Re: [Freesurfer] petsurfer stats for multiple segmentations

2017-07-12 Thread Douglas N Greve 


On 07/12/2017 05:11 PM, Lu Zhao wrote:
> Dear Douglas,
>
> Thank you for your kind reply and instruction. But I still have a few 
> questions:
>
> 1. how can I get the segmentation for BA areas, which have no 
> hemisphere bases?
Not so easy because you need to have complete cortical coverage. If you 
are not doing partial volume correction (or correcting for the volume 
fraction effect), then you can use mri_label2vol to create and ROI of 
the BA in the PET space, then use mri_segstats to extract the mean from 
the ROI (ie, bypass gtmseg and mri_gtmpvc).
> 2. when the cortical atlas is changed, should the '--wm-annot’ be 
> changed accordingly? For instance, use '—wm-annot aparc.a2009s 13100 
> 14100' when use '--ctx-annot  aparc.a2009s 11100 12100’?
No, the --wm-annot is for segmenting white matter.
> 3. is there any function, like aparcstats2table/asegstats2table, can 
> be used to generate the table from the gm.stats.dat file?
https://gate.nmr.mgh.harvard.edu/safelinks/greve/gtmstats2table
> 4. the DKT atlas is the same as the aparc? Please correct me if I was 
> wrong. I think the aparc segmentation is from the Desikan-Killiany 
> Atlas, while the DKT atlas is a different one which is used to produce 
> the aparc.DKTatlas40.annot.
They are not identical but they do segment the same structures. They use 
different atlases derived from  different manual labellings.
>
> Best,
>
> Lu
> */
> /*
> */
> /*
>> On Jul 12, 2017, at 9:41 AM, Douglas N Greve 
>> > wrote:
>>
>> There are several layers of difficulty here:
>>
>> 1. If you just wanted to use a different cortical segmentation, say,
>> aparc.a2009s or aparc.DKTatlas, then you can run gtmseg with --ctx-annot
>> aparc.a2009s 11100 12100 or --ctx-annot aparc.DKTatlas 1000 2000. The
>> numbers are the base  numbers in $FREESURFER_HOME/FreeSurferColorLUT.txt
>> that correspond to these atlases (the DKT atlas is the same as the
>> aparc). Probably you'll want to change the output name with, eg, --o
>> gtmseg.a2009s.
>>
>> 2. If you do not have a whole cortex segmentation, then you will need to
>> create one along with a color table like that in FreeSurferColorLUT.txt
>>
>>
>>
>> On 07/04/2017 06:41 PM, Lu Zhao wrote:
>>> Dear freesurfer support,
>>>
>>> I am using the PetSurfer to process our PET data. But by default, it 
>>> would only generate stats for the segmentation with the aparc atlas.
>>> However, I want to obtain the stats for different freesurfer 
>>> atlases, like in the freesurfer outputs (aseg,stats, 
>>> ?h,BA_exvivo.stats, ?h.aparc.DKTatlas.stats, etc.)
>>> How should I set the ‘gtmseg' to make it produce segmentations for 
>>> the GTM with different freesurfer atlases?
>>> I checked the help doc of gtmseg. The annotation to use for GM/WM 
>>> segmentation can be set using --ctx-annot --wm-annot. However, I 
>>> still don’t know how exactly these should be set. I will be very 
>>> grateful if you could give me some suggestions and detailed guidance 
>>> to help me obtain the PetSurfer stats for different freesurfer 
>>> segmentations.
>>>
>>> Best regards,
>>>
>>> Lu
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu 
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>
>> -- 
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu 
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> 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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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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

Re: [Freesurfer] petsurfer stats for multiple segmentations

2017-07-12 Thread Lu Zhao 
Dear Douglas,

Thank you for your kind reply and instruction. But I still have a few questions:

1. how can I get the segmentation for BA areas, which have no hemisphere bases?
2. when the cortical atlas is changed, should the '--wm-annot’ be changed 
accordingly? For instance, use '—wm-annot aparc.a2009s 13100 14100' when use 
'--ctx-annot  aparc.a2009s 11100 12100’?
3. is there any function, like aparcstats2table/asegstats2table, can be used to 
generate the table from the gm.stats.dat file?
4. the DKT atlas is the same as the aparc? Please correct me if I was wrong. I 
think the aparc segmentation is from the Desikan-Killiany Atlas, while the DKT 
atlas is a different one which is used to produce the aparc.DKTatlas40.annot.

