Re: [Freesurfer] WM parcelleted boundary

[Bruce Fischl]

Yes, that seems reasonable
Bruce



On Dec 15, 2010, at 1:57 PM, "Ingalhalikar, Madhura" 
 wrote:

> Bruce, 
> 
> Please ignore my earlier email. 
> Let me explain what I exactly need. 
> The wmparc.mgz gives me WM parcellation based on cortical parcellation. What 
> I need is just the boundary voxels from wmparc.mgz, such that each voxel in 
> my output has a neighbor in GM and other WM voxels are set to 0. 
> If there is already something available, that would be great. Otherwise I was 
> thinking of proceeding in the following manner,
> 
> Input: WMparc.mgz, WM mask, GM mask. 
> Check if each voxel in WMparc.mgz is inside WM mask. 
> If yes, check if the voxel has atleast one neighbor in GM. 
> If yes, set this voxel as output. 
> else, 
> Output is 0. 
> 
> I hope it makes sense, 
> 
> Madhura
> 
> 
> 
> -Original Message-
> From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
> Sent: Wed 12/15/2010 11:05 AM
> To: Ingalhalikar, Madhura
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: RE: [Freesurfer] WM parcelleted boundary
> 
> Hi Madhura,
> 
> I'm not sure I understand. The ?h.white is the boundary. If you want to 
> create a voxel representation of it you can use mris_fill
> 
> cheers
> Bruce
> On Wed, 15 Dec 
> 2010, Ingalhalikar, Madhura wrote:
> 
>> Bruce and Allison,
>> Thanks for your prompt reply. For me wmparc.mgz is not entirely the correct 
>> solution. I just need the labeled WM boundary (ribbon) to seed my fiber 
>> tracking. So basically I will have to compute the boundary from wmparc.mgz. 
>> Is there anything that does that already?
>> Thanks,
>> Madhura
>> 
>> 
>> -Original Message-
>> From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
>> Sent: Fri 12/10/2010 8:13 PM
>> To: Ingalhalikar, Madhura
>> Cc: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] WM parcelleted boundary
>> 
>> Hi Madhura,
>> 
>> have you looked at the wmparc.mgz? It  might be exactly what you want
>> 
>> Bruce
>> 
>> On
>> Fri, 10 Dec 2010, Ingalhalikar, Madhura wrote:
>> 
>>> Hi,
>>> 
>>> Is there a way to get the cortical parcellations projected onto the WM 
>>> boundary? I need to seed the boundary of the cortical ROI ( in WM) for 
>>> fiber tracking.
>>> Please let me know,
>>> 
>>> Thank you,
>>> Madhura
>>> 
>>> 
>>> The information contained in this e-mail message is intended only for the 
>>> personal and confidential use of the recipient(s) named above. If the 
>>> reader of this message is not the intended recipient or an agent 
>>> responsible for delivering it to the intended recipient, you are hereby 
>>> notified that you have received this document in error and that any review, 
>>> dissemination, distribution, or copying of this message is strictly 
>>> prohibited. If you have received this communication in error, please notify 
>>> us immediately by e-mail, and delete the original message.
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>>> 
>>> 
>> 
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> 
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[Freesurfer] trgicoorder flag in mri_surf2surf

[Joakim Vinberg]

Hi everybody,

 

I am interested in doing sub-sampling of functional data for some new
analyses. Just about the only reference I can find to sub-sampling of
data in FreeSurfer is in mri_surf2surf, which has an optional flag
trgicoorder. The comment for this flag is:

 

"This specifies the size of the icosahedron according to the formula
#vertices=10*4^n+2. In general, it is best to use the largest size
available."

 

It would seem that I might be able to use this flag in order to
sub-sample surface data by using a smaller n (it seems as if the default
for fsaverage is 7 according to the specified formula). Is this correct?

 

Are there any particular guidelines to n? Other surfaces have a variety
of vertices, so it seems that n does not have to be an integer?

 

If I computer a surface of functional data for a given subject with a
specific 'n' and resulting nVertices, should I also calculate an
according anatomical surface with the same number of vertices for
display and analysis?

 

Thanks!

