subject:"Re\: \[Freesurfer\] Anterior \/ Posterior Partition in Hippocampus parcellation atlas"

Re: [Freesurfer] Anterior / Posterior Partition in Hippocampus parcellation atlas

2018-08-03 Thread Iglesias Gonzalez, Eugenio

External Email - Use Caution

Dear Vasudev,
It is expected that you get different volume estimates with different atlases 
(FreeSurfer vs CobraLab), as the manual delineation protocols that were used to 
create them are very different (e.g., see Yushkevich et al., NeuroImage, 2015).
Regarding the differences in p-values between the two methods:
- Do you get a similar effect size / pval when looking at the whole hippocampus?
- Are the volumes of the subfields given by one method highly correlated with 
the volumes given by the other?
- Did you QC the output, for both methods?
- How different were the results you got? While you mention statistical 
significance vs not, I wouldn’t be alarmed if the p-value was 0.04 vs 0.06, 
whereas 0.1 vs 0.5 would be much more worrying.
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From:  on behalf of Dev vasu 

Reply-To: Freesurfer support list 
Date: Thursday, 2 August 2018 at 19:18
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] Anterior / Posterior Partition in Hippocampus 
parcellation atlas


External Email - Use Caution
Dear All,

I have a problem with the Freesurfer hippocampal longitudinal segmentation 
results , when i have done segmentation using following algorithm ( 
https://github.com/CobraLab/antsRegistration-MAGeT) with no anterior/posterior 
partitioning ( Head/body/tail ) , on my subject pool the volumes that i have 
obtained for each subfield is very different from the volumes of corresponding 
subfields that i am getting when i have done subfield segmentation using 
freesurfer. I think algorithm does influence the segmentation procedure, if 
this is the case then i am getting different results for histology based 
segmentation using https://github.com/CobraLab/antsRegistration-MAGeT and 
freesurfer.


When i compare the subfield volumes between healthy and disease patients  that 
i have obtained using first segmentation procedure using ANTS-MAGeT , i notice 
statistical significance   in subfields like CA1,CA2-CA3 but when i do the same 
using freesurfer based algorithm i notice no statistical significance in these 
subfields.

Do you think the algorithm has any influence on segmentation to such a level 
that we get completely different results on two occasions.


Thanks
Vasudev


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Re: [Freesurfer] Anterior / Posterior Partition in Hippocampus parcellation atlas

2018-07-03 Thread Dev vasu

External Email - Use Caution

Dear Sir,

I was able to generate segmentations as cited in the module , I am able
obtain segmentations for CA1 posterior Head and CA1 Posterior body , along
with  CA1 head and CA1 body , what does non posterior parcellations of CA1
head and body indicates, can these be assumed as anterior regions ?, is
there any way to obtain CA1 head and CA1 body etc for both left and right
hemispheres , as per segmentation results i can only see
*[lr]h.hippoSfVolumes-T1.v2x.mgz
files * . Not  (lr)h.CA1_head and body , how can i split these subfields
from  *[lr]h.hippoSfVolumes-T1.v2x.mgz  files.*


*Thanks*
*Vasudev*


On Tue, Jul 3, 2018 at 11:49 AM, Iglesias Gonzalez, Eugenio <
e.igles...@ucl.ac.uk> wrote:

