Re: [Freesurfer] Intensity information of Hippocampal Subfields

2017-02-27 Thread Douglas N Greve 
Is there a T2.prenorm.mgz in the mri folder? If not, you can run

bbregister --mov T2.nativespace.mgz --t2 --s subject --reg t2.reg.lta

mri_vol2vol --mov T2.nativespace.mgz --reg t2.reg.lta --targ orig.mgz 
--o T2.prenorm.mgz

Then run something like

mri_normalize \
 -sigma 0.5 -nonmax_suppress 0 -min_dist 1 \
 -aseg $mdir/aseg.presurf.mgz \
 -surface $sdir/rh.white identity.nofile \
 -surface $sdir/lh.white identity.nofile \
 $mdir/${t2flair}.prenorm.mgz \
 $mdir/${t2flair}.norm.mgz

On 02/27/2017 01:28 PM, ali reza mohammadi nejad wrote:
> I processed the T1-weighted data without T2. Therefore, we do not have 
> T2.norm.mgz in the mri folder of each subject.
> Only for the HP-subfields segmentation, we added additional high-resolution 
> T2-weighted data to increase the accuracy of HP-subfields segmentation.
>
> Thanks!
> Alireza
>
>> On Feb 27, 2017, at 12:53 PM, Douglas N Greve  
>> wrote:
>>
>> There is usually a T2.norm.mgz file in the mri folder. If that is there,
>> then you should use that rather than the raw data that is not bias field
>> corrected
>>
>>
>>> On 02/27/2017 12:30 PM, ali reza mohammadi nejad wrote:
>>> Thank you so much Dr. Doug! I just have one more question:
>>>
>>> Now I want to compute the same information for our second modality (i.e., 
>>> mean and std intensity of different HP_subfields for our additional scan, 
>>> e,g., T2 or FLAIR).
>>> My question is that how could I use .FSspace.mgz (in mri 
>>> folder) and T1_to_.v10.Ita (in transform folder) files in 
>>> mri_segstats command?
>>>
>>> Thank you in advance for any help.
>>> Best regards,
>>> Alireza
>>>
>>>
 On Feb 24, 2017, at 10:51 AM, Douglas N Greve  
 wrote:

 The basic command is

 mri_segstats --seg seg.mgz --default-ctab --sum sum.dat --i input.mgz

 where seg is the hippo sub field seg and input is the input where you
 want to get the intensities from (probably norm.mgz). Note that you need
 to use the hipp sub field output that is 1mm (not the high res one)


> On 02/24/2017 09:53 AM, ali reza mohammadi nejad wrote:
> Dear FreeSurfer Experts,
> I want to compute some intensity information (e.g., mean and std) of each 
> Hippocampal subfields (similar to aseg.stats file).
> I think one option could be mri_segstats command, but I am not sure.
> If it works, what are the inputs of this command?
>
> Thank you in advance for any help.
> Alireza
>
>
>
> ___
> 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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 e-mail
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>>> ___
>>> 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
>
> ___
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> 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:

Re: [Freesurfer] Intensity information of Hippocampal Subfields

2017-02-27 Thread ali reza mohammadi nejad 
I processed the T1-weighted data without T2. Therefore, we do not have 
T2.norm.mgz in the mri folder of each subject.
Only for the HP-subfields segmentation, we added additional high-resolution 
T2-weighted data to increase the accuracy of HP-subfields segmentation.

Thanks!
Alireza

> On Feb 27, 2017, at 12:53 PM, Douglas N Greve  
> wrote:
> 
> There is usually a T2.norm.mgz file in the mri folder. If that is there, 
> then you should use that rather than the raw data that is not bias field 
> corrected
> 
> 
>> On 02/27/2017 12:30 PM, ali reza mohammadi nejad wrote:
>> Thank you so much Dr. Doug! I just have one more question:
>> 
>> Now I want to compute the same information for our second modality (i.e., 
>> mean and std intensity of different HP_subfields for our additional scan, 
>> e,g., T2 or FLAIR).
>> My question is that how could I use .FSspace.mgz (in mri folder) 
>> and T1_to_.v10.Ita (in transform folder) files in mri_segstats 
>> command?
>> 
>> Thank you in advance for any help.
>> Best regards,
>> Alireza
>> 
>> 
>>> On Feb 24, 2017, at 10:51 AM, Douglas N Greve  
>>> wrote:
>>> 
>>> The basic command is
>>> 
>>> mri_segstats --seg seg.mgz --default-ctab --sum sum.dat --i input.mgz
>>> 
>>> where seg is the hippo sub field seg and input is the input where you
>>> want to get the intensities from (probably norm.mgz). Note that you need
>>> to use the hipp sub field output that is 1mm (not the high res one)
>>> 
>>> 
 On 02/24/2017 09:53 AM, ali reza mohammadi nejad wrote:
 Dear FreeSurfer Experts,
 I want to compute some intensity information (e.g., mean and std) of each 
 Hippocampal subfields (similar to aseg.stats file).
 I think one option could be mri_segstats command, but I am not sure.
 If it works, what are the inputs of this command?
 