 

Joakim

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Re: [Freesurfer] Difficulty running FreeSurfer

[Bruce Fischl]

Hi Thomas,

you need to create that file.

cheers
Bruce
On Wed, 15 Dec 2010, Obisesan, Thomas O. 
wrote:

> Thanks Bruce,
>
> Unfortunately, we are unable to locate any such file. Any directives on how 
> to locate the file will be helpful. Additionally, we are unable to paste into 
> the Xterminal.
>
> Thanks
> Thomas Obisesan
>
> - Original Message -
> From: Bruce Fischl 
> To: Nisser ali umar 
> Cc: Freesurfer@nmr.mgh.harvard.edu ; 
> ryorricks...@gmail.com ; Obisesan, Thomas O.
> Sent: Wed Dec 15 20:11:05 2010
> Subject: Re: [Freesurfer] Difficulty running FreeSurfer
>
> Hi Nisser,
>
> put it in a file named $FREESURFER_HOME/.license
>
>
> cheers
> Bruce
>
> On Thu, 16 Dec 2010, Nisser ali
> umar wrote:
>
>> Hi,
>>
>> We installed freesurfer on a mac computer but could not find where to
>> paste the license code, thus have difficulty getting the freesurfer
>> running.
>>
>> Can anyone help, please.
>>
>> Nisser
>>
>>
>>
>>
>>
>>
>
>
> 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] Difficulty running FreeSurfer

[Emily Ward]

If you're having trouble pasting it in there, try:

pico /$FREESURFER_HOME/.license

(Press Crt-X to save)

If there are permission problems, manually go to the folder info and
change permissions at the bottom.

On Wed, Dec 15, 2010 at 8:11 PM, Bruce Fischl
 wrote:
>
> Hi Nisser,
>
> put it in a file named $FREESURFER_HOME/.license
>
>
> cheers
> Bruce
>
> On Thu, 16 Dec 2010, Nisser ali
> umar wrote:
>
> > Hi,
> >
> > We installed freesurfer on a mac computer but could not find where to
> > paste the license code, thus have difficulty getting the freesurfer
> > running.
> >
> > Can anyone help, please.
> >
> > Nisser
> >
> >
> >
> >
> >
> >
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Re: [Freesurfer] Difficulty running FreeSurfer

[Bruce Fischl]

Hi Nisser,

put it in a file named $FREESURFER_HOME/.license


cheers
Bruce

On Thu, 16 Dec 2010, Nisser ali 
umar wrote:

> Hi,
> 
> We installed freesurfer on a mac computer but could not find where to
> paste the license code, thus have difficulty getting the freesurfer
> running.
> 
> Can anyone help, please.
> 
> Nisser
> 
> 
> 
> 
> 
>
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[Freesurfer] Difficulty running FreeSurfer

[Nisser ali umar]

Hi,

We installed freesurfer on a mac computer but could not find where to paste the license code, thus have difficulty getting the freesurfer running.

Can anyone help, please.

Nisser




  

  






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[Freesurfer] Alignment of non whole-brain functional slabs

[Joakim Vinberg]

Hi everybody,

 

I am working towards multi-modal integration of BOLD data. For some of
my data, the entire brain was not recorded (in this case, I have 12
slices covering the superior half of the brain). I have been working to
align this data using bbregister and have had very inconsistent results:
in 1 subject it worked great; in another 6, the alignment failed
(resulting in an alignment that is sometimes close, and sometimes way
off).

 

I am creating a .nii using MRICRON/dcm2niiGUI, and using bbregister. I
have used this method successfully with a number of other sessions so
far (with functional slabs that do cover the entire brain) with
outstanding results.

 

Is this troublesome for bbregister, or is there potentially something
I'm doing incorrectly?

 

Thanks in advance! If I'm repeating well-worn topics, I apologize, I
couldn't find anything following a search through the archives.

 

Joakim

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Re: [Freesurfer] mri_convert float to uchar

[Yang Liu]

Hi,

I found that some of the voxels in my original a.mgz  are negative.
I think that caused some strange behaviors in the float to uchar conversion.
Are there methods in Freesurfer to modify the voxel values ?

