the following text from the License Agreement:

  "Any commercialization of the Software is at the sole risk
   of the party or parties engaged in such commercialization”

In short, commercial entities seeking to make use of FreeSurfer should
seek their own legal council on the interpretation of the license for
their specific circumstance.

-Zeke

> Dear FS experts
>
> I have one concern regarding the license and the Freesurfer usage on
> industry.
>
> We are setting up a start-up specialized with the analysis of brain MRI
> and
> we are interested on using FreeSurfer package as our main neuroimaging
> tool, due to the large amount of utilities it provides.
>
> After reading carefully the Software License provided here (
> https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSoftwareLicense) it is
> not clear for me if we could use yours software to provide a service to an
> external organisation/customer for which payment will be received.
>
> Could someone provide some insight on this issue?
>
> Bests,
> Joss.
>

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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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.

Re: [Freesurfer] Warping an ROI from one subject to another

[Joel Bruss]

Anyone have any thoughts on this?


On 09/21/2016 04:18 PM, Joel Bruss wrote:
> I have two subjects, subA and subB.  subA has a binary ROI mask, native
> space, that I'd like to place in subB's native space. Both subjects have
> been run through all stages of recon, edited, etc. Is there a better or
> easier way to achieve this than what I've run?:
>
>
> #Resample the native space binary ROI file into "brainmask" space
> mri_convert -rl /subA/mri/brainmask.mgz -rt nearest --no_scale 1
> ROI.nii.gz /subA/mri/ROI.mgz
>
> #Convert ROI file into a label
> mri_cor2label --id 1 --c /subA/mri --i ROI.mgz --l ROI.label
>
> #Move label from subA to subB
> mri_label2label --srcsubject subA --srclabel /subA/mri/ROI.label
> --trgsubject subB --trglabel /subB/mri/ROI_to_subB.label --regmethod volume
>
> #Convert warped ROI label to a volume
> mri_label2vol --label /subB/mri/ROI_to_subB.label \
> --subject subB \
> --temp brainmask.mgz \
> --regheader brainmask.mgz \
> --o /subB/mri/ROI_to_subB.mgz
>
> #Convert the volume back to native subB space
> mri_convert -rl subB_native.nii.gz -rt nearest --no_scale 1
> /subB/mri/ROI_to_subB.mgz ROI_to_subB_native.nii.gz
>
> A few follow-up questions:
>
> 1) When running mri_label2label, is better to use surface or volume for
> the "regmethod"?  Which method will give me a better fit for my output?
> 2) The output I'm getting looks striped (there are holes in the binary
> mask) and doesn't quite fit the anatomy (the final file is shifted up
> and away from where I would expect it to be although in the general
> vicinity of what I would expect).  It's almost as if I've chosen a wrong
> target or file along the way.  I don't expect the fit to be perfect, but
> did I do something wrong?
>
> Thanks in advance to any and all replies.
>
>
>
> 
> Notice: This UI Health Care e-mail (including attachments) is covered by the 
> Electronic Communications Privacy Act, 18 U.S.C. 2510-2521 and is intended 
> only for the use of the individual or entity to which it is addressed, and 
> may contain information that is privileged, confidential, and exempt from 
> disclosure under applicable law. If you are not the intended recipient, any 
> dissemination, distribution or copying of this communication is strictly 
> prohibited. If you have received this communication in error, please notify 
> the sender immediately and delete or destroy all copies of the original 
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> retained as required by law or regulation. Thank you.
> 
>
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> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine 
> at
> 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.
>




Notice: This UI Health Care e-mail (including attachments) is covered by the 
Electronic Communications Privacy Act, 18 U.S.C. 2510-2521 and is intended only 
for the use of the individual or entity to which it is addressed, and may 
contain information that is privileged, confidential, and exempt from 
disclosure under applicable law. If you are not the intended recipient, any 
dissemination, distribution or copying of this communication is strictly 
prohibited. If you have received this communication in error, please notify the 
sender immediately and delete or destroy all copies of the original message and 
attachments thereto. Email sent to or from UI Health Care may be retained as 
required by law or regulation. Thank you.


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[Freesurfer] Software License for Industry

[Josseppe Gonsales]

Dear FS experts

I have one concern regarding the license and the Freesurfer usage on
industry.

We are setting up a start-up specialized with the analysis of brain MRI and
we are interested on using FreeSurfer package as our main neuroimaging
tool, due to the large amount of utilities it provides.

After reading carefully the Software License provided here (
https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSoftwareLicense) it is
not clear for me if we could use yours software to provide a service to an
external organisation/customer for which payment will be received.

Could someone provide some insight on this issue?

Bests,
Joss.
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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.

Re: [Freesurfer] Co-registering different source data

[Crawford, Anna]

Hi,

I am having trouble figuring out how to create my own ROI. I can visualize the 
anatomical ROI created automatically. How do I create a new ROI? 

