Re: [Freesurfer] Extract specific LGI and Volume values

[Douglas N. Greve]

what is your command line?

On 3/5/2020 1:50 AM, Tien Pham wrote:


External Email - Use Caution

Thank you for your suggestion.
I tried to use freeview to load surface on the label I created. But 
terminal showed this error '' freadFloat: fread failed '' many times.
I tried to load label with qdec and I got the error (pic 1) I attached 
below.
I also tried to load surface with qdec and this error displayed in 
terminal (pic 2).

I am very appreciated when you helped me before.
I am looking forward to hearing from you.
Thank you very much.

On Mon, Feb 24, 2020 at 11:16 PM Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> wrote:


Try using freeview

On 2/18/2020 8:17 PM, Tien Pham wrote:


External Email - Use Caution

Thank you for your email.
I tried to load the label with qdec and freeview and both were
not worked.
When i tried with qdec, It said '' load the surface first '' then
I did but It did not work and showed some errors.
The other way when I tried to load with qdec, qdec was closed
suddenly without any notification.
I am looking forward to hearing from you.

On Fri, Feb 14, 2020 at 11:44 PM Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>> wrote:

What tool are you trying to use to load the label? What
happens when you try?

On 2/7/2020 10:11 PM, Tien Pham wrote:


External Email - Use Caution

Thank you for your email. I run exactly the command
mri_label2label as you suggested, and the command finished
without any problem.
But I did not know why I could not open the label.
Please help me. Thank you once again.

On Tue, Feb 4, 2020 at 2:55 AM Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>> wrote:

sorry for the delay. You will have to use
mri_label2label to map the label from the fsaverage
space to the individual space


On 1/31/2020 10:01 PM, Tien Pham wrote:


External Email - Use Caution

Can you read my message?
I used longitudinal pipeline for my data set with two
time points and measured the LGI differences between them.
Then I created the label based on significant clusters
which showed in QDEC.
I tried to load the label on the subjects in cross,
base, long steps but it did not work.
I am looking forward to hearing from you. Thank you
very much.

On Sat, Feb 1, 2020 at 8:08 AM Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>> wrote:

Sorry, I do not have the previous emails, can you
repost with previous emails in the message?

On 1/28/2020 7:35 PM, Tien Pham wrote:


External Email - Use Caution

Thank you for your response.
I used longitudinal pipeline for my data set with
two time points and calculated the LGI differences
between them.
Then I created the label based on significant
clusters which showed in QDEC.
I tried to load the label on subjects in cross,
base, long steps but it did not work.
I am looking forward to hearing from you. Thank
you so much.

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Re: [Freesurfer] Extract specific LGI and Volume values

[Tien Pham]

External Email - Use Caution

Thank you for your suggestion.
I tried to use freeview to load surface on the label I created. But
terminal showed this error '' freadFloat: fread failed '' many times.
I tried to load label with qdec and I got the error (pic 1) I attached
below.
I also tried to load surface with qdec and this error displayed in terminal
(pic 2).
I am very appreciated when you helped me before.
I am looking forward to hearing from you.
Thank you very much.

On Mon, Feb 24, 2020 at 11:16 PM Douglas N. Greve 
wrote:

> Try using freeview
>
> On 2/18/2020 8:17 PM, Tien Pham wrote:
>
> External Email - Use Caution
> Thank you for your email.
> I tried to load the label with qdec and freeview and both were not worked.
> When i tried with qdec, It said '' load the surface first '' then I did
> but It did not work and showed some errors.
> The other way when I tried to load with qdec, qdec was closed suddenly
> without any notification.
> I am looking forward to hearing from you.
>
> On Fri, Feb 14, 2020 at 11:44 PM Douglas N. Greve 
> wrote:
>
>> What tool are you trying to use to load the label? What happens when you
>> try?
>>
>> On 2/7/2020 10:11 PM, Tien Pham wrote:
>>
>> External Email - Use Caution
>> Thank you for your email. I run exactly the command mri_label2label as
>> you suggested, and the command finished without any problem.
>> But I did not know why I could not open the label.
>> Please help me. Thank you once again.
>>
>> On Tue, Feb 4, 2020 at 2:55 AM Douglas N. Greve 
>> wrote:
>>
>>> sorry for the delay. You will have to use mri_label2label to map the
>>> label from the fsaverage space to the individual space
>>>
>>>
>>> On 1/31/2020 10:01 PM, Tien Pham wrote:
>>>
>>> External Email - Use Caution
>>> Can you read my message?
>>> I used longitudinal pipeline for my data set with two time points and
>>> measured the LGI differences between them.
>>> Then I created the label based on significant clusters which showed in
>>> QDEC.
>>> I tried to load the label on the subjects in cross, base, long steps
>>> but it did not work.
>>> I am looking forward to hearing from you. Thank you very much.
>>>
>>> On Sat, Feb 1, 2020 at 8:08 AM Douglas N. Greve 
>>> wrote:
>>>
 Sorry, I do not have the previous emails, can you repost with previous
 emails in the message?

 On 1/28/2020 7:35 PM, Tien Pham wrote:

 External Email - Use Caution
 Thank you for your response.

 I used longitudinal pipeline for my data set with two time points and
 calculated the LGI differences between them.
 Then I created the label based on significant clusters which showed in
 QDEC.
 I tried to load the label on subjects in cross, base, long steps but it
 did not work.
 I am looking forward to hearing from you. Thank you so much.

 ___
 Freesurfer mailing 
 listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>> ___
>>> Freesurfer mailing 
>>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
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>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> ___
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>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
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>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
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>
>
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Re: [Freesurfer] Extract specific LGI and Volume values

[Douglas N. Greve]

Try using freeview

On 2/18/2020 8:17 PM, Tien Pham wrote:


External Email - Use Caution

Thank you for your email.
I tried to load the label with qdec and freeview and both were not worked.
When i tried with qdec, It said '' load the surface first '' then I 
did but It did not work and showed some errors.
The other way when I tried to load with qdec, qdec was closed suddenly 
without any notification.

I am looking forward to hearing from you.

On Fri, Feb 14, 2020 at 11:44 PM Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> wrote:


What tool are you trying to use to load the label? What happens
when you try?

On 2/7/2020 10:11 PM, Tien Pham wrote:


External Email - Use Caution

Thank you for your email. I run exactly the command
mri_label2label as you suggested, and the command finished
without any problem.
But I did not know why I could not open the label.
Please help me. Thank you once again.

On Tue, Feb 4, 2020 at 2:55 AM Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>> wrote:

sorry for the delay. You will have to use mri_label2label to
map the label from the fsaverage space to the individual space


On 1/31/2020 10:01 PM, Tien Pham wrote:


External Email - Use Caution

Can you read my message?
I used longitudinal pipeline for my data set with two time
points and measured the LGI differences between them.
Then I created the label based on significant clusters which
showed in QDEC.
I tried to load the label on the subjects in cross, base,
long steps but it did not work.
I am looking forward to hearing from you. Thank you very much.

On Sat, Feb 1, 2020 at 8:08 AM Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>> wrote:

Sorry, I do not have the previous emails, can you repost
with previous emails in the message?

On 1/28/2020 7:35 PM, Tien Pham wrote:


External Email - Use Caution

Thank you for your response.
I used longitudinal pipeline for my data set with two
time points and calculated the LGI differences between
them.
Then I created the label based on significant clusters
which showed in QDEC.
I tried to load the label on subjects in cross, base,
long steps but it did not work.
I am looking forward to hearing from you. Thank you so
much.