Yang



On Wed, Dec 15, 2010 at 11:11 AM, Bruce Fischl
wrote:

> specify -ns 1 (for no scaling)
>
>
> On Wed, 15 Dec 2010, Yang Liu wrote:
>
>  Hello all,
>>
>> I am converting one .mgz file to another like this:
>>
>> mri_convert -i a.mgz -o conformed_a.mgz --conform
>>
>> The data type of a.mgz is float. After the conversion, The conformed_a.mgz
>> is uchar. However, I found that the places surrounding the brain which
>> have
>> 0 grayscale values in the a.mgz are having grayscale value 108 in the
>> confored_a.mgz.
>> This makes the conformed_a.mgz very whitish compared to the original one.
>>
>> Is there a way to make the float 0 to a uchar 0?
>>
>>
>> Thanks.
>>
>> Yang
>>
>>
>
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> is
> addressed. If you believe this e-mail was sent to you in error and the
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Re: [Freesurfer] WM parcelleted boundary

[Bruce Fischl]

yes, the cortical labels in the .annot files apply the ?h.white surfaces

cheers
Bruce
On 
Wed, 15 Dec 2010, Ingalhalikar, Madhura wrote:

>
> Bruce,
> I agree that ?h.white is a boundary. But it is labeled based on cortical 
> labels? If yes, that is exactly what I need.
> Let me know,
>
> Thanks for your response.
> Madhura
>
> -Original Message-
> From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
> Sent: Wed 12/15/2010 11:05 AM
> To: Ingalhalikar, Madhura
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: RE: [Freesurfer] WM parcelleted boundary
>
> Hi Madhura,
>
> I'm not sure I understand. The ?h.white is the boundary. If you want to
> create a voxel representation of it you can use mris_fill
>
> cheers
> Bruce
> On Wed, 15 Dec
> 2010, Ingalhalikar, Madhura wrote:
>
>> Bruce and Allison,
>> Thanks for your prompt reply. For me wmparc.mgz is not entirely the correct 
>> solution. I just need the labeled WM boundary (ribbon) to seed my fiber 
>> tracking. So basically I will have to compute the boundary from wmparc.mgz. 
>> Is there anything that does that already?
>> Thanks,
>> Madhura
>>
>>
>> -Original Message-
>> From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
>> Sent: Fri 12/10/2010 8:13 PM
>> To: Ingalhalikar, Madhura
>> Cc: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] WM parcelleted boundary
>>
>> Hi Madhura,
>>
>> have you looked at the wmparc.mgz? It  might be exactly what you want
>>
>> Bruce
>>
>> On
>> Fri, 10 Dec 2010, Ingalhalikar, Madhura wrote:
>>
>>> Hi,
>>>
>>> Is there a way to get the cortical parcellations projected onto the WM 
>>> boundary? I need to seed the boundary of the cortical ROI ( in WM) for 
>>> fiber tracking.
>>> Please let me know,
>>>
>>> Thank you,
>>> Madhura
>>>
>>>
>>> The information contained in this e-mail message is intended only for the 
>>> personal and confidential use of the recipient(s) named above. If the 
>>> reader of this message is not the intended recipient or an agent 
>>> responsible for delivering it to the intended recipient, you are hereby 
>>> notified that you have received this document in error and that any review, 
>>> dissemination, distribution, or copying of this message is strictly 
>>> prohibited. If you have received this communication in error, please notify 
>>> us immediately by e-mail, and delete the original message.
>>>
>>> ___
>>> 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.
>>
>>
>>
>>
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>> of this message is not the intended recipient or an agent responsible for 
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>> received this communication in error, please notify us immediately by 
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>>
>>
>>
>
>
>
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[Freesurfer] matlab loading problem (mkcontrast, selxavg3-sess)

[Katherine Sledge Moore]

I am having trouble with the interface between freesurfer and matlab. When I 
run mkcontrast-sess and selxavg3-sess, matlab opens, but nothing happens (the 
script does not finish.) When I force it to quit, I get the error "-display: 
Command not found." In both mkcontrast and selxavg3-sess, the command to call 
matlab is something along the lines of "matlab -display iconic". Any thoughts 
as to why the "-display iconic" part is not being interpreted?

Katherine Sledge Moore
Postdoctoral Associate
Visual Cognitive Neuroscience Laboratory
Yale University
http://camplab.psych.yale.edu/
http://pantheon.yale.edu/~khs8


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Re: [Freesurfer] WM parcelleted boundary

[Ingalhalikar, Madhura]

Bruce, 

Please ignore my earlier email. 
Let me explain what I exactly need. 
The wmparc.mgz gives me WM parcellation based on cortical parcellation. What I 
need is just the boundary voxels from wmparc.mgz, such that each voxel in my 
output has a neighbor in GM and other WM voxels are set to 0. 
If there is already something available, that would be great. Otherwise I was 
thinking of proceeding in the following manner,

Input: WMparc.mgz, WM mask, GM mask. 
Check if each voxel in WMparc.mgz is inside WM mask. 
If yes, check if the voxel has atleast one neighbor in GM. 
If yes, set this voxel as output. 
else, 
Output is 0. 

