[Freesurfer] Hc segmentation: crosssectional stream with v4.5, longitudinal with v5.1

[Wenger, Elisabeth]

Dear FreeSurfer experts,

we have processed a dataset crossectionally within version 4.5, and then ran 
the longitudinal stream with v5.1. we are interested in the hippocampus 
segmentations and now i'm wondering whether i should go back and run the whole 
analysis from scratch with the newest version. I understand that it might or 
even will give me slightly different results, but would it also be the 
assumption that the new results would be somewhat more correct, that is 
anatomically more accurate, because maybe for example the processing has been 
optimized for hippocampal segmentation or anything like that in the newer 
version? Or would they just be different, as they would also be different when 
running it on a different computer, Mac or PC, OSX version, etc?

Thank you very much for your help in advance!!

Best wishes,
Elisabeth


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[Freesurfer] hippo-subfield on longitudinally processed brains

[Wenger, Elisabeth]

Dear freesurfer specialists,

I am trying to run the very interesting hippocampus subfield segmentation on 
subjects that have already undergone the standard volumetric pipeline AND the 
longitudinal pipeline. I tried the command "recon-all –subjid  
-hippo-subfields".
Unfortunately, i'm getting the following output message:

"ERROR: Are you trying to run or re-run a longitudinal time point?
   If so, please specify the following parameters:

   \' -long   \'

   where  is the time point id (SAME as cross sectional
   ID) and  is the ID created in the -base run.
   The directory .long. will be created
   automatically or used for output, if it already exists."

Can I just run the -hippo–subfields command on the already longitudinally 
processed brains, and simply include the flags "-long  " 
(without "-all") so freesurfer can use the long-directory as output (as it 
states in the error message)? Or do I have to run the -hippo–subfields command 
on the crosssectionally processed brains and include the flags "-long  
"? Do I then also need to include the flag –all so that it will do 
the whole longitudinal processing again?

Thank you very very much for your help!

Cheers,
Elisabeth



***

Dipl.-Psych. Elisabeth Wenger

Predoctoral Research Fellow

Center for Lifespan Psychology

MPI for Human Development

Lentzeallee 94, 14195 Berlin, Germany

phone: +49-30-82406-427

web: http://www.mpib-berlin.mpg.de
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Re: [Freesurfer] hippo-subfield on longitudinally processed brains

[Wenger, Elisabeth]

Dear Martin,

Thank you very much for your reply!

In my initial try i used the .long. subject, exactly.

So, now i will try to use, as you suggested, "recon-all -long
  -hippo-subfields" and it will
then automatically write the hippo-results in the already existing .long.
folder, right? I'm really curious to see how this goes.

Thank you so much again, and i'll let you know whether it worked.

Best wishes from Berlin,
Elisabeth




Am 01.09.11 18:07 schrieb "Martin Reuter" unter
:

