From pini.lorenzo2 at gmail.com  Mon May  9 09:59:16 2022
From: pini.lorenzo2 at gmail.com (Lorenzo Pini)
Date: Mon, 9 May 2022 15:59:16 +0200
Subject: [Neuroimaging] writing a 1D python array to 3D Nifti file
Message-ID: <CAJR3+oDsY53G-CSzTObPBCTeDDPFbxSCU6Tn_AttrScvu6hEBQ@mail.gmail.com>

Dear experts,

I uploaded a 3D nifti file with nibabel, transformed it into a 1D array and
performed some transformations. My final 1D array has size 902629 (MNI
vector space).

Now, I would like to convert this 1D array back to a 3D nifti image. Any
advice to perform this operation?

Thankx,
L
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://mail.python.org/pipermail/neuroimaging/attachments/20220509/77eba0cf/attachment.html>

From markiewicz at stanford.edu  Mon May  9 10:05:43 2022
From: markiewicz at stanford.edu (Christopher Markiewicz)
Date: Mon, 9 May 2022 14:05:43 +0000
Subject: [Neuroimaging] writing a 1D python array to 3D Nifti file
In-Reply-To: <CAJR3+oDsY53G-CSzTObPBCTeDDPFbxSCU6Tn_AttrScvu6hEBQ@mail.gmail.com>
References: <CAJR3+oDsY53G-CSzTObPBCTeDDPFbxSCU6Tn_AttrScvu6hEBQ@mail.gmail.com>
Message-ID: <DM8PR02MB814020EC3CD9165A79C5DEE1A9C69@DM8PR02MB8140.namprd02.prod.outlook.com>

Hi Lorenzo,

Assuming all you did was flatten the array, you should be able to simply reshape the array to the image shape:

    new_img = Nifti1Image(arr.reshape(old_img.shape), old_img.affine, old_img.header)?

Note that this preserves the affine and type of the input image, so if either of those has changed under your transformations, then you will need to pass the updated affine and call set_data_dtype()? after creation.

Best,
Chris
________________________________
From: Neuroimaging <neuroimaging-bounces+markiewicz=stanford.edu at python.org> on behalf of Lorenzo Pini <pini.lorenzo2 at gmail.com>
Sent: Monday, May 9, 2022 09:59
To: Neuroimaging analysis in Python <neuroimaging at python.org>
Subject: [Neuroimaging] writing a 1D python array to 3D Nifti file

Dear experts,

I uploaded a 3D nifti file with nibabel, transformed it into a 1D array and performed some transformations. My final 1D array has size 902629 (MNI vector space).

Now, I would like to convert this 1D array back to a 3D nifti image. Any advice to perform this operation?

Thankx,
L

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://mail.python.org/pipermail/neuroimaging/attachments/20220509/acf63ecc/attachment.html>

From lists at onerussian.com  Mon May  9 17:44:09 2022
From: lists at onerussian.com (Yaroslav Halchenko)
Date: Mon, 9 May 2022 17:44:09 -0400
Subject: [Neuroimaging] writing a 1D python array to 3D Nifti file
In-Reply-To: <CAJR3+oDsY53G-CSzTObPBCTeDDPFbxSCU6Tn_AttrScvu6hEBQ@mail.gmail.com>
References: <CAJR3+oDsY53G-CSzTObPBCTeDDPFbxSCU6Tn_AttrScvu6hEBQ@mail.gmail.com>
Message-ID: <YnmLKdrWYR1Zuje/@lena.dartmouth.edu>

I would have recommended to "go back" and to avoid explicit flattening /
re-3ding etc.  Why you had to go into 1D?

PS reminded me about an excellent sci-fi book "Three body problem" where
poor folks had to dry up to survive through apocalypses (and being
rolled up and stored deep underground) and then rehydrate, so in
effect do 3D -> 2D -> 3D  ;)  not sure how they survived ;)

On Mon, 09 May 2022, Lorenzo Pini wrote:

>    Dear experts,?
>    I uploaded a 3D nifti file with nibabel, transformed it into a 1D array
>    and performed some transformations. My final 1D array has size 902629 (MNI
>    vector space).?
>    Now, I would like to convert this 1D array back to a 3D nifti image. Any
>    advice to?perform this operation?
>    Thankx,
>    L

> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging


-- 
Yaroslav O. Halchenko
Center for Open Neuroscience     http://centerforopenneuroscience.org
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
WWW:   http://www.linkedin.com/in/yarik        