I hope it makes sense, 

Madhura



-Original Message-
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
Sent: Wed 12/15/2010 11:05 AM
To: Ingalhalikar, Madhura
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] WM parcelleted boundary
 
Hi Madhura,

I'm not sure I understand. The ?h.white is the boundary. If you want to 
create a voxel representation of it you can use mris_fill

cheers
Bruce
On Wed, 15 Dec 
2010, Ingalhalikar, Madhura wrote:

> Bruce and Allison,
> Thanks for your prompt reply. For me wmparc.mgz is not entirely the correct 
> solution. I just need the labeled WM boundary (ribbon) to seed my fiber 
> tracking. So basically I will have to compute the boundary from wmparc.mgz. 
> Is there anything that does that already?
> Thanks,
> Madhura
>
>
> -Original Message-
> From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
> Sent: Fri 12/10/2010 8:13 PM
> To: Ingalhalikar, Madhura
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] WM parcelleted boundary
>
> Hi Madhura,
>
> have you looked at the wmparc.mgz? It  might be exactly what you want
>
> Bruce
>
> On
> Fri, 10 Dec 2010, Ingalhalikar, Madhura wrote:
>
>> Hi,
>>
>> Is there a way to get the cortical parcellations projected onto the WM 
>> boundary? I need to seed the boundary of the cortical ROI ( in WM) for fiber 
>> tracking.
>> Please let me know,
>>
>> Thank you,
>> Madhura
>>
>>
>> The information contained in this e-mail message is intended only for the 
>> personal and confidential use of the recipient(s) named above. If the reader 
>> of this message is not the intended recipient or an agent responsible for 
>> delivering it to the intended recipient, you are hereby notified that you 
>> have received this document in error and that any review, dissemination, 
>> distribution, or copying of this message is strictly prohibited. If you have 
>> received this communication in error, please notify us immediately by 
>> e-mail, and delete the original message.
>>
>> ___
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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.
>
>
>
>
> The information contained in this e-mail message is intended only for the 
> personal and confidential use of the recipient(s) named above. If the reader 
> of this message is not the intended recipient or an agent responsible for 
> delivering it to the intended recipient, you are hereby notified that you 
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> and delete the original message.
>
>
>



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Re: [Freesurfer] WM parcelleted boundary

[Ingalhalikar, Madhura]

Bruce, 
I agree that ?h.white is a boundary. But it is labeled based on cortical 
labels? If yes, that is exactly what I need. 
Let me know, 

Thanks for your response. 
Madhura

-Original Message-
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
Sent: Wed 12/15/2010 11:05 AM
To: Ingalhalikar, Madhura
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] WM parcelleted boundary
 
Hi Madhura,

I'm not sure I understand. The ?h.white is the boundary. If you want to 
create a voxel representation of it you can use mris_fill

cheers
Bruce
On Wed, 15 Dec 
2010, Ingalhalikar, Madhura wrote:

> Bruce and Allison,
> Thanks for your prompt reply. For me wmparc.mgz is not entirely the correct 
> solution. I just need the labeled WM boundary (ribbon) to seed my fiber 
> tracking. So basically I will have to compute the boundary from wmparc.mgz. 
> Is there anything that does that already?
> Thanks,
> Madhura
>
>
> -Original Message-
> From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
> Sent: Fri 12/10/2010 8:13 PM
> To: Ingalhalikar, Madhura
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] WM parcelleted boundary
>
> Hi Madhura,
>
> have you looked at the wmparc.mgz? It  might be exactly what you want
>
> Bruce
>
> On
> Fri, 10 Dec 2010, Ingalhalikar, Madhura wrote:
>
>> Hi,
>>
>> Is there a way to get the cortical parcellations projected onto the WM 
>> boundary? I need to seed the boundary of the cortical ROI ( in WM) for fiber 
>> tracking.
>> Please let me know,
>>
>> Thank you,
>> Madhura
>>
>>
>> The information contained in this e-mail message is intended only for the 
>> personal and confidential use of the recipient(s) named above. If the reader 
>> of this message is not the intended recipient or an agent responsible for 
>> delivering it to the intended recipient, you are hereby notified that you 
>> have received this document in error and that any review, dissemination, 
>> distribution, or copying of this message is strictly prohibited. If you have 
>> received this communication in error, please notify us immediately by 
>> e-mail, and delete the original message.
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>>
>>
>>
>
>
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> 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
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>
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> The information contained in this e-mail message is intended only for the 
> personal and confidential use of the recipient(s) named above. If the reader 
> of this message is not the intended recipient or an agent responsible for 
> delivering it to the intended recipient, you are hereby notified that you 
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Re: [Freesurfer] mri_convert float to uchar