> Yes!
>
>
> Juan Eugenio Iglesias
>
> Centre for Medical Image Computing (CMIC)
>
> University College London
>
> http://www.jeiglesias.com
>
> http://cmictig.cs.ucl.ac.uk/
>
>
> --
> *From:* Dev vasu 
> *Sent:* Tuesday, July 3, 2018 12:22:27 AM
> *To:* Iglesias Gonzalez, Eugenio
> *Cc:* freesurfer@nmr.mgh.harvard.edu
>
> *Subject:* Re: Anterior / Posterior Partition in Hippocampus parcellation
> atlas
>
> Dear Sir,
>
> I have another query if i use "export WRITE_POSTERIORS=1", will it
> generate posterior CA1 and other substructures in the form as cited  
> *posterior_sidev2x.mgz
> , *
>
>
> Thanks
> Vasudev
>
> On Mon, Jul 2, 2018 at 8:30 PM, Dev vasu  gmail.com> wrote:
>
> Dear Sir,
>
> Thanks for your reply Yes,i have run 6.0, Can you send me the link for
> developmental version of freesurfer, also how can i obtain posterior
> regions of subfields like CA1,CA2,CA3,CA4, as the link suggests only CA1
> head and CA1 body were segmented , i need posterior part of CA1 can i
> assume CA1 body as posterior region.
>
>
> Thanks
> Vasudev
>
> On Mon, Jul 2, 2018 at 8:25 PM, Iglesias Gonzalez, Eugenio <
> e.igles...@ucl.ac.uk> wrote:
>
> Ah, now I understand.
>
> To get the division in the wiki (https://surfer.nmr.mgh.harvar
> d.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala), you need to run
> the development version of FreeSurfer. The version you ran (6.0, I
> presume), does not provide such subdivision.
>
> In principle, you could use Garikoitz’s code to subdivide the
> segmentation, but his code is not part of FreeSurfer, so you would have to
> contact him for support. Alternatively, you can also download the
> development version of FreeSurfer, which will provide the segmentation that
> I mentioned earlier.
>
> Kind regards,
>
> /Eugenio
>
>
>
> --
>
> Juan Eugenio Iglesias
>
> ERC Senior Research Fellow
>
> Centre for Medical Image Computing (CMIC)
>
> University College London
>
> http://www.jeiglesias.com
>
> http://cmictig.cs.ucl.ac.uk/
>
>
>
>
>
> *From: *Dev vasu 
> *Date: *Monday, 2 July 2018 at 19:22
> *To: *"Iglesias Gonzalez, Eugenio" 
> *Cc: *"freesurfer@nmr.mgh.harvard.edu" , "
> igles...@nmr.mgh.harvard.edu" 
> *Subject: *Re: Anterior / Posterior Partition in Hippocampus parcellation
> atlas
>
>
>
> Dear sir,
>
>
>
> In the following journal published by you ,procedure for longitudinal
> segmentation was highlighted (https://github.com/garikoitz/hippovol) , I
> have run the module described in wiki and i have obtained
> lh.hippoSfLabels-T1.v10.FSvoxelSpace.mgz and lh.hippoSfLabels-T1.v10.mgz
> files , i would like to know how i can split the labels CA1 head, CA1 body
> and CA1 tail from this file, since individual subfield label numbers for
> CA1 head and CA1 body are not defined ,also can i assure CA1 body as
> posterior region and CA1 head as anterior ?.
>
>
>
>
>
> Thanks
>
> Vasudev
>
>
>
> On Mon, Jul 2, 2018 at 7:39 PM, Iglesias Gonzalez, Eugenio <
> e.igles...@ucl.ac.uk> wrote:
>
> Dear Vasudev,
>
> You can run the module described in that wiki page, and in the output file
> [lr]h.hippoAmygLabels-T1.v2x.mgz you will find segmentations for CA1
> head, CA1 body, CA23 head, CA23 body, CA4 head, CA4 body, and hippocampal
> tail (note that we don’t parcellate the tail).
>
> Cheers,
>
> /Eugenio
>
>
>
> --
>
> Juan Eugenio Iglesias
>
> ERC Senior Research Fellow
>
> Centre for Medical Image Computing (CMIC)
>
> University College London
>
> http://www.jeiglesias.com
>
> http://cmictig.cs.ucl.ac.uk/
>
>
>
>
>
> *From: *Dev vasu 
> *Date: *Monday, 2 July 2018 at 17:09
> *To: *"freesurfer@nmr.mgh.harvard.edu" , "
> igles...@nmr.mgh.harvard.edu" 
> *Subject: *Anterior / Posterior Partition in Hippocampus parcellation
> atlas
>
>
>
> *External Email - Use Caution*
>
> Dear Sir,
>
>
>
>
>
> I have reviewed your journal which detailed about hippocampus parcellation
> ( https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfiel
> dsAndNucleiOfAmygdala ) of subfields ( HBT - Head/body/Tail) , could you
> please let me know how to partition the atlas along the lines of Anterior
> CA1,CA3,CA4  and posterior CA1,CA3,CA4.
>
>
>
>
>
> Thanks
>
> Vasdudev
>
> The information in this e-mail is intended only for the per

Re: [Freesurfer] Anterior / Posterior Partition in Hippocampus parcellation atlas

2018-07-03 Thread Iglesias Gonzalez, Eugenio

External Email - Use Caution

Yes!