Thanks,
Anna

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Sent: Monday, September 26, 2016 10:44 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Co-registering different source data

Hi Anna

I'm not exactly sure what you mean, but if you register EEG electrodes to
the white or pial surface, then you can visualize them on the inflated
surface trivially. That is, you can create your ROI on any surface of the
same hemisphere/subject and visualize it on any other

cheers
Bruce


On Mon, 26 Sep 2016, Crawford, Anna
wrote:

> Hello,
>
> I am trying to create a new surface area on the inflated brain given by 
> freesurfer
> using recon-all. I make to create my own ROI that is co-registered onto this 
> surfer.
> Ultimately, I want to be able to take information from a different data 
> source such as
> EEG and have it co-registered onto the inflated surface. How do I go about 
> creating
> this new ROI surface?
>
> Thanks,
> Anna
>
> ===
>
> Please consider the environment before printing this e-mail
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===


 Please consider the environment before printing this e-mail

Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & 
World Report (2015).  
Visit us online at http://www.clevelandclinic.org for a complete listing of our 
services, staff and locations.


Confidentiality Note:  This message is intended for use only by the individual 
or entity to which it is addressed and may contain information that is 
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Re: [Freesurfer] Co-registering different source data

[Bruce Fischl]

Hi Anna

I'm not exactly sure what you mean, but if you register EEG electrodes to 
the white or pial surface, then you can visualize them on the inflated 
surface trivially. That is, you can create your ROI on any surface of the 
same hemisphere/subject and visualize it on any other

cheers
Bruce


On Mon, 26 Sep 2016, Crawford, Anna 
wrote:

> Hello,
> 
> I am trying to create a new surface area on the inflated brain given by 
> freesurfer
> using recon-all. I make to create my own ROI that is co-registered onto this 
> surfer.
> Ultimately, I want to be able to take information from a different data 
> source such as
> EEG and have it co-registered onto the inflated surface. How do I go about 
> creating
> this new ROI surface?
> 
> Thanks,
> Anna
> 
> ===
> 
> Please consider the environment before printing this e-mail
> 
> Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News 
> & World
> Report (2015). Visit us online at http://www.clevelandclinic.org for a 
> complete listing
> of our services, staff and locations. Confidentiality Note: This message is 
> intended
> for use only by the individual or entity to which it is addressed and may 
> contain
> information that is privileged, confidential, and exempt from disclosure under
> applicable law. If the reader of this message is not the intended recipient 
> or the
> employee or agent responsible for delivering the message to the intended 
> recipient, you
> are hereby notified that any dissemination, distribution or copying of this
> communication is strictly prohibited. If you have received this communication 
> in error,
> please contact the sender immediately and destroy the material in its 
> entirety, whether
> electronic or hard copy. Thank you.
> 
>
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[Freesurfer] Postdoctoral Positions -- Baby Brain Connectome

[gangli]

Postdoctoral research associate positions are available in the Department
of Radiology and Biomedical Research Imaging Center (BRIC) at the
University of North Carolina at Chapel Hill (UNC-Chapel Hill). Our current
focuses are to better understand the dynamic development of brain
structure, function and connectivity during critical early postnatal
stages, via computational analysis of high-quality multimodal neuroimaging
data acquired by UNC/UMN Baby Connectome Project. We are seeking highly
motivated individuals who have extensive research experience in
neuroimaging analysis (e.g., structural, diffusion or functional MRI) and
demonstrated academic excellence, including publications in first-class
journals and conferences. The postdoctoral candidate should have a Ph.D.
(or equivalent) in Neuroscience, Computer Science, Applied
Mathematics/Statistics, Electrical Engineering, Biomedical Engineering, or
related fields. Good command of programming tools including Matlab, C++,
Linux, and scripting are necessary to carry out the research work in this
group. The candidate will support our efforts either in advancing
neuroimaging analysis technologies or in neuroscience applications.



The successful candidate will be part of a diverse group including
neuroscientists, radiologists, psychologists, physicists, biostatistician,
and computer scientists, and will build upon the group's extensive
foundation on neuroimaging analysis. If interested, please email resume to
Dr. Gang Li (gang...@med.unc.edu).
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[Freesurfer] Co-registering different source data

[Crawford, Anna]

Hello,

I am trying to create a new surface area on the inflated brain given by 
freesurfer using recon-all. I make to create my own ROI that is co-registered 
onto this surfer. Ultimately, I want to be able to take information from a 
different data source such as EEG and have it co-registered onto the inflated 
surface. How do I go about creating this new ROI surface?

Thanks,
Anna

===


 Please consider the environment before printing this e-mail

Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & 
World Report (2015).  
Visit us online at http://www.clevelandclinic.org for a complete listing of our 
services, staff and locations.


Confidentiality Note:  This message is intended for use only by the individual 
or entity to which it is addressed and may contain information that is 
privileged, confidential, and exempt from disclosure under applicable law.  If 
the reader of this message is not the intended recipient or the employee or 
agent responsible for delivering the message to the intended recipient, you are 
hereby notified that any dissemination, distribution or copying of this 
communication is strictly prohibited.  If you have received this communication 
in error,  please contact the sender immediately and destroy the material in 
its entirety, whether electronic or hard copy.  

Thank you.
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The information in this e-mail is intended only for the person to whom it is
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[Freesurfer] White matter editing using control points

[Jannike Ausland]

Hi,


I am having some trouble with white matter editing using control points. I am 
placing control points in white matter with intensity <110, and I find that it 
seems to have different effects in different slices/subjects, which makes it 
hard to develop a general standard for control point editing. Additionally, the 
curve outlining white matter is often less correct after control point edit, 
also some distance away from where control points are added. So, how does 
Freesurfer interpret control points and what exactly happens when control 
points are added? How does the number of control points used and the intensity 
of the voxels in which the control points are placed determine the outcome?


Thanks,


Jannike
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