[Bruce Fischl]

specify -ns 1 (for no scaling)

On Wed, 15 Dec 2010, Yang Liu wrote:

> Hello all,
>
> I am converting one .mgz file to another like this:
>
> mri_convert -i a.mgz -o conformed_a.mgz --conform
>
> The data type of a.mgz is float. After the conversion, The conformed_a.mgz
> is uchar. However, I found that the places surrounding the brain which have
> 0 grayscale values in the a.mgz are having grayscale value 108 in the
> confored_a.mgz.
> This makes the conformed_a.mgz very whitish compared to the original one.
>
> Is there a way to make the float 0 to a uchar 0?
>
>
> Thanks.
>
> Yang
>
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Re: [Freesurfer] mri_convert float to uchar

[Yang Liu]

Hi Bruce,

Thank you.

I did try

mri_convert -i a.mgz conformed_a.mgz --conform -ns 1

the pixels with 0 grayscale in a.mgz are still turned into pixels with 108
grayscale in conformed_a.mgz.


Yang

On Wed, Dec 15, 2010 at 11:11 AM, Bruce Fischl
wrote:

> specify -ns 1 (for no scaling)
>
>
> On Wed, 15 Dec 2010, Yang Liu wrote:
>
>  Hello all,
>>
>> I am converting one .mgz file to another like this:
>>
>> mri_convert -i a.mgz -o conformed_a.mgz --conform
>>
>> The data type of a.mgz is float. After the conversion, The conformed_a.mgz
>> is uchar. However, I found that the places surrounding the brain which
>> have
>> 0 grayscale values in the a.mgz are having grayscale value 108 in the
>> confored_a.mgz.
>> This makes the conformed_a.mgz very whitish compared to the original one.
>>
>> Is there a way to make the float 0 to a uchar 0?
>>
>>
>> Thanks.
>>
>> Yang
>>
>>
>
> 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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> dispose of the e-mail.
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Re: [Freesurfer] WM parcelleted boundary

[Bruce Fischl]

Hi Madhura,

I'm not sure I understand. The ?h.white is the boundary. If you want to 
create a voxel representation of it you can use mris_fill

cheers
Bruce
On Wed, 15 Dec 
2010, Ingalhalikar, Madhura wrote:

> Bruce and Allison,
> Thanks for your prompt reply. For me wmparc.mgz is not entirely the correct 
> solution. I just need the labeled WM boundary (ribbon) to seed my fiber 
> tracking. So basically I will have to compute the boundary from wmparc.mgz. 
> Is there anything that does that already?
> Thanks,
> Madhura
>
>
> -Original Message-
> From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
> Sent: Fri 12/10/2010 8:13 PM
> To: Ingalhalikar, Madhura
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] WM parcelleted boundary
>
> Hi Madhura,
>
> have you looked at the wmparc.mgz? It  might be exactly what you want
>
> Bruce
>
> On
> Fri, 10 Dec 2010, Ingalhalikar, Madhura wrote:
>
>> Hi,
>>
>> Is there a way to get the cortical parcellations projected onto the WM 
>> boundary? I need to seed the boundary of the cortical ROI ( in WM) for fiber 
>> tracking.
>> Please let me know,
>>
>> Thank you,
>> Madhura
>>
>>
>> The information contained in this e-mail message is intended only for the 
>> personal and confidential use of the recipient(s) named above. If the reader 
>> of this message is not the intended recipient or an agent responsible for 
>> delivering it to the intended recipient, you are hereby notified that you 
>> have received this document in error and that any review, dissemination, 
>> distribution, or copying of this message is strictly prohibited. If you have 
>> received this communication in error, please notify us immediately by 
>> e-mail, and delete the original message.
>>
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
>
>
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> contains patient information, please contact the Partners Compliance HelpLine 
> at
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[Freesurfer] mri_convert float to uchar

[Yang Liu]

Hello all,

I am converting one .mgz file to another like this:

mri_convert -i a.mgz -o conformed_a.mgz --conform

The data type of a.mgz is float. After the conversion, The conformed_a.mgz
is uchar. However, I found that the places surrounding the brain which have
0 grayscale values in the a.mgz are having grayscale value 108 in the
confored_a.mgz.
This makes the conformed_a.mgz very whitish compared to the original one.