Juan Eugenio Iglesias

Centre for Medical Image Computing (CMIC)

University College London

http://www.jeiglesias.com

http://cmictig.cs.ucl.ac.uk/



From: Dev vasu 
Sent: Tuesday, July 3, 2018 12:22:27 AM
To: Iglesias Gonzalez, Eugenio
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: Anterior / Posterior Partition in Hippocampus parcellation atlas

Dear Sir,

I have another query if i use "export WRITE_POSTERIORS=1", will it generate 
posterior CA1 and other substructures in the form as cited  
posterior_sidev2x.mgz ,


Thanks
Vasudev

On Mon, Jul 2, 2018 at 8:30 PM, Dev vasu 
mailto:vasudevamurthy.devulapa...@gmail.com>>
 wrote:
Dear Sir,

Thanks for your reply Yes,i have run 6.0, Can you send me the link for 
developmental version of freesurfer, also how can i obtain posterior regions of 
subfields like CA1,CA2,CA3,CA4, as the link suggests only CA1 head and CA1 body 
were segmented , i need posterior part of CA1 can i assume CA1 body as 
posterior region.


Thanks
Vasudev

On Mon, Jul 2, 2018 at 8:25 PM, Iglesias Gonzalez, Eugenio 
mailto:e.igles...@ucl.ac.uk>> wrote:

Ah, now I understand.

To get the division in the wiki 
(https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala),
 you need to run the development version of FreeSurfer. The version you ran 
(6.0, I presume), does not provide such subdivision.

In principle, you could use Garikoitz’s code to subdivide the segmentation, but 
his code is not part of FreeSurfer, so you would have to contact him for 
support. Alternatively, you can also download the development version of 
FreeSurfer, which will provide the segmentation that I mentioned earlier.

Kind regards,

/Eugenio



--

Juan Eugenio Iglesias

ERC Senior Research Fellow

Centre for Medical Image Computing (CMIC)

University College London

http://www.jeiglesias.com

http://cmictig.cs.ucl.ac.uk/





From: Dev vasu 
mailto:vasudevamurthy.devulapa...@gmail.com>>
Date: Monday, 2 July 2018 at 19:22
To: "Iglesias Gonzalez, Eugenio" 
mailto:e.igles...@ucl.ac.uk>>
Cc: "freesurfer@nmr.mgh.harvard.edu" 
mailto:freesurfer@nmr.mgh.harvard.edu>>, 
"igles...@nmr.mgh.harvard.edu" 
mailto:igles...@nmr.mgh.harvard.edu>>
Subject: Re: Anterior / Posterior Partition in Hippocampus parcellation atlas



Dear sir,



In the following journal published by you ,procedure for longitudinal 
segmentation was highlighted (https://github.com/garikoitz/hippovol) , I have 
run the module described in wiki and i have obtained 
lh.hippoSfLabels-T1.v10.FSvoxelSpace.mgz and lh.hippoSfLabels-T1.v10.mgz files 
, i would like to know how i can split the labels CA1 head, CA1 body and CA1 
tail from this file, since individual subfield label numbers for CA1 head and 
CA1 body are not defined ,also can i assure CA1 body as posterior region and 
CA1 head as anterior ?.





Thanks

Vasudev



On Mon, Jul 2, 2018 at 7:39 PM, Iglesias Gonzalez, Eugenio 
mailto:e.igles...@ucl.ac.uk>> wrote:

Dear Vasudev,

You can run the module described in that wiki page, and in the output file 
[lr]h.hippoAmygLabels-T1.v2x.mgz you will find segmentations for CA1 head, CA1 
body, CA23 head, CA23 body, CA4 head, CA4 body, and hippocampal tail (note that 
we don’t parcellate the tail).

Cheers,

/Eugenio



--

Juan Eugenio Iglesias

ERC Senior Research Fellow

Centre for Medical Image Computing (CMIC)

University College London

http://www.jeiglesias.com

http://cmictig.cs.ucl.ac.uk/





From: Dev vasu 
mailto:vasudevamurthy.devulapa...@gmail.com>>
Date: Monday, 2 July 2018 at 17:09
To: "freesurfer@nmr.mgh.harvard.edu" 
mailto:freesurfer@nmr.mgh.harvard.edu>>, 
"igles...@nmr.mgh.harvard.edu" 
mailto:igles...@nmr.mgh.harvard.edu>>
Subject: Anterior / Posterior Partition in Hippocampus parcellation atlas



External Email - Use Caution

Dear Sir,





I have reviewed your journal which detailed about hippocampus parcellation ( 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala
 ) of subfields ( HBT - Head/body/Tail) , could you please let me know how to 
partition the atlas along the lines of Anterior CA1,CA3,CA4  and posterior 
CA1,CA3,CA4.





