Re: [Freesurfer] How to run part of TRACULA

[Athanasia Metoki]

Dear Anastasia,

Now I understand and it makes perfect sense! Thank you very much for your
answers.

Best,
Nasia Metoki

*Athanasia Metoki*
Psychology Doctoral Student - Brain and Cognitive Sciences Program
Cognitive Neuroscience Laboratory
Temple University
Department of Psychology
1701 N 13th St.
Philadelphia, PA 19122
Email: athanasia.met...@temple.edu

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On Mon, Aug 15, 2016 at 8:49 AM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:

>
> Hi Nasia - They both have preprocessing steps because recon-all runs on
> the T1 and trac-all runs on the DWIs, so they preprocess different images.
>
> You cannot skip any of the steps in recon-all and still get a
> segmentation. The point of the autorecon schemes is mostly to repeat only
> one part of the processing if you change something in between, not to skip
> part of the processing entirely.
>
> Best,
>
> a.y
>
>
> On Sun, 14 Aug 2016, Athanasia Metoki wrote:
>
> Dear Anastasia,
>>
>> Thank you so much for responding so fast!
>> I see what you're saying and thank you for your input.
>>
>> I have one more question if you don't mind taking a moment to respond. I
>> noticed that both trac-all and recon-all include some preprocessing steps
>> (eg. motion correction, eddy current correction, skull stripping). How
>> come
>> and they both have these steps if one is supposed to run both commands? My
>> understandind is, if someone wants to run TRACULA from scratch, they would
>> need to run both recon-all (first) and trac-all (second). One would have
>> to
>> run recon-all in order to get the cortical parcellation and subcortical
>> segmentation (mri/aparc+aseg.mgz) file  which will be used from trac-all
>> in
>> the mask creation step.
>>
>> In my case where I have some preprocessed data, is there a particular
>> -autorecon# command which only does some of the recon steps that would
>> help
>> me get the cortical parcellation and subcortical segmentation
>> (mri/aparc+aseg.mgz) file that I am missing?
>>
>> I understand I may be asking a lot! Once more thank you very much for your
>> initial response and your time!
>>
>> Best,
>> Nasia Metoki
>>
>>
>> On Sat, Aug 13, 2016 at 8:03 PM, Anastasia Yendiki
>>  wrote:
>>
>>   Hi Athanasia - TRACULA expects certains files named a certain
>>   way to be
>>   there at the end of each preprocessing step. These are described
>>   here:
>>
>> https://surfer.nmr.mgh.harvard.edu/fswiki/trac-all#Outputdir
>> ectoriesandfile
>>   s
>>
>>   If you are using pre-existing files, you have to make sure that
>>   they
>>   follow the same file/directory naming convention.
>>
>>   You just run recon-all with the default settings. The aparc+aseg
>>   is
>>   created in one of the last steps of recon-all, so all the
>>   previous steps
>>   have to run as well.
>>
>>   Hope this helps!
>>
>>   a.y
>>
>>   On Sat, 13 Aug 2016, Athanasia Metoki wrote:
>>
>>   > Dear Freesurfer Developers,
>>   >
>>   > I am fairly new to image analysis and this is the first time I
>>   use
>>   > Freesurfer.
>>   >
>>   > I have some DTI data and I have already preprocessed them and
>>   ran bedpostX
>>   > using FSL. I ran probabilistic tractography on FSL as well to
>>   get the
>>   > connectivity between two distinct brain areas.
>>   >
>>   > I am also interested in getting the probability distribution
>>   for the
>>   > uncinate fasciculi so I am trying to use TRACULA.
>>   > My question is: Can I use TRCULA without doing preprocessing
>>   and dedpostX
>>   > again? If so, will I need to do the cortical parcelation and
>>   subcortical
>>   > segmentation with recon-all and get the aparc+aseg.mgz file in
>>   order to use
>>   > TRACULA? Which argument would I need to use when I run
>>   recon-all?
>>   >
>>   > Thank you!
>>   >
>>   > Athanasia Metoki
>>   > Psychology Doctoral Student - Brain and Cognitive Sciences
>>   Program
>>   > Cognitive Neuroscience Laboratory
>>   > Temple University
>>   > Department of Psychology
>>   > 1701 N 13th St.
>>   > Philadelphia, PA 19122
>>   > Email: athanasia.met...@temple.edu
>>   >
>>   

Re: [Freesurfer] How to run part of TRACULA

[Anastasia Yendiki]

Hi Nasia - They both have preprocessing steps because recon-all runs on 
the T1 and trac-all runs on the DWIs, so they preprocess different images.


You cannot skip any of the steps in recon-all and still get a 
segmentation. The point of the autorecon schemes is mostly to repeat only 
one part of the processing if you change something in between, not to skip 
part of the processing entirely.


Best,

a.y

On Sun, 14 Aug 2016, Athanasia Metoki wrote:


Dear Anastasia,

Thank you so much for responding so fast!
I see what you're saying and thank you for your input.