Is there a way to make the float 0 to a uchar 0?


Thanks.

Yang
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[Freesurfer] .xdebug_tkmedit

[Paola Valsasina]

Dear List,

I installed version 5.0 of freesurfer on my Linux machine, when I tried to
run tkmedit I got the attached error. Do you have any suggestion?
Kind regards,
Paola


  

---
SOSTIENI ANCHE TU LA RICERCA DEL SAN RAFFAELE.
NON C'E' CURA SENZA RICERCA.
Per donazioni: ccp 42437681 intestato a Fondazione Arete' Onlus del San 
Raffaele.
Per informazioni: tel. 02.2643.4461 - www.sanraffaele.org


.xdebug_tkmedit
Description: Binary data
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Re: [Freesurfer] WM parcelleted boundary

[Ingalhalikar, Madhura]

Bruce and Allison, 
Thanks for your prompt reply. For me wmparc.mgz is not entirely the correct 
solution. I just need the labeled WM boundary (ribbon) to seed my fiber 
tracking. So basically I will have to compute the boundary from wmparc.mgz. Is 
there anything that does that already?
Thanks, 
Madhura


-Original Message-
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
Sent: Fri 12/10/2010 8:13 PM
To: Ingalhalikar, Madhura
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] WM parcelleted boundary
 
Hi Madhura,

have you looked at the wmparc.mgz? It  might be exactly what you want

Bruce

On 
Fri, 10 Dec 2010, Ingalhalikar, Madhura wrote:

> Hi,
>
> Is there a way to get the cortical parcellations projected onto the WM 
> boundary? I need to seed the boundary of the cortical ROI ( in WM) for fiber 
> tracking.
> Please let me know,
>
> Thank you,
> Madhura
>
>
> The information contained in this e-mail message is intended only for the 
> personal and confidential use of the recipient(s) named above. If the reader 
> of this message is not the intended recipient or an agent responsible for 
> delivering it to the intended recipient, you are hereby notified that you 
> have received this document in error and that any review, dissemination, 
> distribution, or copying of this message is strictly prohibited. If you have 
> received this communication in error, please notify us immediately by e-mail, 
> and delete the original message.
>
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>
>
>


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Re: [Freesurfer] CUDA on Mac

[Nick Schmansky]

yes, its in the works for the next release.

n.

On Wed, 2010-12-15 at 11:34 +0100, Martin Kavec wrote:
> Hi all,
> 
> I wonder if there are any plans to support CUDA on Mac platform. I see
> there are libraries available for the platform.
> 
> Thanks a lot for feedback,
> 
> Martin
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Re: [Freesurfer] the usage of mri_surf2vol program

[Nick Schmansky]

another option is to convert the thickness file to gifti format.  see
mris_convert --help. 

n.

On Wed, 2010-12-15 at 01:26 -0800, qizhu wu wrote:
> Dear all,
> 
> Continue with my previous question in "To use the file thickness.mgh
> outside Freesurfer". Thanks for Doug's recommedation to use the
> mri_surf2vol program to convert mgh files into image format, such as
> NIFTI.
> But I failed due to wrong setting on several arguments:
> 
> 1,  '--volreg': I do not understand what file it requires. It's
> declared in --help that "Contains the matrix that maps XYZ in the
> reference anatomical to XYZ in the functional volume". But I am only
> dealing with the structural volumes, and has this file been created in
> any step during the previous processing? Or could anyone tell me
> clearly how to set this argument?
> 
> 2, --surfval: if only pthname rather than single file is allowed as
> input here?
> 
> 3, --template: couldI use mni305.cor.mgz, or just left these optional
> arguments empty?
> 
> thanks in advance.
> 
> Qizhu Wu
> 
> 
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Re: [Freesurfer] another recon-all error

[Nick Schmansky]

this is a problem that will be fixed in the upcoming 5.1 release
(*hopefully* by the end of the year).

the workaround is to run mri_nu_correct.mni adding the -nofloat flag.  

n.