Thanks

Vasdudev

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] Anterior / Posterior Partition in Hippocampus parcellation atlas

2018-07-02 Thread Dev vasu

External Email - Use Caution

Dear Sir,

I have another query if i use "export WRITE_POSTERIORS=1", will it generate
posterior CA1 and other substructures in the form as cited
*posterior_sidev2x.mgz
, *


Thanks
Vasudev

On Mon, Jul 2, 2018 at 8:30 PM, Dev vasu <
vasudevamurthy.devulapa...@gmail.com> wrote:

> Dear Sir,
>
> Thanks for your reply Yes,i have run 6.0, Can you send me the link for
> developmental version of freesurfer, also how can i obtain posterior
> regions of subfields like CA1,CA2,CA3,CA4, as the link suggests only CA1
> head and CA1 body were segmented , i need posterior part of CA1 can i
> assume CA1 body as posterior region.
>
>
> Thanks
> Vasudev
>
> On Mon, Jul 2, 2018 at 8:25 PM, Iglesias Gonzalez, Eugenio <
> e.igles...@ucl.ac.uk> wrote:
>
>> Ah, now I understand.
>>
>> To get the division in the wiki (https://surfer.nmr.mgh.harvar
>> d.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala), you need to run
>> the development version of FreeSurfer. The version you ran (6.0, I
>> presume), does not provide such subdivision.
>>
>> In principle, you could use Garikoitz’s code to subdivide the
>> segmentation, but his code is not part of FreeSurfer, so you would have to
>> contact him for support. Alternatively, you can also download the
>> development version of FreeSurfer, which will provide the segmentation that
>> I mentioned earlier.
>>
>> Kind regards,
>>
>> /Eugenio
>>
>>
>>
>> --
>>
>> Juan Eugenio Iglesias
>>
>> ERC Senior Research Fellow
>>
>> Centre for Medical Image Computing (CMIC)
>>
>> University College London
>>
>> http://www.jeiglesias.com
>>
>> http://cmictig.cs.ucl.ac.uk/
>>
>>
>>
>>
>>
>> *From: *Dev vasu 
>> *Date: *Monday, 2 July 2018 at 19:22
>> *To: *"Iglesias Gonzalez, Eugenio" 
>> *Cc: *"freesurfer@nmr.mgh.harvard.edu" ,
>> "igles...@nmr.mgh.harvard.edu" 
>> *Subject: *Re: Anterior / Posterior Partition in Hippocampus
>> parcellation atlas
>>
>>
>>
>> Dear sir,
>>
>>
>>
>> In the following journal published by you ,procedure for longitudinal
>> segmentation was highlighted (https://github.com/garikoitz/hippovol) , I
>> have run the module described in wiki and i have obtained
>> lh.hippoSfLabels-T1.v10.FSvoxelSpace.mgz and lh.hippoSfLabels-T1.v10.mgz
>> files , i would like to know how i can split the labels CA1 head, CA1 body
>> and CA1 tail from this file, since individual subfield label numbers for
>> CA1 head and CA1 body are not defined ,also can i assure CA1 body as
>> posterior region and CA1 head as anterior ?.
>>
>>
>>
>>
>>
>> Thanks
>>
>> Vasudev
>>
>>
>>
>> On Mon, Jul 2, 2018 at 7:39 PM, Iglesias Gonzalez, Eugenio <
>> e.igles...@ucl.ac.uk> wrote:
>>
>> Dear Vasudev,
>>
>> You can run the module described in that wiki page, and in the output
>> file [lr]h.hippoAmygLabels-T1.v2x.mgz you will find segmentations for
>> CA1 head, CA1 body, CA23 head, CA23 body, CA4 head, CA4 body, and
>> hippocampal tail (note that we don’t parcellate the tail).
>>
>> Cheers,
>>
>> /Eugenio
>>
>>
>>
>> --
>>
>> Juan Eugenio Iglesias
>>
>> ERC Senior Research Fellow
>>
>> Centre for Medical Image Computing (CMIC)
>>
>> University College London
>>
>> http://www.jeiglesias.com
>>
>> http://cmictig.cs.ucl.ac.uk/
>>
>>
>>
>>
>>
>> *From: *Dev vasu 
>> *Date: *Monday, 2 July 2018 at 17:09
>> *To: *"freesurfer@nmr.mgh.harvard.edu" ,
>> "igles...@nmr.mgh.harvard.edu" 
>> *Subject: *Anterior / Posterior Partition in Hippocampus parcellation
>> atlas
>>
>>
>>
>> *External Email - Use Caution*
>>
>> Dear Sir,
>>
>>
>>
>>
>>
>> I have reviewed your journal which detailed about hippocampus
>> parcellation ( https://surfer.nmr.mgh.harvard
>> .edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala ) of subfields ( HBT
>> - Head/body/Tail) , could you please let me know how to partition the atlas
>> along the lines of Anterior CA1,CA3,CA4  and posterior CA1,CA3,CA4.
>>
>>
>>
>>
>>
>> Thanks
>>
>> Vasdudev
>>
>> 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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Freesurfer@nmr.mgh.harvard.edu
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Anterior / Posterior Partition in Hippocampus parcellation atlas