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Re: [Freesurfer] Extract specific LGI and Volume values

[Tien Pham]

External Email - Use Caution

Thank you for your email.
I tried to load the label with qdec and freeview and both were not worked.
When i tried with qdec, It said '' load the surface first '' then I did but
It did not work and showed some errors.
The other way when I tried to load with qdec, qdec was closed suddenly
without any notification.
I am looking forward to hearing from you.

On Fri, Feb 14, 2020 at 11:44 PM Douglas N. Greve 
wrote:

> What tool are you trying to use to load the label? What happens when you
> try?
>
> On 2/7/2020 10:11 PM, Tien Pham wrote:
>
> External Email - Use Caution
> Thank you for your email. I run exactly the command mri_label2label as
> you suggested, and the command finished without any problem.
> But I did not know why I could not open the label.
> Please help me. Thank you once again.
>
> On Tue, Feb 4, 2020 at 2:55 AM Douglas N. Greve 
> wrote:
>
>> sorry for the delay. You will have to use mri_label2label to map the
>> label from the fsaverage space to the individual space
>>
>>
>> On 1/31/2020 10:01 PM, Tien Pham wrote:
>>
>> External Email - Use Caution
>> Can you read my message?
>> I used longitudinal pipeline for my data set with two time points and
>> measured the LGI differences between them.
>> Then I created the label based on significant clusters which showed in
>> QDEC.
>> I tried to load the label on the subjects in cross, base, long steps
>> but it did not work.
>> I am looking forward to hearing from you. Thank you very much.
>>
>> On Sat, Feb 1, 2020 at 8:08 AM Douglas N. Greve 
>> wrote:
>>
>>> Sorry, I do not have the previous emails, can you repost with previous
>>> emails in the message?
>>>
>>> On 1/28/2020 7:35 PM, Tien Pham wrote:
>>>
>>> External Email - Use Caution
>>> Thank you for your response.
>>>
>>> I used longitudinal pipeline for my data set with two time points and
>>> calculated the LGI differences between them.
>>> Then I created the label based on significant clusters which showed in
>>> QDEC.
>>> I tried to load the label on subjects in cross, base, long steps but it
>>> did not work.
>>> I am looking forward to hearing from you. Thank you so much.
>>>
>>> ___
>>> Freesurfer mailing 
>>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> ___
>> Freesurfer mailing 
>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
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>
>
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Re: [Freesurfer] Extract specific LGI and Volume values

[Douglas N. Greve]

What tool are you trying to use to load the label? What happens when you 
try?


On 2/7/2020 10:11 PM, Tien Pham wrote:


External Email - Use Caution

Thank you for your email. I run exactly the command mri_label2label as 
you suggested, and the command finished without any problem.

But I did not know why I could not open the label.
Please help me. Thank you once again.

On Tue, Feb 4, 2020 at 2:55 AM Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> wrote:


sorry for the delay. You will have to use mri_label2label to map
the label from the fsaverage space to the individual space


On 1/31/2020 10:01 PM, Tien Pham wrote:


External Email - Use Caution

Can you read my message?
I used longitudinal pipeline for my data set with two time points
and measured the LGI differences between them.
Then I created the label based on significant clusters which
showed in QDEC.
I tried to load the label on the subjects in cross, base, long
steps but it did not work.
I am looking forward to hearing from you. Thank you very much.

On Sat, Feb 1, 2020 at 8:08 AM Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>> wrote:

Sorry, I do not have the previous emails, can you repost with
previous emails in the message?

On 1/28/2020 7:35 PM, Tien Pham wrote:


External Email - Use Caution

Thank you for your response.
I used longitudinal pipeline for my data set with two time
points and calculated the LGI differences between them.
Then I created the label based on significant clusters which
showed in QDEC.
I tried to load the label on subjects in cross, base, long
steps but it did not work.
I am looking forward to hearing from you. Thank you so much.

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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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Re: [Freesurfer] Extract specific LGI and Volume values

[Tien Pham]

External Email - Use Caution

Thank you for your email. I run exactly the command mri_label2label as
you suggested, and the command finished without any problem.
But I did not know why I could not open the label.
Please help me. Thank you once again.

On Tue, Feb 4, 2020 at 2:55 AM Douglas N. Greve 
wrote:

> sorry for the delay. You will have to use mri_label2label to map the label
> from the fsaverage space to the individual space
>
>
> On 1/31/2020 10:01 PM, Tien Pham wrote:
>
> External Email - Use Caution
> Can you read my message?
> I used longitudinal pipeline for my data set with two time points and
> measured the LGI differences between them.
> Then I created the label based on significant clusters which showed in
> QDEC.
> I tried to load the label on the subjects in cross, base, long steps
> but it did not work.
> I am looking forward to hearing from you. Thank you very much.
>
> On Sat, Feb 1, 2020 at 8:08 AM Douglas N. Greve 
> wrote:
>
>> Sorry, I do not have the previous emails, can you repost with previous
>> emails in the message?
>>
>> On 1/28/2020 7:35 PM, Tien Pham wrote:
>>
>> External Email - Use Caution
>> Thank you for your response.
>>
>> I used longitudinal pipeline for my data set with two time points and
>> calculated the LGI differences between them.
>> Then I created the label based on significant clusters which showed in
>> QDEC.
>> I tried to load the label on subjects in cross, base, long steps but it
>> did not work.
>> I am looking forward to hearing from you. Thank you so much.
>>
>> ___
>> Freesurfer mailing 
>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Re: [Freesurfer] Extract specific LGI and Volume values

[Douglas N. Greve]

sorry for the delay. You will have to use mri_label2label to map the 
label from the fsaverage space to the individual space


On 1/31/2020 10:01 PM, Tien Pham wrote:


External Email - Use Caution

Can you read my message?
I used longitudinal pipeline for my data set with two time points and 
measured the LGI differences between them.
Then I created the label based on significant clusters which showed in 
QDEC.
I tried to load the label on the subjects in cross, base, long steps 
but it did not work.

I am looking forward to hearing from you. Thank you very much.

On Sat, Feb 1, 2020 at 8:08 AM Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> wrote:


Sorry, I do not have the previous emails, can you repost with
previous emails in the message?

On 1/28/2020 7:35 PM, Tien Pham wrote:


External Email - Use Caution

Thank you for your response.
I used longitudinal pipeline for my data set with two time points
and calculated the LGI differences between them.
Then I created the label based on significant clusters which
showed in QDEC.
I tried to load the label on subjects in cross, base, long steps
but it did not work.
I am looking forward to hearing from you. Thank you so much.

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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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Re: [Freesurfer] Extract specific LGI and Volume values

[Tien Pham]

External Email - Use Caution

Can you read my message?
I used longitudinal pipeline for my data set with two time points and
measured the LGI differences between them.
Then I created the label based on significant clusters which showed in QDEC.
I tried to load the label on the subjects in cross, base, long steps but it
did not work.
I am looking forward to hearing from you. Thank you very much.

On Sat, Feb 1, 2020 at 8:08 AM Douglas N. Greve 
wrote:

> Sorry, I do not have the previous emails, can you repost with previous
> emails in the message?
>
> On 1/28/2020 7:35 PM, Tien Pham wrote:
>
> External Email - Use Caution
> Thank you for your response.
>
> I used longitudinal pipeline for my data set with two time points and
> calculated the LGI differences between them.
> Then I created the label based on significant clusters which showed in
> QDEC.
> I tried to load the label on subjects in cross, base, long steps but it
> did not work.
> I am looking forward to hearing from you. Thank you so much.
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Re: [Freesurfer] Extract specific LGI and Volume values

[Tien Pham]

External Email - Use Caution

Thank you for your response.
I used longitudinal pipeline for my data set with two time points and
calculated the LGI differences between them.
Then I created the label based on significant clusters which showed in QDEC.
I tried to load the label on subjects in cross, base, long steps but it did
not work.
I am looking forward to hearing from you. Thank you so much.