On Wed, 2010-12-15 at 02:57 -0500, Thomas, Adam (NIH/NIMH) [E] wrote:
> Bruce et al,
> 
>  
> 
> Did you ever get to the bottom of Joakim’s problem? I’m getting the
> same error. I checked the talairach and it looks fine. But for some
> reason mri_normalize can’t find any peaks so T1.mgz comes out as all
> zeros.
> 
>  
> 
> I just uploaded the subject to your anon FTP server.: ex03.2.tgz
> 
>  
> 
> Thanks and let me know,
> 
> -Adam
> 
>  
> 
>  
> 
>  
> 
>  
> 
> On Thu, Nov 2010, Bruce Fischl wrote:
> 
>  
> 
> Hi Joakim,
> 
>  
> 
> you need to visualize the talairach.xfm applied to the orig.mgz in
> either tkregister2 or tkmedit to see if it is ok. mri_normalize
> clearly failed, and this is usually because of a failure in the
> talairach. It could also be that the nu intensity correction failed,
> so make sure to look at the nu.mgz as well. Or if you rather you can
> send us the nu.mgz and we can see what happened.
> 
> cheers
> 
> Bruce
> 
>  
> 
>  
> 
>  
> 
> On Thu, 11 Nov 2010, Joakim Vinberg wrote:
> 
>  
> 
> Bruce,
> 
>  
> 
> I had quickly scanned the talairach.xfm, but I have to admit that I'm
> new to 
> 
> the process and wasn't sure what I was looking for. Here are the
> recon-all.log 
> 
> and talairach.xfm from this subject. Thank you for all the help!
> 
>  
> 
> oakimJ
> 
>  
> 
> -Original Message-
> 
> From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
> 
> Sent: Wednesday, November 10, 2010 7:09 PM
> 
> To: Joakim Vinberg
> 
> Cc: 
> 
> Subject: Re: [Freesurfer] another recon-all error
> 
>  
> 
> Did you check the talairach.xfm? Can you send us the recon-all.log
> file?
> 
>  
> 
>  
> 
>  
> 
> On Nov 10, 2010, at 9:35 PM, "Joakim Vinberg" 
> wrote:
> 
>  
> 
> Sorry to add another!
> 
>  
> 
>  
> 
>  
> 
> I ran recon-all on a subject of mine, and have recon-all exit with the
> error 
> 
> below. Based on the message, I examined both T1 and nu.mgz. T1.mgz is
> in fact 
> 
> totally emptyÿÿdefinitely not enough values of 110. Is this due to a
> specific 
> 
> error that I might be able to bypass, or will adding in WM control
> points fix 
> 
> things?
> 
>  
> 
>  
> 
>  
> 
> Thanks in advance!
> 
>  
> 
>  
> 
>  
> 
> Joakim
> 
>  
> 
>  
> 
>  
> 
> //
> 
>  
> 
>  
> 
>  
> 
> mri_watershed -T1 -brain_atlas 
> 
> /usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca 
> 
> transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz
> 
>  
> 
>  
> 
>  
> 
>  
> 
>  
> 
> Mode:  T1 normalized volume
> 
>  
> 
> Mode:  Use the information of atlas (default parms, --help for
> details)
> 
>  
> 
>  
> 
>  
> 
> *
> 
>  
> 
> The input file is T1.mgz
> 
>  
> 
> The output file is brainmask.auto.mgz
> 
>  
> 
> Weighting the input with atlas information before watershed
> 
>  
> 
>  
> 
>  
> 
> *WATERSHED**
> 
>  
> 
> Sorting...
> 
>  
> 
> mri_watershed Error:
> 
>  
> 
> Problem in the COG calculation:
> 
>  
> 
> T1.mgz may not contain properly normalized white-matter.
> 
>  
> 
> Confirm that T1.mgz has enough white-matter voxels of value 110.
> 
>  
> 
> If white-matter contains few if any voxels of value 110,
> 
>  
> 
> try adding wm control-points to nu.mgz, and re-run recon-all.
> 
>  
> 
>  
> 
>  
> 
> Linux penguin 2.6.34.6-54.fc13.i686 #1 SMP Sun Sep 5 17:52:31 UTC 2010
> i686 
> 
> i686 i386 GNU/Linux
> 
>  
> 
>  
> 
>  
> 
> recon-all -s 0142 exited with ERRORS at Wed Nov 10 16:55:08 PST 2010
> 
>  
> 
>  
> 
>  
> 
>  
> 
> 
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Re: [Freesurfer] running in the background?

[Nick Schmansky]

i use nohup with recon-all remotely, with:

nohup recon-all -s subj -all >& /dev/null &

notice the >& /dev/null, which redirects stdout and stderr to null.
i've found this is necessary.  note that recon-all output still goes to
its log.   after launching this way, you can close the terminal, and
recon-all will still be running on whereever you launched it.

n.