2018-07-02 Thread Iglesias Gonzalez, Eugenio

External Email - Use Caution

You can download dev from here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev

Whether you can use CA1 body as posterior CA1… you’d be making an approximation 
that may or may not be valid, depending on the application. I honestly don’t 
know.

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From: Dev vasu 
Date: Monday, 2 July 2018 at 19:30
To: "Iglesias Gonzalez, Eugenio" 
Cc: "freesurfer@nmr.mgh.harvard.edu" , 
"igles...@nmr.mgh.harvard.edu" 
Subject: Re: Anterior / Posterior Partition in Hippocampus parcellation atlas

Dear Sir,

Thanks for your reply Yes,i have run 6.0, Can you send me the link for 
developmental version of freesurfer, also how can i obtain posterior regions of 
subfields like CA1,CA2,CA3,CA4, as the link suggests only CA1 head and CA1 body 
were segmented , i need posterior part of CA1 can i assume CA1 body as 
posterior region.


Thanks
Vasudev

On Mon, Jul 2, 2018 at 8:25 PM, Iglesias Gonzalez, Eugenio 
mailto:e.igles...@ucl.ac.uk>> wrote:
Ah, now I understand.
To get the division in the wiki 
(https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala),
 you need to run the development version of FreeSurfer. The version you ran 
(6.0, I presume), does not provide such subdivision.
In principle, you could use Garikoitz’s code to subdivide the segmentation, but 
his code is not part of FreeSurfer, so you would have to contact him for 
support. Alternatively, you can also download the development version of 
FreeSurfer, which will provide the segmentation that I mentioned earlier.
Kind regards,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From: Dev vasu 
mailto:vasudevamurthy.devulapa...@gmail.com>>
Date: Monday, 2 July 2018 at 19:22
To: "Iglesias Gonzalez, Eugenio" 
mailto:e.igles...@ucl.ac.uk>>
Cc: "freesurfer@nmr.mgh.harvard.edu" 
mailto:freesurfer@nmr.mgh.harvard.edu>>, 
"igles...@nmr.mgh.harvard.edu" 
mailto:igles...@nmr.mgh.harvard.edu>>
Subject: Re: Anterior / Posterior Partition in Hippocampus parcellation atlas

Dear sir,

In the following journal published by you ,procedure for longitudinal 
segmentation was highlighted (https://github.com/garikoitz/hippovol) , I have 
run the module described in wiki and i have obtained 
lh.hippoSfLabels-T1.v10.FSvoxelSpace.mgz and lh.hippoSfLabels-T1.v10.mgz files 
, i would like to know how i can split the labels CA1 head, CA1 body and CA1 
tail from this file, since individual subfield label numbers for CA1 head and 
CA1 body are not defined ,also can i assure CA1 body as posterior region and 
CA1 head as anterior ?.