From christophe at pallier.org  Tue May 10 01:45:47 2022
From: christophe at pallier.org (Christophe Pallier)
Date: Tue, 10 May 2022 07:45:47 +0200
Subject: [Neuroimaging] writing a 1D python array to 3D Nifti file
In-Reply-To: <YnmLKdrWYR1Zuje/@lena.dartmouth.edu>
References: <CAJR3+oDsY53G-CSzTObPBCTeDDPFbxSCU6Tn_AttrScvu6hEBQ@mail.gmail.com>
 <YnmLKdrWYR1Zuje/@lena.dartmouth.edu>
Message-ID: <CALyk9bzPTdanTUfO+knTV7zc9+3zFQGavNDzX0f_df6u0mCgJw@mail.gmail.com>

Well there  are scenarios where it totally makes sense to transform to 1D,
for example to use some sklearn functions that require vectors.

In such cases, I find that nilearn's niftimaskers are a simple tool to go
from 3d (or 4d) to 1d (or 2d), and vice versa.



On Tue, May 10, 2022, 00:03 Yaroslav Halchenko <lists at onerussian.com> wrote:

> I would have recommended to "go back" and to avoid explicit flattening /
> re-3ding etc.  Why you had to go into 1D?
>
> PS reminded me about an excellent sci-fi book "Three body problem" where
> poor folks had to dry up to survive through apocalypses (and being
> rolled up and stored deep underground) and then rehydrate, so in
> effect do 3D -> 2D -> 3D  ;)  not sure how they survived ;)
>
> On Mon, 09 May 2022, Lorenzo Pini wrote:
>
> >    Dear experts,
> >    I uploaded a 3D nifti file with nibabel, transformed it into a 1D
> array
> >    and performed some transformations. My final 1D array has size 902629
> (MNI
> >    vector space).
> >    Now, I would like to convert this 1D array back to a 3D nifti image.
> Any
> >    advice to perform this operation?
> >    Thankx,
> >    L
>
> > _______________________________________________
> > Neuroimaging mailing list
> > Neuroimaging at python.org
> > https://mail.python.org/mailman/listinfo/neuroimaging
>
>
> --
> Yaroslav O. Halchenko
> Center for Open Neuroscience     http://centerforopenneuroscience.org
> Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
> WWW:   http://www.linkedin.com/in/yarik
>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://mail.python.org/pipermail/neuroimaging/attachments/20220510/3a680136/attachment.html>

From pini.lorenzo2 at gmail.com  Tue May 10 07:28:42 2022
From: pini.lorenzo2 at gmail.com (Lorenzo Pini)
Date: Tue, 10 May 2022 13:28:42 +0200
Subject: [Neuroimaging] writing a 1D python array to 3D Nifti file
In-Reply-To: <CALyk9bzPTdanTUfO+knTV7zc9+3zFQGavNDzX0f_df6u0mCgJw@mail.gmail.com>
References: <CAJR3+oDsY53G-CSzTObPBCTeDDPFbxSCU6Tn_AttrScvu6hEBQ@mail.gmail.com>
 <YnmLKdrWYR1Zuje/@lena.dartmouth.edu>
 <CALyk9bzPTdanTUfO+knTV7zc9+3zFQGavNDzX0f_df6u0mCgJw@mail.gmail.com>
Message-ID: <CAJR3+oAzQTHdZws5FyYqnG6tGkHpAhy2TSHYJjQStQN8r7G3gg@mail.gmail.com>

Thanks a lot for the clarification!
I was able to "go back" to the original nifti image.

Il giorno mar 10 mag 2022 alle ore 07:46 Christophe Pallier <
christophe at pallier.org> ha scritto:

> Well there  are scenarios where it totally makes sense to transform to 1D,
> for example to use some sklearn functions that require vectors.
>
> In such cases, I find that nilearn's niftimaskers are a simple tool to go
> from 3d (or 4d) to 1d (or 2d), and vice versa.
>
>
>
> On Tue, May 10, 2022, 00:03 Yaroslav Halchenko <lists at onerussian.com>
> wrote:
>
>> I would have recommended to "go back" and to avoid explicit flattening /
>> re-3ding etc.  Why you had to go into 1D?
>>
>> PS reminded me about an excellent sci-fi book "Three body problem" where
>> poor folks had to dry up to survive through apocalypses (and being
>> rolled up and stored deep underground) and then rehydrate, so in
>> effect do 3D -> 2D -> 3D  ;)  not sure how they survived ;)
>>
>> On Mon, 09 May 2022, Lorenzo Pini wrote:
>>
>> >    Dear experts,
>> >    I uploaded a 3D nifti file with nibabel, transformed it into a 1D
>> array
>> >    and performed some transformations. My final 1D array has size
>> 902629 (MNI
>> >    vector space).
>> >    Now, I would like to convert this 1D array back to a 3D nifti image.
>> Any
>> >    advice to perform this operation?
>> >    Thankx,
>> >    L
>>
>> > _______________________________________________
>> > Neuroimaging mailing list
>> > Neuroimaging at python.org
>> > https://mail.python.org/mailman/listinfo/neuroimaging
>>
>>
>> --
>> Yaroslav O. Halchenko
>> Center for Open Neuroscience     http://centerforopenneuroscience.org
>> Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
>> WWW:   http://www.linkedin.com/in/yarik
>>
>> _______________________________________________
>> Neuroimaging mailing list
>> Neuroimaging at python.org
>> https://mail.python.org/mailman/listinfo/neuroimaging
>>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>