On Sat, Feb 1, 2020 at 8:08 AM Douglas N. Greve 
wrote:

> Sorry, I do not have the previous emails, can you repost with previous
> emails in the message?
>
> On 1/28/2020 7:35 PM, Tien Pham wrote:
>
> External Email - Use Caution
> Thank you for your response.
>
> I used longitudinal pipeline for my data set with two time points and
> calculated the LGI differences between them.
> Then I created the label based on significant clusters which showed in
> QDEC.
> I tried to load the label on subjects in cross, base, long steps but it
> did not work.
> I am looking forward to hearing from you. Thank you so much.
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Re: [Freesurfer] Extract specific LGI and Volume values

[Douglas N. Greve]

Sorry, I do not have the previous emails, can you repost with previous 
emails in the message?


On 1/28/2020 7:35 PM, Tien Pham wrote:


External Email - Use Caution

Thank you for your response.
I used longitudinal pipeline for my data set with two time points and 
calculated the LGI differences between them.
Then I created the label based on significant clusters which showed in 
QDEC.
I tried to load the label on subjects in cross, base, long steps 
but it did not work.

I am looking forward to hearing from you. Thank you so much.

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

Re: [Freesurfer] Extract specific LGI and Volume values

[Tien Pham]

External Email - Use Caution

Thank you for your response.
I used longitudinal pipeline for my data set with two time points and
calculated the LGI differences between them.
Then I created the label based on significant clusters which showed in QDEC.
I tried to load the label on subjects in cross, base, long steps but it did
not work.
I am looking forward to hearing from you. Thank you so much.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Extract specific LGI and Volume values

[Greve, Douglas N.,Ph.D.]

I cannot see anything wrong with the label. How did you create it? Are you sure 
that the label belongs to the same subject's surface that you loading it onto?

On 1/26/2020 12:10 AM, Tien Pham wrote:

External Email - Use Caution

Thank you for your e-mail.
Yes, of course. I send the label I created to you in attachment.
Please, let me know if you have any problem with it.
Thank you.

On Sat, Jan 25, 2020 at 12:24 AM Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> wrote:
I'm guessing that there is something wrong with the label. Can you send it?

On 1/21/2020 8:08 PM, Tien Pham wrote:

External Email - Use Caution

Thank you for your e-mail.
I also could not load the label in freeview. The terminal showed the following 
error:

2020-01-22 09:56:18.064 Freeview[51338:303] modalSession has been exited 
prematurely - check for a reentrant call to endModalSession:
2020-01-22 09:56:26.655 Freeview[51338:303] modalSession has been exited 
prematurely - check for a reentrant call to endModalSession:
freadFloat: fread failed
freadFloat: fread failed

This error was still showing like it never end until I close freeview.

 I draw the ROI in qdec, then add selection to ROI , and save the current 
label. That was how I created the label.
I am looking forward to hearing from you. Thank you.

On Wed, Jan 22, 2020 at 12:17 AM Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> wrote:
You can try freeview, but there might be something wrong with the label. How 
was it created?

On 1/16/2020 11:51 PM, Tien Pham wrote:

External Email - Use Caution

Thank you for your help.
I cannot load the label on surface, this is the error:

[toyama-no-iMac:/applications/freesurfer/subjects] toyama% qdec

Reading /applications/freesurfer/tktools/tkUtils.tcl

Using /applications/freesurfer/lib/tcl/fsgdfPlot.tcl
qdec.bin(41334,0xa15971a8) malloc: *** mach_vm_map(size=114944) failed 
(error code=3)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
MRISalloc(15124178, 76): could not allocate faces
Cannot allocate memory

What do you mean how many point? How do I find it?

On Fri, Jan 17, 2020 at 1:17 PM Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> wrote:
Is the label valid? Can you load it on a surface? How many points are in it?

On 1/16/2020 9:51 PM, Tien Pham wrote:

External Email - Use Caution

Thank you for your e-mail.
It seems I got another error. This is what it showed in terminal:

[toyama-no-iMac:/applications/freesurfer/subjects] toyama% mri_segstats --i 
lh.pial_lgi --slabel VC001_1 lh lh.frontoinsula.label --id 1 --sum sum.dat

$Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $
cwd
cmdline mri_segstats --i lh.pial_lgi --slabel VC001_1 lh lh.frontoinsula.label 
--id 1 --sum sum.dat
sysname  Darwin
hostname toyama-no-iMac.local
machine  x86_64
user toyama
UseRobust  0
Constructing seg from label
Segmentation fault

Could you help me please?

On Fri, Jan 17, 2020 at 11:56 AM Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> wrote:
Sorry, it should have been --sum instead of --o
the subject name is subject_id
--id 1 just means to take the vertices in the label (--id 0 would mean to take 
the background)

On 1/16/2020 7:07 PM, Tien Pham wrote:

External Email - Use Caution

Thank you very much for your e-mail.
I tried, but this '' --o '' is unknown showing in terminal and the '' --id '' 
flag is subject name?
Could you please help me?
For example, I found the change in frontoinsula region between 2 groups in my 
dataset and I want to extract the values of this region.

On Fri, Jan 17, 2020 at 8:30 AM Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> wrote:
It might be easier to use mri_segstats, eg,

mri_segstats --i lh.pial_lgi --slabel subject_id lh lh.untitled.label --id 1 
--o sum.dat

The mean value will be in the "Mean" column of the sum.dat


On 1/14/2020 7:08 PM, Tien Pham wrote:

External Email - Use Caution

Dear FreeSurfer Experts,

I am Tien Pham, I am stucked at this situation. I calculated longitudinal LGI 
changes in my data set with two time points using longitudinal pipeline. Now I 
would like to extract the regional LGI and gray matter volume in my 
longitudinal results using QDEC to draw the ROIs which is showed significant 
differences, label it and map to all subjects. Then I get the LGI value of the 
ROI I saved before using the command below:

cd $SUBJECTS_DIR
mris_anatomical_stats -l lh.untitled.label \
 -t lh.pial_lgi \
 -b \
 -f subject_id/stats/lh.untitled.stats subject_id lh

And this is the result:

[toyama-no-iMac:/applications/freesurfer/subjects] toyama% 
mris_anatomical_stats -l lh.frontoinsula.label \
? -t lh.pial_lgi \
? -b \
? -f VC019_1/stats/lh.frontoinsula.stats VC019_1 lh
limiting computations to label lh.frontoinsula.label.
using thickness file lh.pial_lgi.
reading volume /applications/freesurfer/subjects/VC019_1/mri/wm.mgz...
reading input surface 

Re: [Freesurfer] Extract specific LGI and Volume values

[Greve, Douglas N.,Ph.D.]

I'm guessing that there is something wrong with the label. Can you send it?

On 1/21/2020 8:08 PM, Tien Pham wrote:

External Email - Use Caution

Thank you for your e-mail.
I also could not load the label in freeview. The terminal showed the following 
error:

2020-01-22 09:56:18.064 Freeview[51338:303] modalSession has been exited 
prematurely - check for a reentrant call to endModalSession:
2020-01-22 09:56:26.655 Freeview[51338:303] modalSession has been exited 
prematurely - check for a reentrant call to endModalSession:
freadFloat: fread failed
freadFloat: fread failed

This error was still showing like it never end until I close freeview.

 I draw the ROI in qdec, then add selection to ROI , and save the current 
label. That was how I created the label.
I am looking forward to hearing from you. Thank you.