On Tue, 2010-12-14 at 21:54 -0500, Scott Burns wrote:
> You can make it work with nohup? In the past I've had trouble and my
> thinking was that because recon-all starts many child processes, the
>  currently continues after the terminal is closed, but any subsequent
> process can't start.  That's why I've been using screen, but YMMV.
> 
> 
> Scott Burns
> Kuperberg Lab
> Martinos Center, MGH
> sbu...@nmr.mgh.harvard.edu
> 
> 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.
> 
> 
> 
> On Tue, Dec 14, 2010 at 9:02 PM, Watson, Christopher
>  wrote:
> You can also just run e.g. "nohup recon-all -autorecon-all -s
> doe_j &"
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Scott
> Burns [sbu...@nmr.mgh.harvard.edu]
> Sent: Tuesday, December 14, 2010 8:05 PM
> To: Nathan Dankner
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] running in the background?
> 
> This tip comes from Sam at the helpdesk...
> 
> At the command prompt, type 'screen' and press enter.  This
> opens the terminal emulation program, aptly named screen.  In
> this new terminal, start your recon as you would normally,
> whether that's invoking a script of your making or typing in
> the standard 'recon -all '.  Once the job starts, either
> close the terminal window or press Ctrl-A followed by 'd'.
>  This detaches the screen session but safely keeps the
>  reconstruction pipeline going.
> 
> When you get back to your desk, type 'screen -r' at the
> command prompt to reattach to the screen session you created
> previously.  A new terminal will open and will contain all the
> output from the recon pipeline. Good luck.
> 
> 
> Scott Burns
> Kuperberg Lab
> Martinos Center, MGH
> 
> sbu...@nmr.mgh.harvard.edu
> 
> 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.
> 
> 
> 
> 
> On Tue, Dec 14, 2010 at 5:51 PM, Nathan Dankner
> mailto:nathan.dank...@vanderbilt.edu>> 
> wrote:
> Hi All,
> 
> I'm running freesurfer on a public station, so I need to sign
> out when I'm finished with sessions.  Has anyone found a
> suitable way to run freesurfer in the background?  I know that
> I can run matlab in the background here, so if there is a way
> to run the pipeline through matlab that may work... Thanks,
> 
> Nathan
> 
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Re: [Freesurfer] aparc+aseg

[Lilla Zollei]

Hi Pedro Paulo,

The aparc+aseg file describes a single volume with parcellation and 
segmentation information combined.


--Lilla

On Wed, 15 Dec 2010, Pedro Paulo de Magalhães Oliveira Junior wrote:


Hi,

One quick question: In the aparc+aseg file I suppose we have two volumes
(one for aparc and other for aseg). Are those volumes overlapped or one
after another?

thanks

PPJ
-
Pedro Paulo de Magalhães Oliveira Junior
Diretor de Operações
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://www.netfilter.com.br/mobile
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[Freesurfer] aparc+aseg

[Pedro Paulo de Magalhães Oliveira Junior]

Hi,

One quick question: In the aparc+aseg file I suppose we have two volumes
(one for aparc and other for aseg). Are those volumes overlapped or one
after another?

thanks

PPJ
-
Pedro Paulo de Magalhães Oliveira Junior
Diretor de Operações
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://www.netfilter.com.br/mobile
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[Freesurfer] CUDA on Mac

[Martin Kavec]

Hi all,

I wonder if there are any plans to support CUDA on Mac platform. I see there
are libraries available for the platform.

Thanks a lot for feedback,

Martin
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[Freesurfer] the usage of mri_surf2vol program

[qizhu wu]

Dear all,

Continue with my previous question in "To use the file thickness.mgh outside 
Freesurfer". Thanks for Doug's recommedation to use the mri_surf2vol program to 
convert mgh files into image format, such as NIFTI.
But I failed due to wrong setting on several arguments:

1,  '--volreg': I do not understand what file it requires. It's declared in 
--help that "Contains the matrix that maps XYZ in the reference anatomical to 
XYZ in the functional volume". But I am only dealing with the structural 
volumes, and has this file been created in any step during the previous 
processing? Or could anyone tell me clearly how to set this argument?

2, --surfval: if only pthname rather than single file is allowed as input here?

3, --template: couldI use mni305.cor.mgz, or just left these optional arguments 
empty?

thanks in advance.

Qizhu Wu



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