Best,

Lu


> On Jul 12, 2017, at 9:41 AM, Douglas N Greve  
> wrote:
> 
> There are several layers of difficulty here:
> 
> 1. If you just wanted to use a different cortical segmentation, say, 
> aparc.a2009s or aparc.DKTatlas, then you can run gtmseg with --ctx-annot 
> aparc.a2009s 11100 12100 or --ctx-annot aparc.DKTatlas 1000 2000. The 
> numbers are the base  numbers in $FREESURFER_HOME/FreeSurferColorLUT.txt 
> that correspond to these atlases (the DKT atlas is the same as the 
> aparc). Probably you'll want to change the output name with, eg, --o 
> gtmseg.a2009s.
> 
> 2. If you do not have a whole cortex segmentation, then you will need to 
> create one along with a color table like that in FreeSurferColorLUT.txt
> 
> 
> 
> On 07/04/2017 06:41 PM, Lu Zhao wrote:
>> Dear freesurfer support,
>> 
>> I am using the PetSurfer to process our PET data. But by default, it would 
>> only generate stats for the segmentation with the aparc atlas.
>> However, I want to obtain the stats for different freesurfer atlases, like 
>> in the freesurfer outputs (aseg,stats, ?h,BA_exvivo.stats, 
>> ?h.aparc.DKTatlas.stats, etc.)
>> How should I set the ‘gtmseg' to make it produce segmentations for the GTM 
>> with different freesurfer atlases?
>> I checked the help doc of gtmseg. The annotation to use for GM/WM 
>> segmentation can be set using --ctx-annot --wm-annot. However, I still don’t 
>> know how exactly these should be set. I will be very grateful if you could 
>> give me some suggestions and detailed guidance to help me obtain the 
>> PetSurfer stats for different freesurfer segmentations.
>> 
>> Best regards,
>> 
>> Lu
>> 
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> 
>> 
> 
> -- 
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
> 
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> 
> ___
> Freesurfer mailing list
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> 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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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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Re: [Freesurfer] petsurfer stats for multiple segmentations

2017-07-12 Thread Douglas N Greve 
There are several layers of difficulty here:

1. If you just wanted to use a different cortical segmentation, say, 
aparc.a2009s or aparc.DKTatlas, then you can run gtmseg with --ctx-annot 
aparc.a2009s 11100 12100 or --ctx-annot aparc.DKTatlas 1000 2000. The 
numbers are the base  numbers in $FREESURFER_HOME/FreeSurferColorLUT.txt 
that correspond to these atlases (the DKT atlas is the same as the 
aparc). Probably you'll want to change the output name with, eg, --o 
gtmseg.a2009s.

2. If you do not have a whole cortex segmentation, then you will need to 
create one along with a color table like that in FreeSurferColorLUT.txt



On 07/04/2017 06:41 PM, Lu Zhao wrote:
> Dear freesurfer support,
>
> I am using the PetSurfer to process our PET data. But by default, it would 
> only generate stats for the segmentation with the aparc atlas.
> However, I want to obtain the stats for different freesurfer atlases, like in 
> the freesurfer outputs (aseg,stats, ?h,BA_exvivo.stats, 
> ?h.aparc.DKTatlas.stats, etc.)
> How should I set the ‘gtmseg' to make it produce segmentations for the GTM 
> with different freesurfer atlases?
> I checked the help doc of gtmseg. The annotation to use for GM/WM 
> segmentation can be set using --ctx-annot --wm-annot. However, I still don’t 
> know how exactly these should be set. I will be very grateful if you could 
> give me some suggestions and detailed guidance to help me obtain the 
> PetSurfer stats for different freesurfer segmentations.
>
> Best regards,
>
> Lu
>   
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

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

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

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

[Freesurfer] petsurfer stats for multiple segmentations

2017-07-09 Thread Lu Zhao 
Dear freesurfer support,

I am using the PetSurfer to process our PET data. But by default, it would only 
generate stats for the segmentation with the aparc atlas. 
However, I want to obtain the stats for different freesurfer atlases, like in 
the freesurfer outputs (aseg,stats, ?h,BA_exvivo.stats, 
?h.aparc.DKTatlas.stats, etc.)
How should I set the ‘gtmseg' to make it produce segmentations for the GTM with 
different freesurfer atlases? 
I checked the help doc of gtmseg. The annotation to use for GM/WM segmentation 
can be set using --ctx-annot --wm-annot. However, I still don’t know how 
exactly these should be set. I will be very grateful if you could give me some 
suggestions and detailed guidance to help me obtain the PetSurfer stats for 
different freesurfer segmentations.

Best regards,

Lu
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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.

[Freesurfer] petsurfer stats for multiple segmentations

2017-07-04 Thread Lu Zhao 
Dear freesurfer support,

I am using the PetSurfer to process our PET data. But by default, it would only 
generate stats for the segmentation with the aparc atlas. 
However, I want to obtain the stats for different freesurfer atlases, like in 
the freesurfer outputs (aseg,stats, ?h,BA_exvivo.stats, 
?h.aparc.DKTatlas.stats, etc.)
How should I set the ‘gtmseg' to make it produce segmentations for the GTM with 
different freesurfer atlases? 
I checked the help doc of gtmseg. The annotation to use for GM/WM segmentation 
can be set using --ctx-annot --wm-annot. However, I still don’t know how 
exactly these should be set. I will be very grateful if you could give me some 
suggestions and detailed guidance to help me obtain the PetSurfer stats for 
different freesurfer segmentations.

Best regards,

Lu
 
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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.