On Wed, Jan 22, 2020 at 12:17 AM Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> wrote:
You can try freeview, but there might be something wrong with the label. How 
was it created?

On 1/16/2020 11:51 PM, Tien Pham wrote:

External Email - Use Caution

Thank you for your help.
I cannot load the label on surface, this is the error:

[toyama-no-iMac:/applications/freesurfer/subjects] toyama% qdec

Reading /applications/freesurfer/tktools/tkUtils.tcl

Using /applications/freesurfer/lib/tcl/fsgdfPlot.tcl
qdec.bin(41334,0xa15971a8) malloc: *** mach_vm_map(size=114944) failed 
(error code=3)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
MRISalloc(15124178, 76): could not allocate faces
Cannot allocate memory

What do you mean how many point? How do I find it?

On Fri, Jan 17, 2020 at 1:17 PM Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> wrote:
Is the label valid? Can you load it on a surface? How many points are in it?

On 1/16/2020 9:51 PM, Tien Pham wrote:

External Email - Use Caution

Thank you for your e-mail.
It seems I got another error. This is what it showed in terminal:

[toyama-no-iMac:/applications/freesurfer/subjects] toyama% mri_segstats --i 
lh.pial_lgi --slabel VC001_1 lh lh.frontoinsula.label --id 1 --sum sum.dat

$Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $
cwd
cmdline mri_segstats --i lh.pial_lgi --slabel VC001_1 lh lh.frontoinsula.label 
--id 1 --sum sum.dat
sysname  Darwin
hostname toyama-no-iMac.local
machine  x86_64
user toyama
UseRobust  0
Constructing seg from label
Segmentation fault

Could you help me please?

On Fri, Jan 17, 2020 at 11:56 AM Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> wrote:
Sorry, it should have been --sum instead of --o
the subject name is subject_id
--id 1 just means to take the vertices in the label (--id 0 would mean to take 
the background)

On 1/16/2020 7:07 PM, Tien Pham wrote:

External Email - Use Caution

Thank you very much for your e-mail.
I tried, but this '' --o '' is unknown showing in terminal and the '' --id '' 
flag is subject name?
Could you please help me?
For example, I found the change in frontoinsula region between 2 groups in my 
dataset and I want to extract the values of this region.

On Fri, Jan 17, 2020 at 8:30 AM Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> wrote:
It might be easier to use mri_segstats, eg,

mri_segstats --i lh.pial_lgi --slabel subject_id lh lh.untitled.label --id 1 
--o sum.dat

The mean value will be in the "Mean" column of the sum.dat


On 1/14/2020 7:08 PM, Tien Pham wrote:

External Email - Use Caution

Dear FreeSurfer Experts,

I am Tien Pham, I am stucked at this situation. I calculated longitudinal LGI 
changes in my data set with two time points using longitudinal pipeline. Now I 
would like to extract the regional LGI and gray matter volume in my 
longitudinal results using QDEC to draw the ROIs which is showed significant 
differences, label it and map to all subjects. Then I get the LGI value of the 
ROI I saved before using the command below:

cd $SUBJECTS_DIR
mris_anatomical_stats -l lh.untitled.label \
 -t lh.pial_lgi \
 -b \
 -f subject_id/stats/lh.untitled.stats subject_id lh

And this is the result:

[toyama-no-iMac:/applications/freesurfer/subjects] toyama% 
mris_anatomical_stats -l lh.frontoinsula.label \
? -t lh.pial_lgi \
? -b \
? -f VC019_1/stats/lh.frontoinsula.stats VC019_1 lh
limiting computations to label lh.frontoinsula.label.
using thickness file lh.pial_lgi.
reading volume /applications/freesurfer/subjects/VC019_1/mri/wm.mgz...
reading input surface /applications/freesurfer/subjects/VC019_1/surf/lh.white...
reading input pial surface 
/applications/freesurfer/subjects/VC019_1/surf/lh.pial...
reading input white surface 
/applications/freesurfer/subjects/VC019_1/surf/lh.white...

table columns are:
number of vertices
total surface area (mm^2)
total gray matter volume (mm^3)
average cortical thickness +- standard deviation (mm)
integrated rectified mean curvature
integrated rectified Gaussian curvature

Re: [Freesurfer] Extract specific LGI and Volume values

[Tien Pham]

External Email - Use Caution

Thank you for your e-mail.
I also could not load the label in freeview. The terminal showed the
following error:

2020-01-22 09:56:18.064 Freeview[51338:303] modalSession has been exited
prematurely - check for a reentrant call to endModalSession:

2020-01-22 09:56:26.655 Freeview[51338:303] modalSession has been exited
prematurely - check for a reentrant call to endModalSession:

freadFloat: fread failed

freadFloat: fread failed


This error was still showing like it never end until I close freeview.


 I draw the ROI in qdec, then add selection to ROI , and save the current
label. That was how I created the label.

I am looking forward to hearing from you. Thank you.

On Wed, Jan 22, 2020 at 12:17 AM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> You can try freeview, but there might be something wrong with the label.
> How was it created?
>
> On 1/16/2020 11:51 PM, Tien Pham wrote:
>
> External Email - Use Caution
> Thank you for your help.
> I cannot load the label on surface, this is the error:
>
> [toyama-no-iMac:/applications/freesurfer/subjects] toyama% qdec
>
>
>
> Reading /applications/freesurfer/tktools/tkUtils.tcl
>
>
>
> Using /applications/freesurfer/lib/tcl/fsgdfPlot.tcl
>
> qdec.bin(41334,0xa15971a8) malloc: *** mach_vm_map(size=114944) failed
> (error code=3)
>
> *** error: can't allocate region
>
> *** set a breakpoint in malloc_error_break to debug
>
> MRISalloc(15124178, 76): could not allocate faces
>
> Cannot allocate memory
>
>
> What do you mean how many point? How do I find it?
>
> On Fri, Jan 17, 2020 at 1:17 PM Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu> wrote:
>
>> Is the label valid? Can you load it on a surface? How many points are in
>> it?
>>
>> On 1/16/2020 9:51 PM, Tien Pham wrote:
>>
>> External Email - Use Caution
>> Thank you for your e-mail.
>> It seems I got another error. This is what it showed in terminal:
>>
>> [toyama-no-iMac:/applications/freesurfer/subjects] toyama% mri_segstats
>> --i lh.pial_lgi --slabel VC001_1 lh lh.frontoinsula.label --id 1 --sum
>> sum.dat
>>
>>
>>
>> $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $
>>
>> cwd
>>
>> cmdline mri_segstats --i lh.pial_lgi --slabel VC001_1 lh
>> lh.frontoinsula.label --id 1 --sum sum.dat
>>
>> sysname  Darwin
>>
>> hostname toyama-no-iMac.local
>>
>> machine  x86_64
>>
>> user toyama
>>
>> UseRobust  0
>>
>> Constructing seg from label
>>
>> Segmentation fault
>>
>>
>> Could you help me please?
>>
>> On Fri, Jan 17, 2020 at 11:56 AM Greve, Douglas N.,Ph.D. <
>> dgr...@mgh.harvard.edu> wrote:
>>
>>> Sorry, it should have been --sum instead of --o
>>> the subject name is subject_id
>>> --id 1 just means to take the vertices in the label (--id 0 would mean
>>> to take the background)
>>>
>>> On 1/16/2020 7:07 PM, Tien Pham wrote:
>>>
>>> External Email - Use Caution
>>> Thank you very much for your e-mail.
>>> I tried, but this '' --o '' is unknown showing in terminal and the ''
>>> --id '' flag is subject name?
>>> Could you please help me?
>>> For example, I found the change in frontoinsula region between 2 groups
>>> in my dataset and I want to extract the values of this region.
>>>
>>> On Fri, Jan 17, 2020 at 8:30 AM Greve, Douglas N.,Ph.D. <
>>> dgr...@mgh.harvard.edu> wrote:
>>>
 It might be easier to use mri_segstats, eg,

 mri_segstats --i lh.pial_lgi --slabel subject_id lh lh.untitled.label
 --id 1 --o sum.dat