Thanks
Vasudev

On Mon, Jul 2, 2018 at 7:39 PM, Iglesias Gonzalez, Eugenio 
mailto:e.igles...@ucl.ac.uk>> wrote:
Dear Vasudev,
You can run the module described in that wiki page, and in the output file 
[lr]h.hippoAmygLabels-T1.v2x.mgz you will find segmentations for CA1 head, CA1 
body, CA23 head, CA23 body, CA4 head, CA4 body, and hippocampal tail (note that 
we don’t parcellate the tail).
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From: Dev vasu 
mailto:vasudevamurthy.devulapa...@gmail.com>>
Date: Monday, 2 July 2018 at 17:09
To: "freesurfer@nmr.mgh.harvard.edu" 
mailto:freesurfer@nmr.mgh.harvard.edu>>, 
"igles...@nmr.mgh.harvard.edu" 
mailto:igles...@nmr.mgh.harvard.edu>>
Subject: Anterior / Posterior Partition in Hippocampus parcellation atlas


External Email - Use Caution
Dear Sir,


I have reviewed your journal which detailed about hippocampus parcellation ( 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala
 ) of subfields ( HBT - Head/body/Tail) , could you please let me know how to 
partition the atlas along the lines of Anterior CA1,CA3,CA4  and posterior 
CA1,CA3,CA4.


Thanks
Vasdudev

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
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The information in this e-mail is intended only for the person to

Re: [Freesurfer] Anterior / Posterior Partition in Hippocampus parcellation atlas

2018-07-02 Thread Dev vasu

External Email - Use Caution

Dear Sir,

Thanks for your reply Yes,i have run 6.0, Can you send me the link for
developmental version of freesurfer, also how can i obtain posterior
regions of subfields like CA1,CA2,CA3,CA4, as the link suggests only CA1
head and CA1 body were segmented , i need posterior part of CA1 can i
assume CA1 body as posterior region.


Thanks
Vasudev

On Mon, Jul 2, 2018 at 8:25 PM, Iglesias Gonzalez, Eugenio <
e.igles...@ucl.ac.uk> wrote:

> Ah, now I understand.
>
> To get the division in the wiki (https://surfer.nmr.mgh.
> harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala), you need to
> run the development version of FreeSurfer. The version you ran (6.0, I
> presume), does not provide such subdivision.
>
> In principle, you could use Garikoitz’s code to subdivide the
> segmentation, but his code is not part of FreeSurfer, so you would have to
> contact him for support. Alternatively, you can also download the
> development version of FreeSurfer, which will provide the segmentation that
> I mentioned earlier.
>
> Kind regards,
>
> /Eugenio
>
>
>
> --
>
> Juan Eugenio Iglesias
>
> ERC Senior Research Fellow
>
> Centre for Medical Image Computing (CMIC)
>
> University College London
>
> http://www.jeiglesias.com
>
> http://cmictig.cs.ucl.ac.uk/
>
>
>
>
>
> *From: *Dev vasu 
> *Date: *Monday, 2 July 2018 at 19:22
> *To: *"Iglesias Gonzalez, Eugenio" 
> *Cc: *"freesurfer@nmr.mgh.harvard.edu" , "
> igles...@nmr.mgh.harvard.edu" 
> *Subject: *Re: Anterior / Posterior Partition in Hippocampus parcellation
> atlas
>
>
>
> Dear sir,
>
>
>
> In the following journal published by you ,procedure for longitudinal
> segmentation was highlighted (https://github.com/garikoitz/hippovol) , I
> have run the module described in wiki and i have obtained
> lh.hippoSfLabels-T1.v10.FSvoxelSpace.mgz and lh.hippoSfLabels-T1.v10.mgz
> files , i would like to know how i can split the labels CA1 head, CA1 body
> and CA1 tail from this file, since individual subfield label numbers for
> CA1 head and CA1 body are not defined ,also can i assure CA1 body as
> posterior region and CA1 head as anterior ?.
>
>
>
>
>
> Thanks
>
> Vasudev
>
>
>
> On Mon, Jul 2, 2018 at 7:39 PM, Iglesias Gonzalez, Eugenio <
> e.igles...@ucl.ac.uk> wrote:
>
> Dear Vasudev,
>
> You can run the module described in that wiki page, and in the output file
> [lr]h.hippoAmygLabels-T1.v2x.mgz you will find segmentations for CA1
> head, CA1 body, CA23 head, CA23 body, CA4 head, CA4 body, and hippocampal
> tail (note that we don’t parcellate the tail).
>
> Cheers,
>
> /Eugenio
>
>
>
> --
>
> Juan Eugenio Iglesias
>
> ERC Senior Research Fellow
>
> Centre for Medical Image Computing (CMIC)
>
> University College London
>
> http://www.jeiglesias.com
>
> http://cmictig.cs.ucl.ac.uk/
>
>
>
>
>
> *From: *Dev vasu 
> *Date: *Monday, 2 July 2018 at 17:09
> *To: *"freesurfer@nmr.mgh.harvard.edu" , "
> igles...@nmr.mgh.harvard.edu" 
> *Subject: *Anterior / Posterior Partition in Hippocampus parcellation
> atlas
>
>
>
> *External Email - Use Caution*
>
> Dear Sir,
>
>
>
>
>
> I have reviewed your journal which detailed about hippocampus parcellation
> ( https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiO
> fAmygdala ) of subfields ( HBT - Head/body/Tail) , could you please let
> me know how to partition the atlas along the lines of Anterior CA1,CA3,CA4
> and posterior CA1,CA3,CA4.
>
>
>
>
>
> Thanks
>
> Vasdudev
>
> 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