>Hi Elisabeth,
>
>the hippo stuff was never tested with the long stream. But I don't see a
>reason why it should not work.
>I don't know your command. is subjid the long or the cross subject?
>Probably you passed the .long. subject and that is why you see that
>error.
>
>I would recommend to
>
>recon-all -long   -hippo-subfields
>
>(so run the hippo subfield segementation on the improved longitudinal
>results instead of the cross sectionals).
>Let me know how it goes.
>
>Best, Martin
>
>On Tue, 2011-08-30 at 10:44 +, Wenger, Elisabeth wrote:
>> Dear freesurfer specialists,
>> 
>> 
>> I am trying to run the very interesting hippocampus subfield
>> segmentation on subjects that have already undergone the standard
>> volumetric pipeline AND the longitudinal pipeline. I tried the
>> command "recon-all ­subjid  -hippo-subfields".
>> Unfortunately, i'm getting the following output message:
>> 
>> 
>> "ERROR: Are you trying to run or re-run a longitudinal time point?
>>If so, please specify the following parameters:
>> 
>> 
>>\' -long   \'
>> 
>> 
>>where  is the time point id (SAME as cross sectional
>>ID) and  is the ID created in the -base run.
>>The directory .long. will be created
>>automatically or used for output, if it already exists."
>> 
>> 
>> Can I just run the -hippo­subfields command on the already
>> longitudinally processed brains, and simply include the flags "-long
>>  " (without "-all") so freesurfer can use the
>> long-directory as output (as it states in the error message)? Or do I
>> have to run the -hippo­subfields command on the crosssectionally
>> processed brains and include the flags "-long  "?
>> Do I then also need to include the flag ­all so that it will do the
>> whole longitudinal processing again?
>> 
>> 
>> Thank you very very much for your help!
>> 
>> 
>> Cheers,
>> Elisabeth
>> 
>> 
>> 
>> 
>> ***
>> 
>> Dipl.-Psych. Elisabeth Wenger
>> 
>> Predoctoral Research Fellow
>> 
>> Center for Lifespan Psychology
>> 
>> MPI for Human Development
>> 
>> Lentzeallee 94, 14195 Berlin, Germany
>> 
>> phone: +49-30-82406-427
>> 
>> web: http://www.mpib-berlin.mpg.de
>> 
>> 
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>> Freesurfer mailing list
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>
>
>
>The information in this e-mail is intended only for the person to whom it
>is
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>e-mail
>contains patient information, please contact the Partners Compliance
>HelpLine at
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[Freesurfer] atlas used for subcortical segmentation

[Wenger, Elisabeth]

Dear Freesurfer specialists,


we are currently working on a comparison paper between manual segmentations and 
freesurfer segmentations of the hippocampus. In the paper by Jovicich and 
colleagues (2009) they mention that they generated their own segmentation atlas 
for the full brain freesurfer segmentation that consisted of different people 
of different age groups. We found this really interesting and wondered which 
segmentation atlas is used in the default stream of Freesurfer for subcortical 
segmentation? How many people were in that sample that created this atlas and 
which age were they? As we are specifically working with the hippocampus 
segmentations, it would also be very interesting to know what the mean size of 
their hippocampi was? Or is there maybe a paper that specifically describes in 
detail the descriptives of the used subjects for the standard atlas you could 
recommend us?


Thank you very much for all your help and your time!


Cheers,

Johan and Elisabeth

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[Freesurfer] manually labeled brains for segmentation atlas

[Wenger, Elisabeth]

Dear Freesurfer specialists,

I'm currently working on a comparison between manual segmentations and 
freesurfer segmentations of the hippocampus. Therefore i would be very 
interested in the atlas used for subcortical segmentation. On the wiki i read 
that the manually labeled brains used to build this atlas are about but not 
completely the same as the ones in the Desikan atlas, namely 39 manually 
labeled brains by Rahul Desikan. Could you please provide me with some rough 
sample descriptives on the brains used in the subcortical segmentation atlas, 
i.e. Age of subjects, male/female? That would be wonderful!

Has this atlas changed in any way between version 4.5 and 5.1?

As I am specifically working with the hippocampus segmentations, it would also 
be very interesting to know what the mean size of the hippocampus in this 
sample was – do you by any chance have some information on this?

Thank you very much for your help!

Cheers,
Elisabeth


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[Freesurfer] optimal voxel size

[Wenger, Elisabeth]

Dear Freesurfer experts,

I am currently planning a study in which I want to investigate changes in gray 
matter due to training on structural MR images. I heard some rumors that 
although FreeSurfer can of course process images with different voxel sizes, it 
always somehow "transforms" the voxel size to 1 x 1 x 1, irrespective of the 
originally obtained image resolution. I've been wondering if something has 
changed in this regard, that is, whether FreeSurfer is now capable of 
maintaining a higher resolution (eg, 0.8 mm) throughout all the analysis steps?
As I am looking for very very tiny changes I would like to acquire images with 
0.8mm resolution. But if FreeSurfer has to convert these images with the help 
of some estimation processes at some point of the reconstruction, I would 
rather like to acquire 1 x 1 x 1 images in the first place.

Thank you so much for your help!

All the best,
Elisabeth

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