 The mean value will be in the "Mean" column of the sum.dat


 On 1/14/2020 7:08 PM, Tien Pham wrote:

 External Email - Use Caution
 Dear FreeSurfer Experts,

 I am Tien Pham, I am stucked at this situation. I calculated
 longitudinal LGI changes in my data set with two time points using
 longitudinal pipeline. Now I would like to extract the regional LGI and
 gray matter volume in my longitudinal results using QDEC to draw the ROIs
 which is showed significant differences, label it and map to all subjects.
 Then I get the LGI value of the ROI I saved before using the command below:

 cd $SUBJECTS_DIR
 mris_anatomical_stats -l lh.untitled.label \
  -t lh.pial_lgi \
  -b \
  -f subject_id/stats/lh.untitled.stats subject_id lh

 And this is the result:

 [toyama-no-iMac:/applications/freesurfer/subjects] toyama%
 mris_anatomical_stats -l lh.frontoinsula.label \

 ? -t lh.pial_lgi \

 ? -b \

 ? -f VC019_1/stats/lh.frontoinsula.stats VC019_1 lh

 limiting computations to label lh.frontoinsula.label.

 using thickness file lh.pial_lgi.

 reading volume /applications/freesurfer/subjects/VC019_1/mri/wm.mgz...

 reading input surface
 /applications/freesurfer/subjects/VC019_1/surf/lh.white...

 reading input pial surface
 /applications/freesurfer/subjects/VC019_1/surf/lh.pial...

 

Re: [Freesurfer] Extract specific LGI and Volume values

[Greve, Douglas N.,Ph.D.]

You can try freeview, but there might be something wrong with the label. How 
was it created?

On 1/16/2020 11:51 PM, Tien Pham wrote:

External Email - Use Caution

Thank you for your help.
I cannot load the label on surface, this is the error:

[toyama-no-iMac:/applications/freesurfer/subjects] toyama% qdec

Reading /applications/freesurfer/tktools/tkUtils.tcl

Using /applications/freesurfer/lib/tcl/fsgdfPlot.tcl
qdec.bin(41334,0xa15971a8) malloc: *** mach_vm_map(size=114944) failed 
(error code=3)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
MRISalloc(15124178, 76): could not allocate faces
Cannot allocate memory

What do you mean how many point? How do I find it?

On Fri, Jan 17, 2020 at 1:17 PM Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> wrote:
Is the label valid? Can you load it on a surface? How many points are in it?

On 1/16/2020 9:51 PM, Tien Pham wrote:

External Email - Use Caution

Thank you for your e-mail.
It seems I got another error. This is what it showed in terminal:

[toyama-no-iMac:/applications/freesurfer/subjects] toyama% mri_segstats --i 
lh.pial_lgi --slabel VC001_1 lh lh.frontoinsula.label --id 1 --sum sum.dat

$Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $
cwd
cmdline mri_segstats --i lh.pial_lgi --slabel VC001_1 lh lh.frontoinsula.label 
--id 1 --sum sum.dat
sysname  Darwin
hostname toyama-no-iMac.local
machine  x86_64
user toyama
UseRobust  0
Constructing seg from label
Segmentation fault

Could you help me please?

On Fri, Jan 17, 2020 at 11:56 AM Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> wrote:
Sorry, it should have been --sum instead of --o
the subject name is subject_id
--id 1 just means to take the vertices in the label (--id 0 would mean to take 
the background)

On 1/16/2020 7:07 PM, Tien Pham wrote:

External Email - Use Caution

Thank you very much for your e-mail.
I tried, but this '' --o '' is unknown showing in terminal and the '' --id '' 
flag is subject name?
Could you please help me?
For example, I found the change in frontoinsula region between 2 groups in my 
dataset and I want to extract the values of this region.

On Fri, Jan 17, 2020 at 8:30 AM Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> wrote:
It might be easier to use mri_segstats, eg,

mri_segstats --i lh.pial_lgi --slabel subject_id lh lh.untitled.label --id 1 
--o sum.dat

The mean value will be in the "Mean" column of the sum.dat


On 1/14/2020 7:08 PM, Tien Pham wrote:

External Email - Use Caution

Dear FreeSurfer Experts,

I am Tien Pham, I am stucked at this situation. I calculated longitudinal LGI 
changes in my data set with two time points using longitudinal pipeline. Now I 
would like to extract the regional LGI and gray matter volume in my 
longitudinal results using QDEC to draw the ROIs which is showed significant 
differences, label it and map to all subjects. Then I get the LGI value of the 
ROI I saved before using the command below:

cd $SUBJECTS_DIR
mris_anatomical_stats -l lh.untitled.label \
 -t lh.pial_lgi \
 -b \
 -f subject_id/stats/lh.untitled.stats subject_id lh

And this is the result:

[toyama-no-iMac:/applications/freesurfer/subjects] toyama% 
mris_anatomical_stats -l lh.frontoinsula.label \
? -t lh.pial_lgi \
? -b \
? -f VC019_1/stats/lh.frontoinsula.stats VC019_1 lh
limiting computations to label lh.frontoinsula.label.
using thickness file lh.pial_lgi.
reading volume /applications/freesurfer/subjects/VC019_1/mri/wm.mgz...
reading input surface /applications/freesurfer/subjects/VC019_1/surf/lh.white...
reading input pial surface 
/applications/freesurfer/subjects/VC019_1/surf/lh.pial...
reading input white surface 
/applications/freesurfer/subjects/VC019_1/surf/lh.white...

table columns are:
number of vertices
total surface area (mm^2)
total gray matter volume (mm^3)
average cortical thickness +- standard deviation (mm)
integrated rectified mean curvature
integrated rectified Gaussian curvature
folding index
intrinsic curvature index
structure name

 6595   4368  15935  3.311 0.895 0.158 0.077  13519.7  
lh.frontoinsula.label

As I saw there was no columns showing the LGI value, I did similar with gray 
matter volume, the result displayed the different in some values of the columns.
Could you please help me to explain about this?
Thank you very much.

Best regards,
Tien Pham



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



___
Freesurfer mailing list

Re: [Freesurfer] Extract specific LGI and Volume values

[Tien Pham]

External Email - Use Caution

Thank you for your help.
I cannot load the label on surface, this is the error:

[toyama-no-iMac:/applications/freesurfer/subjects] toyama% qdec



Reading /applications/freesurfer/tktools/tkUtils.tcl



Using /applications/freesurfer/lib/tcl/fsgdfPlot.tcl

qdec.bin(41334,0xa15971a8) malloc: *** mach_vm_map(size=114944) failed
(error code=3)

*** error: can't allocate region

*** set a breakpoint in malloc_error_break to debug

MRISalloc(15124178, 76): could not allocate faces

Cannot allocate memory


What do you mean how many point? How do I find it?