I have one more question if you don't mind taking a moment to respond. I
noticed that both trac-all and recon-all include some preprocessing steps
(eg. motion correction, eddy current correction, skull stripping). How come
and they both have these steps if one is supposed to run both commands? My
understandind is, if someone wants to run TRACULA from scratch, they would
need to run both recon-all (first) and trac-all (second). One would have to
run recon-all in order to get the cortical parcellation and subcortical
segmentation (mri/aparc+aseg.mgz) file  which will be used from trac-all in
the mask creation step.

In my case where I have some preprocessed data, is there a particular
-autorecon# command which only does some of the recon steps that would help
me get the cortical parcellation and subcortical segmentation
(mri/aparc+aseg.mgz) file that I am missing?

I understand I may be asking a lot! Once more thank you very much for your
initial response and your time!

Best,
Nasia Metoki


On Sat, Aug 13, 2016 at 8:03 PM, Anastasia Yendiki
 wrote:

  Hi Athanasia - TRACULA expects certains files named a certain
  way to be
  there at the end of each preprocessing step. These are described
  here:

https://surfer.nmr.mgh.harvard.edu/fswiki/trac-all#Outputdirectoriesandfile
  s

  If you are using pre-existing files, you have to make sure that
  they
  follow the same file/directory naming convention.

  You just run recon-all with the default settings. The aparc+aseg
  is
  created in one of the last steps of recon-all, so all the
  previous steps
  have to run as well.

  Hope this helps!

  a.y

  On Sat, 13 Aug 2016, Athanasia Metoki wrote:

  > Dear Freesurfer Developers,
  >
  > I am fairly new to image analysis and this is the first time I
  use
  > Freesurfer.
  >
  > I have some DTI data and I have already preprocessed them and
  ran bedpostX
  > using FSL. I ran probabilistic tractography on FSL as well to
  get the
  > connectivity between two distinct brain areas.
  >
  > I am also interested in getting the probability distribution
  for the
  > uncinate fasciculi so I am trying to use TRACULA.
  > My question is: Can I use TRCULA without doing preprocessing
  and dedpostX
  > again? If so, will I need to do the cortical parcelation and
  subcortical
  > segmentation with recon-all and get the aparc+aseg.mgz file in
  order to use
  > TRACULA? Which argument would I need to use when I run
  recon-all?
  >
  > Thank you!
  >
  > Athanasia Metoki
  > Psychology Doctoral Student - Brain and Cognitive Sciences
  Program
  > Cognitive Neuroscience Laboratory
  > Temple University
  > Department of Psychology
  > 1701 N 13th St.
  > Philadelphia, PA 19122
  > Email: athanasia.met...@temple.edu
  >
  
>___

  > 
  > The contents of this email message and any attachments are
  intended solely
  > for the addressee(s) and may contain confidential and/or
  privileged
  > information and may be legally protected from disclosure. If
  you are not the
  > intended recipient of this message or their agent, or if this
  message has
  > been addressed to you in error, please immediately alert the
  sender by reply
  > email and then delete this message and any attachments. If you
  are not the
  > intended recipient, you are hereby notified that any use,
  dissemination,
  > copying, or storage of this message or its attachments is
  strictly
  > prohibited.
  >
  >
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Re: [Freesurfer] How to run part of TRACULA

[Athanasia Metoki]

Dear Anastasia,

Thank you so much for responding so fast!
I see what you're saying and thank you for your input.

I have one more question if you don't mind taking a moment to respond. I
noticed that both trac-all and recon-all include some preprocessing steps
(eg. motion correction, eddy current correction, skull stripping). How come
and they both have these steps if one is supposed to run both commands? My
understandind is, if someone wants to run TRACULA from scratch, they would
need to run *both* recon-all (first) and trac-all (second). One would have
to run recon-all in order to get the cortical parcellation and subcortical
segmentation (mri/aparc+aseg.mgz) file  which will be used from trac-all in
the mask creation step.

In my case where I have some preprocessed data, is there a particular
-autorecon# command which only does some of the recon steps that would help
me get the cortical parcellation and subcortical segmentation
(mri/aparc+aseg.mgz) file that I am missing?

I understand I may be asking a lot! Once more thank you very much for your
initial response and your time!

Best,
Nasia Metoki


On Sat, Aug 13, 2016 at 8:03 PM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:

>
> Hi Athanasia - TRACULA expects certains files named a certain way to be
> there at the end of each preprocessing step. These are described here:
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/trac-all#
> Outputdirectoriesandfiles
>
> If you are using pre-existing files, you have to make sure that they
> follow the same file/directory naming convention.
>
> You just run recon-all with the default settings. The aparc+aseg is
> created in one of the last steps of recon-all, so all the previous steps
> have to run as well.
>
> Hope this helps!
>
> a.y
>
> On Sat, 13 Aug 2016, Athanasia Metoki wrote:
>
> > Dear Freesurfer Developers,
> >
> > I am fairly new to image analysis and this is the first time I use
> > Freesurfer.
> >
> > I have some DTI data and I have already preprocessed them and ran
> bedpostX
> > using FSL. I ran probabilistic tractography on FSL as well to get the
> > connectivity between two distinct brain areas.
> >
> > I am also interested in getting the probability distribution for the
> > uncinate fasciculi so I am trying to use TRACULA.
> > My question is: Can I use TRCULA without doing preprocessing and dedpostX
> > again? If so, will I need to do the cortical parcelation and subcortical
> > segmentation with recon-all and get the aparc+aseg.mgz file in order to
> use
> > TRACULA? Which argument would I need to use when I run recon-all?
> >
> > Thank you!
> >
> > Athanasia Metoki
> > Psychology Doctoral Student - Brain and Cognitive Sciences Program
> > Cognitive Neuroscience Laboratory
> > Temple University
> > Department of Psychology
> > 1701 N 13th St.
> > Philadelphia, PA 19122
> > Email: athanasia.met...@temple.edu
> >
> > 
> ___
> > 
> > The contents of this email message and any attachments are intended
> solely
> > for the addressee(s) and may contain confidential and/or privileged
> > information and may be legally protected from disclosure. If you are not
> the
> > intended recipient of this message or their agent, or if this message has
> > been addressed to you in error, please immediately alert the sender by
> reply
> > email and then delete this message and any attachments. If you are not
> the
> > intended recipient, you are hereby notified that any use, dissemination,
> > copying, or storage of this message or its attachments is strictly
> > prohibited.
> >
> >
> ___
> 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 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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> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
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>
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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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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] How to run part of TRACULA

[Anastasia Yendiki]

Hi Athanasia - TRACULA expects certains files named a certain way to be 
there at the end of each preprocessing step. These are described here:

https://surfer.nmr.mgh.harvard.edu/fswiki/trac-all#Outputdirectoriesandfiles

If you are using pre-existing files, you have to make sure that they 
follow the same file/directory naming convention.

You just run recon-all with the default settings. The aparc+aseg is 
created in one of the last steps of recon-all, so all the previous steps 
have to run as well.

Hope this helps!

a.y

On Sat, 13 Aug 2016, Athanasia Metoki wrote:

> Dear Freesurfer Developers,
> 
> I am fairly new to image analysis and this is the first time I use
> Freesurfer.
> 
> I have some DTI data and I have already preprocessed them and ran bedpostX
> using FSL. I ran probabilistic tractography on FSL as well to get the
> connectivity between two distinct brain areas.
> 
> I am also interested in getting the probability distribution for the
> uncinate fasciculi so I am trying to use TRACULA.
> My question is: Can I use TRCULA without doing preprocessing and dedpostX
> again? If so, will I need to do the cortical parcelation and subcortical
> segmentation with recon-all and get the aparc+aseg.mgz file in order to use
> TRACULA? Which argument would I need to use when I run recon-all?
> 
> Thank you!
> 
> Athanasia Metoki
> Psychology Doctoral Student - Brain and Cognitive Sciences Program
> Cognitive Neuroscience Laboratory
> Temple University
> Department of Psychology
> 1701 N 13th St.
> Philadelphia, PA 19122
> Email: athanasia.met...@temple.edu
> 
> ___
> 
> The contents of this email message and any attachments are intended solely
> for the addressee(s) and may contain confidential and/or privileged
> information and may be legally protected from disclosure. If you are not the
> intended recipient of this message or their agent, or if this message has
> been addressed to you in error, please immediately alert the sender by reply
> email and then delete this message and any attachments. If you are not the
> intended recipient, you are hereby notified that any use, dissemination,
> copying, or storage of this message or its attachments is strictly
> prohibited.
> 
>
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[Freesurfer] How to run part of TRACULA

[Athanasia Metoki]

Dear Freesurfer Developers,

I am fairly new to image analysis and this is the first time I use
Freesurfer.

I have some DTI data and I have already preprocessed them and ran bedpostX
using FSL. I ran probabilistic tractography on FSL as well to get the
connectivity between two distinct brain areas.

I am also interested in getting the probability distribution for the
uncinate fasciculi so I am trying to use TRACULA.
My question is: Can I use TRCULA without doing preprocessing and dedpostX
again? If so, will I need to do the cortical parcelation and subcortical
segmentation with recon-all and get the aparc+aseg.mgz file in order to use
TRACULA? Which argument would I need to use when I run recon-all?

Thank you!

*Athanasia Metoki*
Psychology Doctoral Student - Brain and Cognitive Sciences Program
Cognitive Neuroscience Laboratory
Temple University
Department of Psychology
1701 N 13th St.
Philadelphia, PA 19122
Email: athanasia.met...@temple.edu

___
The contents of this email message and any attachments are intended solely
for the addressee(s) and may contain confidential and/or privileged
information and may be legally protected from disclosure. If you are not
the intended recipient of this message or their agent, or if this message has
been addressed to you in error, please immediately alert the sender by
reply email and then delete this message and any attachments. If you are
not the intended recipient, you are hereby notified that any use,
dissemination, copying, or storage of this message or its attachments is
strictly prohibited.
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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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