 Thank you in advance for any help.
 Alireza
 
 
 
 ___
 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.
>>> 
>> 
>> ___
>> 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


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Re: [Freesurfer] Intensity information of Hippocampal Subfields

2017-02-27 Thread Douglas N Greve 
There is usually a T2.norm.mgz file in the mri folder. If that is there, 
then you should use that rather than the raw data that is not bias field 
corrected


On 02/27/2017 12:30 PM, ali reza mohammadi nejad wrote:
> Thank you so much Dr. Doug! I just have one more question:
>
> Now I want to compute the same information for our second modality (i.e., 
> mean and std intensity of different HP_subfields for our additional scan, 
> e,g., T2 or FLAIR).
> My question is that how could I use .FSspace.mgz (in mri folder) 
> and T1_to_.v10.Ita (in transform folder) files in mri_segstats 
> command?
>
> Thank you in advance for any help.
> Best regards,
> Alireza
>
>
>> On Feb 24, 2017, at 10:51 AM, Douglas N Greve  
>> wrote:
>>
>> The basic command is
>>
>> mri_segstats --seg seg.mgz --default-ctab --sum sum.dat --i input.mgz
>>
>> where seg is the hippo sub field seg and input is the input where you
>> want to get the intensities from (probably norm.mgz). Note that you need
>> to use the hipp sub field output that is 1mm (not the high res one)
>>
>>
>>> On 02/24/2017 09:53 AM, ali reza mohammadi nejad wrote:
>>> Dear FreeSurfer Experts,
>>> I want to compute some intensity information (e.g., mean and std) of each 
>>> Hippocampal subfields (similar to aseg.stats file).
>>> I think one option could be mri_segstats command, but I am not sure.
>>> If it works, what are the inputs of this command?
>>>
>>> Thank you in advance for any help.
>>> Alireza
>>>
>>>
>>>
>>> ___
>>> 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.
>>
>
> ___
> 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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Re: [Freesurfer] Intensity information of Hippocampal Subfields

2017-02-27 Thread ali reza mohammadi nejad 
Thank you so much Dr. Doug! I just have one more question:

Now I want to compute the same information for our second modality (i.e., mean 
and std intensity of different HP_subfields for our additional scan, e,g., T2 
or FLAIR).
My question is that how could I use .FSspace.mgz (in mri folder) 
and T1_to_.v10.Ita (in transform folder) files in mri_segstats 
command?

Thank you in advance for any help.
Best regards,
Alireza


> On Feb 24, 2017, at 10:51 AM, Douglas N Greve  
> wrote:
> 
> The basic command is
> 
> mri_segstats --seg seg.mgz --default-ctab --sum sum.dat --i input.mgz
> 
> where seg is the hippo sub field seg and input is the input where you 
> want to get the intensities from (probably norm.mgz). Note that you need 
> to use the hipp sub field output that is 1mm (not the high res one)
> 
> 
>> On 02/24/2017 09:53 AM, ali reza mohammadi nejad wrote:
>> Dear FreeSurfer Experts,
>> I want to compute some intensity information (e.g., mean and std) of each 
>> Hippocampal subfields (similar to aseg.stats file).
>> I think one option could be mri_segstats command, but I am not sure.
>> If it works, what are the inputs of this command?
>> 
>> Thank you in advance for any help.
>> Alireza
>> 
>> 
>> 
>> ___
>> 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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Re: [Freesurfer] Intensity information of Hippocampal Subfields

2017-02-25 Thread Ali-Reza Mohammadi-Nejad 
Thank you so much Dr. Doug! I just have one more question:
Now I want to compute the same information for our second modality (i.e., mean 
and std intensity of different HP_subfields for our additional scan, e,g., T2 
or FLAIR).My question is that how could I use .FSspace.mgz (in mri 
folder) and T1_to_.v10.Ita (in transform folder) files in 
mri_segstats command?
Thank you in advance for any help.Best regards,Alireza
   

On Friday, February 24, 2017 10:51 AM, Douglas N Greve 
 wrote:
 

 The basic command is

mri_segstats --seg seg.mgz --default-ctab --sum sum.dat --i input.mgz

where seg is the hippo sub field seg and input is the input where you 
want to get the intensities from (probably norm.mgz). Note that you need 
to use the hipp sub field output that is 1mm (not the high res one)


On 02/24/2017 09:53 AM, ali reza mohammadi nejad wrote:
> Dear FreeSurfer Experts,
> I want to compute some intensity information (e.g., mean and std) of each 
> Hippocampal subfields (similar to aseg.stats file).
> I think one option could be mri_segstats command, but I am not sure.
> If it works, what are the inputs of this command?
>
> Thank you in advance for any help.
> Alireza
>
>
>
> ___
> 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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Re: [Freesurfer] Intensity information of Hippocampal Subfields

2017-02-24 Thread Douglas N Greve 
The basic command is

mri_segstats --seg seg.mgz --default-ctab --sum sum.dat --i input.mgz

where seg is the hippo sub field seg and input is the input where you 
want to get the intensities from (probably norm.mgz). Note that you need 
to use the hipp sub field output that is 1mm (not the high res one)


On 02/24/2017 09:53 AM, ali reza mohammadi nejad wrote:
> Dear FreeSurfer Experts,
> I want to compute some intensity information (e.g., mean and std) of each 
> Hippocampal subfields (similar to aseg.stats file).
> I think one option could be mri_segstats command, but I am not sure.
> If it works, what are the inputs of this command?
>
> Thank you in advance for any help.
> Alireza
>
>
>
> ___
> 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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[Freesurfer] Intensity information of Hippocampal Subfields

2017-02-24 Thread ali reza mohammadi nejad 
Dear FreeSurfer Experts,
I want to compute some intensity information (e.g., mean and std) of each 
Hippocampal subfields (similar to aseg.stats file).
I think one option could be mri_segstats command, but I am not sure. 
If it works, what are the inputs of this command?

Thank you in advance for any help.
Alireza



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contains patient information, please contact the Partners Compliance HelpLine at
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