On Fri, Jan 17, 2020 at 1:17 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> Is the label valid? Can you load it on a surface? How many points are in
> it?
>
> On 1/16/2020 9:51 PM, Tien Pham wrote:
>
> External Email - Use Caution
> Thank you for your e-mail.
> It seems I got another error. This is what it showed in terminal:
>
> [toyama-no-iMac:/applications/freesurfer/subjects] toyama% mri_segstats
> --i lh.pial_lgi --slabel VC001_1 lh lh.frontoinsula.label --id 1 --sum
> sum.dat
>
>
>
> $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $
>
> cwd
>
> cmdline mri_segstats --i lh.pial_lgi --slabel VC001_1 lh
> lh.frontoinsula.label --id 1 --sum sum.dat
>
> sysname  Darwin
>
> hostname toyama-no-iMac.local
>
> machine  x86_64
>
> user toyama
>
> UseRobust  0
>
> Constructing seg from label
>
> Segmentation fault
>
>
> Could you help me please?
>
> On Fri, Jan 17, 2020 at 11:56 AM Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu> wrote:
>
>> Sorry, it should have been --sum instead of --o
>> the subject name is subject_id
>> --id 1 just means to take the vertices in the label (--id 0 would mean to
>> take the background)
>>
>> On 1/16/2020 7:07 PM, Tien Pham wrote:
>>
>> External Email - Use Caution
>> Thank you very much for your e-mail.
>> I tried, but this '' --o '' is unknown showing in terminal and the ''
>> --id '' flag is subject name?
>> Could you please help me?
>> For example, I found the change in frontoinsula region between 2 groups
>> in my dataset and I want to extract the values of this region.
>>
>> On Fri, Jan 17, 2020 at 8:30 AM Greve, Douglas N.,Ph.D. <
>> dgr...@mgh.harvard.edu> wrote:
>>
>>> It might be easier to use mri_segstats, eg,
>>>
>>> mri_segstats --i lh.pial_lgi --slabel subject_id lh lh.untitled.label
>>> --id 1 --o sum.dat
>>>
>>> The mean value will be in the "Mean" column of the sum.dat
>>>
>>>
>>> On 1/14/2020 7:08 PM, Tien Pham wrote:
>>>
>>> External Email - Use Caution
>>> Dear FreeSurfer Experts,
>>>
>>> I am Tien Pham, I am stucked at this situation. I calculated
>>> longitudinal LGI changes in my data set with two time points using
>>> longitudinal pipeline. Now I would like to extract the regional LGI and
>>> gray matter volume in my longitudinal results using QDEC to draw the ROIs
>>> which is showed significant differences, label it and map to all subjects.
>>> Then I get the LGI value of the ROI I saved before using the command below:
>>>
>>> cd $SUBJECTS_DIR
>>> mris_anatomical_stats -l lh.untitled.label \
>>>  -t lh.pial_lgi \
>>>  -b \
>>>  -f subject_id/stats/lh.untitled.stats subject_id lh
>>>
>>> And this is the result:
>>>
>>> [toyama-no-iMac:/applications/freesurfer/subjects] toyama%
>>> mris_anatomical_stats -l lh.frontoinsula.label \
>>>
>>> ? -t lh.pial_lgi \
>>>
>>> ? -b \
>>>
>>> ? -f VC019_1/stats/lh.frontoinsula.stats VC019_1 lh
>>>
>>> limiting computations to label lh.frontoinsula.label.
>>>
>>> using thickness file lh.pial_lgi.
>>>
>>> reading volume /applications/freesurfer/subjects/VC019_1/mri/wm.mgz...
>>>
>>> reading input surface
>>> /applications/freesurfer/subjects/VC019_1/surf/lh.white...
>>>
>>> reading input pial surface
>>> /applications/freesurfer/subjects/VC019_1/surf/lh.pial...
>>>
>>> reading input white surface
>>> /applications/freesurfer/subjects/VC019_1/surf/lh.white...
>>>
>>>
>>>
>>> table columns are:
>>>
>>> number of vertices
>>>
>>> total surface area (mm^2)
>>>
>>> total gray matter volume (mm^3)
>>>
>>> average cortical thickness +- standard deviation (mm)
>>>
>>> integrated rectified mean curvature
>>>
>>> integrated rectified Gaussian curvature
>>>
>>> folding index
>>>
>>> intrinsic curvature index
>>>
>>> structure name
>>>
>>>
>>>
>>>  6595   4368  15935  3.311 0.895 0.158 0.077  13519.7
>>> lh.frontoinsula.label
>>>
>>>
>>> As I saw there was no columns showing the LGI value, I did similar with
>>> gray matter volume, the result displayed the different in some values of
>>> the columns.
>>> Could you please help me to explain about this?
>>>
>>> Thank you very much.
>>>
>>>
>>> Best regards,
>>>
>>> Tien Pham
>>>
>>> ___
>>> Freesurfer mailing 
>>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>> 

Re: [Freesurfer] Extract specific LGI and Volume values

[Greve, Douglas N.,Ph.D.]

Is the label valid? Can you load it on a surface? How many points are in it?

On 1/16/2020 9:51 PM, Tien Pham wrote:

External Email - Use Caution

Thank you for your e-mail.
It seems I got another error. This is what it showed in terminal:

[toyama-no-iMac:/applications/freesurfer/subjects] toyama% mri_segstats --i 
lh.pial_lgi --slabel VC001_1 lh lh.frontoinsula.label --id 1 --sum sum.dat

$Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $
cwd
cmdline mri_segstats --i lh.pial_lgi --slabel VC001_1 lh lh.frontoinsula.label 
--id 1 --sum sum.dat
sysname  Darwin
hostname toyama-no-iMac.local
machine  x86_64
user toyama
UseRobust  0
Constructing seg from label
Segmentation fault

Could you help me please?

On Fri, Jan 17, 2020 at 11:56 AM Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> wrote:
Sorry, it should have been --sum instead of --o
the subject name is subject_id
--id 1 just means to take the vertices in the label (--id 0 would mean to take 
the background)

On 1/16/2020 7:07 PM, Tien Pham wrote:

External Email - Use Caution

Thank you very much for your e-mail.
I tried, but this '' --o '' is unknown showing in terminal and the '' --id '' 
flag is subject name?
Could you please help me?
For example, I found the change in frontoinsula region between 2 groups in my 
dataset and I want to extract the values of this region.

On Fri, Jan 17, 2020 at 8:30 AM Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> wrote:
It might be easier to use mri_segstats, eg,

mri_segstats --i lh.pial_lgi --slabel subject_id lh lh.untitled.label --id 1 
--o sum.dat

The mean value will be in the "Mean" column of the sum.dat


On 1/14/2020 7:08 PM, Tien Pham wrote:

External Email - Use Caution

Dear FreeSurfer Experts,

I am Tien Pham, I am stucked at this situation. I calculated longitudinal LGI 
changes in my data set with two time points using longitudinal pipeline. Now I 
would like to extract the regional LGI and gray matter volume in my 
longitudinal results using QDEC to draw the ROIs which is showed significant 
differences, label it and map to all subjects. Then I get the LGI value of the 
ROI I saved before using the command below:

cd $SUBJECTS_DIR
mris_anatomical_stats -l lh.untitled.label \
 -t lh.pial_lgi \
 -b \
 -f subject_id/stats/lh.untitled.stats subject_id lh

And this is the result:

[toyama-no-iMac:/applications/freesurfer/subjects] toyama% 
mris_anatomical_stats -l lh.frontoinsula.label \
? -t lh.pial_lgi \
? -b \
? -f VC019_1/stats/lh.frontoinsula.stats VC019_1 lh
limiting computations to label lh.frontoinsula.label.
using thickness file lh.pial_lgi.
reading volume /applications/freesurfer/subjects/VC019_1/mri/wm.mgz...
reading input surface /applications/freesurfer/subjects/VC019_1/surf/lh.white...
reading input pial surface 
/applications/freesurfer/subjects/VC019_1/surf/lh.pial...
reading input white surface 
/applications/freesurfer/subjects/VC019_1/surf/lh.white...

table columns are:
number of vertices
total surface area (mm^2)
total gray matter volume (mm^3)
average cortical thickness +- standard deviation (mm)
integrated rectified mean curvature
integrated rectified Gaussian curvature
folding index
intrinsic curvature index
structure name

 6595   4368  15935  3.311 0.895 0.158 0.077  13519.7  
lh.frontoinsula.label

As I saw there was no columns showing the LGI value, I did similar with gray 
matter volume, the result displayed the different in some values of the columns.
Could you please help me to explain about this?
Thank you very much.