-- 
*Lorenzo Pini, PhD *
*Padova Neuroscience Center, PNC*
Universit? degli Studi di Padova
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://mail.python.org/pipermail/neuroimaging/attachments/20220510/ba8b3e94/attachment.html>

From lists at onerussian.com  Tue May 10 10:58:01 2022
From: lists at onerussian.com (Yaroslav Halchenko)
Date: Tue, 10 May 2022 10:58:01 -0400
Subject: [Neuroimaging] writing a 1D python array to 3D Nifti file
In-Reply-To: <CALyk9bzPTdanTUfO+knTV7zc9+3zFQGavNDzX0f_df6u0mCgJw@mail.gmail.com>
References: <CAJR3+oDsY53G-CSzTObPBCTeDDPFbxSCU6Tn_AttrScvu6hEBQ@mail.gmail.com>
 <YnmLKdrWYR1Zuje/@lena.dartmouth.edu>
 <CALyk9bzPTdanTUfO+knTV7zc9+3zFQGavNDzX0f_df6u0mCgJw@mail.gmail.com>
Message-ID: <Ynp9ec/uKOpAR7Yl@lena.dartmouth.edu>


On Tue, 10 May 2022, Christophe Pallier wrote:

>    Well there? are scenarios where it totally makes sense to transform to 1D,
>    for example to use some sklearn functions that require vectors.
>    In such cases, I find that nilearn's niftimaskers are a simple tool to go
>    from 3d (or 4d) to 1d (or 2d), and vice versa.

FAIR ENOUGH!  Indeed in those cases -- flattening might be
required and the use of tools for transformations of such kind is
advisable (especially whenever masking is involved).

I guess I just saw way too many unnecessary uses of flattening whenever
data could have been manipulated in their native ND form thanks to
super-powerful broadcasting numpy supports.

Cheers,
-- 
Yaroslav O. Halchenko
Center for Open Neuroscience     http://centerforopenneuroscience.org
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
WWW:   http://www.linkedin.com/in/yarik        


From redhatw at gmail.com  Wed May 25 15:47:45 2022
From: redhatw at gmail.com (Ze Wang)
Date: Wed, 25 May 2022 19:47:45 +0000
Subject: [Neuroimaging] postdoc position in University of Maryland
 School of Medicine
In-Reply-To: <emc034c169-6f6e-40da-8461-68a0faa07d79@laptop-cm30trfu>
References: <emc034c169-6f6e-40da-8461-68a0faa07d79@laptop-cm30trfu>
Message-ID: <emff190a41-fb8d-4be5-8b13-31eb25009611@laptop-cm30trfu>

>We are still looking for a highly motivated Postdoc Research Fellow or 
>Research Associate in neuroimaging data processing. We are particularly 
>interested in time series analysis, graph theory, gradient analysis, 
>connectome analysis, and machine learning. The position is immediately 
>available from June 2022 until filled. The candidate will be supported 
>by a NIH R01 project. The ideal candidate should method development 
>experience in fMRI or neuroimaging signal processing. Experience of 
>clustering and graph analysis will be preferred. Python, Matlab 
>programming skills are required. Experience on multi-band fMRI data 
>processing is considered a plus.
>
>Candidates for these positions are expected to have good communication 
>skills and have good writing skills. We are willing to provide 
>competitive salary.
>
>Interested candidates should send CV and a brief introduction to Ze 
>Wang: ze.wang at som.umaryland.edu.
>
>
>Information about Dr. Wang?s lab can be found in:
>
>
>https://www.medschool.umaryland.edu/pi/Ze-Wang-PhD/
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://mail.python.org/pipermail/neuroimaging/attachments/20220525/39f1d720/attachment.html>