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

Re: [Freesurfer] Anterior / Posterior Partition in Hippocampus parcellation atlas

2018-07-02 Thread Iglesias Gonzalez, Eugenio

External Email - Use Caution

Ah, now I understand.
To get the division in the wiki 
(https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala),
 you need to run the development version of FreeSurfer. The version you ran 
(6.0, I presume), does not provide such subdivision.
In principle, you could use Garikoitz’s code to subdivide the segmentation, but 
his code is not part of FreeSurfer, so you would have to contact him for 
support. Alternatively, you can also download the development version of 
FreeSurfer, which will provide the segmentation that I mentioned earlier.
Kind regards,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From: Dev vasu 
Date: Monday, 2 July 2018 at 19:22
To: "Iglesias Gonzalez, Eugenio" 
Cc: "freesurfer@nmr.mgh.harvard.edu" , 
"igles...@nmr.mgh.harvard.edu" 
Subject: Re: Anterior / Posterior Partition in Hippocampus parcellation atlas

Dear sir,

In the following journal published by you ,procedure for longitudinal 
segmentation was highlighted (https://github.com/garikoitz/hippovol) , I have 
run the module described in wiki and i have obtained 
lh.hippoSfLabels-T1.v10.FSvoxelSpace.mgz and lh.hippoSfLabels-T1.v10.mgz files 
, i would like to know how i can split the labels CA1 head, CA1 body and CA1 
tail from this file, since individual subfield label numbers for CA1 head and 
CA1 body are not defined ,also can i assure CA1 body as posterior region and 
CA1 head as anterior ?.


Thanks
Vasudev

On Mon, Jul 2, 2018 at 7:39 PM, Iglesias Gonzalez, Eugenio 
mailto:e.igles...@ucl.ac.uk>> wrote:
Dear Vasudev,
You can run the module described in that wiki page, and in the output file 
[lr]h.hippoAmygLabels-T1.v2x.mgz you will find segmentations for CA1 head, CA1 
body, CA23 head, CA23 body, CA4 head, CA4 body, and hippocampal tail (note that 
we don’t parcellate the tail).
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From: Dev vasu 
mailto:vasudevamurthy.devulapa...@gmail.com>>
Date: Monday, 2 July 2018 at 17:09
To: "freesurfer@nmr.mgh.harvard.edu" 
mailto:freesurfer@nmr.mgh.harvard.edu>>, 
"igles...@nmr.mgh.harvard.edu" 
mailto:igles...@nmr.mgh.harvard.edu>>
Subject: Anterior / Posterior Partition in Hippocampus parcellation atlas


External Email - Use Caution
Dear Sir,


I have reviewed your journal which detailed about hippocampus parcellation ( 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala
 ) of subfields ( HBT - Head/body/Tail) , could you please let me know how to 
partition the atlas along the lines of Anterior CA1,CA3,CA4  and posterior 
CA1,CA3,CA4.