Best regards,
Tien Pham



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Re: [Freesurfer] Extract specific LGI and Volume values

[Tien Pham]

External Email - Use Caution

Thank you for your e-mail.
It seems I got another error. This is what it showed in terminal:

[toyama-no-iMac:/applications/freesurfer/subjects] toyama% mri_segstats --i
lh.pial_lgi --slabel VC001_1 lh lh.frontoinsula.label --id 1 --sum sum.dat



$Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $

cwd

cmdline mri_segstats --i lh.pial_lgi --slabel VC001_1 lh
lh.frontoinsula.label --id 1 --sum sum.dat

sysname  Darwin

hostname toyama-no-iMac.local

machine  x86_64

user toyama

UseRobust  0

Constructing seg from label

Segmentation fault


Could you help me please?

On Fri, Jan 17, 2020 at 11:56 AM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> Sorry, it should have been --sum instead of --o
> the subject name is subject_id
> --id 1 just means to take the vertices in the label (--id 0 would mean to
> take the background)
>
> On 1/16/2020 7:07 PM, Tien Pham wrote:
>
> External Email - Use Caution
> Thank you very much for your e-mail.
> I tried, but this '' --o '' is unknown showing in terminal and the '' --id
> '' flag is subject name?
> Could you please help me?
> For example, I found the change in frontoinsula region between 2 groups in
> my dataset and I want to extract the values of this region.
>
> On Fri, Jan 17, 2020 at 8:30 AM Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu> wrote:
>
>> It might be easier to use mri_segstats, eg,
>>
>> mri_segstats --i lh.pial_lgi --slabel subject_id lh lh.untitled.label
>> --id 1 --o sum.dat
>>
>> The mean value will be in the "Mean" column of the sum.dat
>>
>>
>> On 1/14/2020 7:08 PM, Tien Pham wrote:
>>
>> External Email - Use Caution
>> Dear FreeSurfer Experts,
>>
>> I am Tien Pham, I am stucked at this situation. I calculated longitudinal
>> LGI changes in my data set with two time points using longitudinal
>> pipeline. Now I would like to extract the regional LGI and gray matter
>> volume in my longitudinal results using QDEC to draw the ROIs which is
>> showed significant differences, label it and map to all subjects. Then I
>> get the LGI value of the ROI I saved before using the command below:
>>
>> cd $SUBJECTS_DIR
>> mris_anatomical_stats -l lh.untitled.label \
>>  -t lh.pial_lgi \
>>  -b \
>>  -f subject_id/stats/lh.untitled.stats subject_id lh
>>
>> And this is the result:
>>
>> [toyama-no-iMac:/applications/freesurfer/subjects] toyama%
>> mris_anatomical_stats -l lh.frontoinsula.label \
>>
>> ? -t lh.pial_lgi \
>>
>> ? -b \
>>
>> ? -f VC019_1/stats/lh.frontoinsula.stats VC019_1 lh
>>
>> limiting computations to label lh.frontoinsula.label.
>>
>> using thickness file lh.pial_lgi.
>>
>> reading volume /applications/freesurfer/subjects/VC019_1/mri/wm.mgz...
>>
>> reading input surface
>> /applications/freesurfer/subjects/VC019_1/surf/lh.white...
>>
>> reading input pial surface
>> /applications/freesurfer/subjects/VC019_1/surf/lh.pial...
>>
>> reading input white surface
>> /applications/freesurfer/subjects/VC019_1/surf/lh.white...
>>
>>
>>
>> table columns are:
>>
>> number of vertices
>>
>> total surface area (mm^2)
>>
>> total gray matter volume (mm^3)
>>
>> average cortical thickness +- standard deviation (mm)
>>
>> integrated rectified mean curvature
>>
>> integrated rectified Gaussian curvature
>>
>> folding index
>>
>> intrinsic curvature index
>>
>> structure name
>>
>>
>>
>>  6595   4368  15935  3.311 0.895 0.158 0.077  13519.7
>> lh.frontoinsula.label
>>
>>
>> As I saw there was no columns showing the LGI value, I did similar with
>> gray matter volume, the result displayed the different in some values of
>> the columns.
>> Could you please help me to explain about this?
>>
>> Thank you very much.
>>
>>
>> Best regards,
>>
>> Tien Pham
>>
>> ___
>> Freesurfer mailing 
>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
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Re: [Freesurfer] Extract specific LGI and Volume values

[Greve, Douglas N.,Ph.D.]

Sorry, it should have been --sum instead of --o
the subject name is subject_id
--id 1 just means to take the vertices in the label (--id 0 would mean to take 
the background)

On 1/16/2020 7:07 PM, Tien Pham wrote:

External Email - Use Caution

Thank you very much for your e-mail.
I tried, but this '' --o '' is unknown showing in terminal and the '' --id '' 
flag is subject name?
Could you please help me?
For example, I found the change in frontoinsula region between 2 groups in my 
dataset and I want to extract the values of this region.

On Fri, Jan 17, 2020 at 8:30 AM Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> wrote:
It might be easier to use mri_segstats, eg,

mri_segstats --i lh.pial_lgi --slabel subject_id lh lh.untitled.label --id 1 
--o sum.dat

The mean value will be in the "Mean" column of the sum.dat


On 1/14/2020 7:08 PM, Tien Pham wrote:

External Email - Use Caution

Dear FreeSurfer Experts,

I am Tien Pham, I am stucked at this situation. I calculated longitudinal LGI 
changes in my data set with two time points using longitudinal pipeline. Now I 
would like to extract the regional LGI and gray matter volume in my 
longitudinal results using QDEC to draw the ROIs which is showed significant 
differences, label it and map to all subjects. Then I get the LGI value of the 
ROI I saved before using the command below:

cd $SUBJECTS_DIR
mris_anatomical_stats -l lh.untitled.label \
 -t lh.pial_lgi \
 -b \
 -f subject_id/stats/lh.untitled.stats subject_id lh

And this is the result:

[toyama-no-iMac:/applications/freesurfer/subjects] toyama% 
mris_anatomical_stats -l lh.frontoinsula.label \
? -t lh.pial_lgi \
? -b \
? -f VC019_1/stats/lh.frontoinsula.stats VC019_1 lh
limiting computations to label lh.frontoinsula.label.
using thickness file lh.pial_lgi.
reading volume /applications/freesurfer/subjects/VC019_1/mri/wm.mgz...
reading input surface /applications/freesurfer/subjects/VC019_1/surf/lh.white...
reading input pial surface 
/applications/freesurfer/subjects/VC019_1/surf/lh.pial...
reading input white surface 
/applications/freesurfer/subjects/VC019_1/surf/lh.white...

table columns are:
number of vertices
total surface area (mm^2)
total gray matter volume (mm^3)
average cortical thickness +- standard deviation (mm)
integrated rectified mean curvature
integrated rectified Gaussian curvature
folding index
intrinsic curvature index
structure name

 6595   4368  15935  3.311 0.895 0.158 0.077  13519.7  
lh.frontoinsula.label

As I saw there was no columns showing the LGI value, I did similar with gray 
matter volume, the result displayed the different in some values of the columns.
Could you please help me to explain about this?
Thank you very much.