Thanks
Vasdudev

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


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

Re: [Freesurfer] Anterior / Posterior Partition in Hippocampus parcellation atlas

2018-07-02 Thread Dev vasu

External Email - Use Caution

Dear sir,

In the following journal published by you ,procedure for longitudinal
segmentation was highlighted (https://github.com/garikoitz/hippovol) , I
have run the module described in wiki and i have obtained
lh.hippoSfLabels-T1.v10.FSvoxelSpace.mgz and lh.hippoSfLabels-T1.v10.mgz
files , i would like to know how i can split the labels CA1 head, CA1 body
and CA1 tail from this file, since individual subfield label numbers for
CA1 head and CA1 body are not defined ,also can i assure CA1 body as
posterior region and CA1 head as anterior ?.

Thanks
Vasudev

On Mon, Jul 2, 2018 at 7:39 PM, Iglesias Gonzalez, Eugenio <
e.igles...@ucl.ac.uk> wrote:

> Dear Vasudev,
>
> You can run the module described in that wiki page, and in the output file
> [lr]h.hippoAmygLabels-T1.v2x.mgz you will find segmentations for CA1
> head, CA1 body, CA23 head, CA23 body, CA4 head, CA4 body, and hippocampal
> tail (note that we don’t parcellate the tail).
>
> Cheers,
>
> /Eugenio
>
>
>
> --
>
> Juan Eugenio Iglesias
>
> ERC Senior Research Fellow
>
> Centre for Medical Image Computing (CMIC)
>
> University College London
>
> http://www.jeiglesias.com
>
> http://cmictig.cs.ucl.ac.uk/
>
>
>
>
>
> *From: *Dev vasu 
> *Date: *Monday, 2 July 2018 at 17:09
> *To: *"freesurfer@nmr.mgh.harvard.edu" , "
> igles...@nmr.mgh.harvard.edu" 
> *Subject: *Anterior / Posterior Partition in Hippocampus parcellation
> atlas
>
>
>
> *External Email - Use Caution*
>
> Dear Sir,
>
>
>
>
>
> I have reviewed your journal which detailed about hippocampus parcellation
> ( https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiO
> fAmygdala ) of subfields ( HBT - Head/body/Tail) , could you please let
> me know how to partition the atlas along the lines of Anterior CA1,CA3,CA4
> and posterior CA1,CA3,CA4.
>
>
>
>
>
> Thanks
>
> Vasdudev
>
> 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

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

Re: [Freesurfer] Anterior / Posterior Partition in Hippocampus parcellation atlas

2018-07-02 Thread Iglesias Gonzalez, Eugenio

External Email - Use Caution

Dear Vasudev,
You can run the module described in that wiki page, and in the output file 
[lr]h.hippoAmygLabels-T1.v2x.mgz you will find segmentations for CA1 head, CA1 
body, CA23 head, CA23 body, CA4 head, CA4 body, and hippocampal tail (note that 
we don’t parcellate the tail).
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From: Dev vasu 
Date: Monday, 2 July 2018 at 17:09
To: "freesurfer@nmr.mgh.harvard.edu" , 
"igles...@nmr.mgh.harvard.edu" 
Subject: Anterior / Posterior Partition in Hippocampus parcellation atlas


External Email - Use Caution
Dear Sir,


I have reviewed your journal which detailed about hippocampus parcellation ( 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala
 ) of subfields ( HBT - Head/body/Tail) , could you please let me know how to 
partition the atlas along the lines of Anterior CA1,CA3,CA4  and posterior 
CA1,CA3,CA4.


Thanks
Vasdudev

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


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

Re: [Freesurfer] Anterior / Posterior Partition in Hippocampus parcellation atlas

Re: [Freesurfer] Anterior / Posterior Partition in Hippocampus parcellation atlas

Re: [Freesurfer] Anterior / Posterior Partition in Hippocampus parcellation atlas

Re: [Freesurfer] Anterior / Posterior Partition in Hippocampus parcellation atlas

Re: [Freesurfer] Anterior / Posterior Partition in Hippocampus parcellation atlas

Re: [Freesurfer] Anterior / Posterior Partition in Hippocampus parcellation atlas

Re: [Freesurfer] Anterior / Posterior Partition in Hippocampus parcellation atlas

Re: [Freesurfer] Anterior / Posterior Partition in Hippocampus parcellation atlas

Re: [Freesurfer] Anterior / Posterior Partition in Hippocampus parcellation atlas

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