Best regards,
Tien Pham



___
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Extract specific LGI and Volume values

[Tien Pham]

External Email - Use Caution

Thank you very much for your e-mail.
I tried, but this '' --o '' is unknown showing in terminal and the '' --id
'' flag is subject name?
Could you please help me?
For example, I found the change in frontoinsula region between 2 groups in
my dataset and I want to extract the values of this region.

On Fri, Jan 17, 2020 at 8:30 AM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> It might be easier to use mri_segstats, eg,
>
> mri_segstats --i lh.pial_lgi --slabel subject_id lh lh.untitled.label --id
> 1 --o sum.dat
>
> The mean value will be in the "Mean" column of the sum.dat
>
>
> On 1/14/2020 7:08 PM, Tien Pham wrote:
>
> External Email - Use Caution
> Dear FreeSurfer Experts,
>
> I am Tien Pham, I am stucked at this situation. I calculated longitudinal
> LGI changes in my data set with two time points using longitudinal
> pipeline. Now I would like to extract the regional LGI and gray matter
> volume in my longitudinal results using QDEC to draw the ROIs which is
> showed significant differences, label it and map to all subjects. Then I
> get the LGI value of the ROI I saved before using the command below:
>
> cd $SUBJECTS_DIR
> mris_anatomical_stats -l lh.untitled.label \
>  -t lh.pial_lgi \
>  -b \
>  -f subject_id/stats/lh.untitled.stats subject_id lh
>
> And this is the result:
>
> [toyama-no-iMac:/applications/freesurfer/subjects] toyama%
> mris_anatomical_stats -l lh.frontoinsula.label \
>
> ? -t lh.pial_lgi \
>
> ? -b \
>
> ? -f VC019_1/stats/lh.frontoinsula.stats VC019_1 lh
>
> limiting computations to label lh.frontoinsula.label.
>
> using thickness file lh.pial_lgi.
>
> reading volume /applications/freesurfer/subjects/VC019_1/mri/wm.mgz...
>
> reading input surface
> /applications/freesurfer/subjects/VC019_1/surf/lh.white...
>
> reading input pial surface
> /applications/freesurfer/subjects/VC019_1/surf/lh.pial...
>
> reading input white surface
> /applications/freesurfer/subjects/VC019_1/surf/lh.white...
>
>
>
> table columns are:
>
> number of vertices
>
> total surface area (mm^2)
>
> total gray matter volume (mm^3)
>
> average cortical thickness +- standard deviation (mm)
>
> integrated rectified mean curvature
>
> integrated rectified Gaussian curvature
>
> folding index
>
> intrinsic curvature index
>
> structure name
>
>
>
>  6595   4368  15935  3.311 0.895 0.158 0.077  13519.7
> lh.frontoinsula.label
>
>
> As I saw there was no columns showing the LGI value, I did similar with
> gray matter volume, the result displayed the different in some values of
> the columns.
> Could you please help me to explain about this?
>
> Thank you very much.
>
>
> Best regards,
>
> Tien Pham
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
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Re: [Freesurfer] Extract specific LGI and Volume values

[Greve, Douglas N.,Ph.D.]

It might be easier to use mri_segstats, eg,

mri_segstats --i lh.pial_lgi --slabel subject_id lh lh.untitled.label --id 1 
--o sum.dat

The mean value will be in the "Mean" column of the sum.dat


On 1/14/2020 7:08 PM, Tien Pham wrote:

External Email - Use Caution

Dear FreeSurfer Experts,

I am Tien Pham, I am stucked at this situation. I calculated longitudinal LGI 
changes in my data set with two time points using longitudinal pipeline. Now I 
would like to extract the regional LGI and gray matter volume in my 
longitudinal results using QDEC to draw the ROIs which is showed significant 
differences, label it and map to all subjects. Then I get the LGI value of the 
ROI I saved before using the command below:

cd $SUBJECTS_DIR
mris_anatomical_stats -l lh.untitled.label \
 -t lh.pial_lgi \
 -b \
 -f subject_id/stats/lh.untitled.stats subject_id lh

And this is the result:

[toyama-no-iMac:/applications/freesurfer/subjects] toyama% 
mris_anatomical_stats -l lh.frontoinsula.label \
? -t lh.pial_lgi \
? -b \
? -f VC019_1/stats/lh.frontoinsula.stats VC019_1 lh
limiting computations to label lh.frontoinsula.label.
using thickness file lh.pial_lgi.
reading volume /applications/freesurfer/subjects/VC019_1/mri/wm.mgz...
reading input surface /applications/freesurfer/subjects/VC019_1/surf/lh.white...
reading input pial surface 
/applications/freesurfer/subjects/VC019_1/surf/lh.pial...
reading input white surface 
/applications/freesurfer/subjects/VC019_1/surf/lh.white...

table columns are:
number of vertices
total surface area (mm^2)
total gray matter volume (mm^3)
average cortical thickness +- standard deviation (mm)
integrated rectified mean curvature
integrated rectified Gaussian curvature
folding index
intrinsic curvature index
structure name

 6595   4368  15935  3.311 0.895 0.158 0.077  13519.7  
lh.frontoinsula.label

As I saw there was no columns showing the LGI value, I did similar with gray 
matter volume, the result displayed the different in some values of the columns.
Could you please help me to explain about this?
Thank you very much.

Best regards,
Tien Pham



___
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Extract specific LGI and Volume values

[Tien Pham]

External Email - Use Caution

Dear FreeSurfer Experts,

I am Tien Pham, I am stucked at this situation. I calculated longitudinal
LGI changes in my data set with two time points using longitudinal
pipeline. Now I would like to extract the regional LGI and gray matter
volume in my longitudinal results using QDEC to draw the ROIs which is
showed significant differences, label it and map to all subjects. Then I
get the LGI value of the ROI I saved before using the command below:

cd $SUBJECTS_DIR
mris_anatomical_stats -l lh.untitled.label \
 -t lh.pial_lgi \
 -b \
 -f subject_id/stats/lh.untitled.stats subject_id lh

And this is the result:

[toyama-no-iMac:/applications/freesurfer/subjects] toyama%
mris_anatomical_stats -l lh.frontoinsula.label \

? -t lh.pial_lgi \

? -b \

? -f VC019_1/stats/lh.frontoinsula.stats VC019_1 lh

limiting computations to label lh.frontoinsula.label.

using thickness file lh.pial_lgi.

reading volume /applications/freesurfer/subjects/VC019_1/mri/wm.mgz...

reading input surface
/applications/freesurfer/subjects/VC019_1/surf/lh.white...

reading input pial surface
/applications/freesurfer/subjects/VC019_1/surf/lh.pial...

reading input white surface
/applications/freesurfer/subjects/VC019_1/surf/lh.white...



table columns are:

number of vertices

total surface area (mm^2)

total gray matter volume (mm^3)

average cortical thickness +- standard deviation (mm)

integrated rectified mean curvature

integrated rectified Gaussian curvature

folding index

intrinsic curvature index

structure name



 6595   4368  15935  3.311 0.895 0.158 0.077  13519.7
lh.frontoinsula.label


As I saw there was no columns showing the LGI value, I did similar with
gray matter volume, the result displayed the different in some values of
the columns.
Could you please help me to explain about this?

Thank you very much.


Best regards,

Tien Pham
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