[Freesurfer] squirrel data sharing format available in beta

[Gregory Book]

External Email - Use Caution

The squirrel data sharing format is now available in beta format and we're
looking for public comment. The squirrel format is designed to use the
minimum number of objects to describe all parts of neuroimaging analysis.
From experiments and raw data to analysis methods and results, all
information can be categorized into 10 object types. Using a
hierarchical storage, the format can store any number of subjects, any
number of imaging sessions, any number of visits, and any modality of data.
It handles not just imaging data, but demographics, measures, vitals, and
drugs.

Simple to use, simple to share.
* convert from DICOM to squirrel
* convert from BIDS to squirrel
* modify existing packages
* packages are in 7zip format, and JSON is human readable
* available for RHEL8, RHEL9, and Debian12/Ubuntu22

The squirrel utilities are in beta, so not all parts work, but we're
looking for testers and feedback!

Download the squirrel utils from 
https://secure-web.cisco.com/1WRNkvQPK4BOcCo4fgUYLyLTBlLdPW7fwixbJiXy16MAKLgW3vnRY88djSv8H3AqH0gZVy-pzMUEyuPetB0N5Oaep_D-NWZAj8VucoVvxwpwOzyRV-s8PNAZ2vOcKM2kBI4we1pf9dCtrikVem_lXGJ1sgGJzvdzcr8rIL1dhNWeDil6oYvXOp4nUROsrmTsRxvkssv33mnQPdh3Vwr-rwlc5Lwtzi8UvD22-77WDge9qDmVD7IAH1XnQtjhDrB8SYu8lhbxceEcMwSTyIgPcZenfSSKYzbwSiO3yjoVzFL68HZ1Jaj4WXEXw_5MJI3JHNhF2OL-I1Wo9koTjSoox8g/https%3A%2F%2Fgithub.com%2Fgbook%2Fsquirrel%2Freleases
Documentation and the squirrel specification:
https://secure-web.cisco.com/1uAU1-QCnkUDsyb1PHsY1vqWB553FNwLN1raYY7xR1zBejLyjEw2NI4mS72nELnQg7JTBKhTPOkat4vugEaOaC1pL7IYxb1u2yDZReVeHk7jk5rPFowK4WTXAB_46YIjS9lRlhfkm4DLr1juxP1BNUR7HaIQ2ehNhrrvP0VTTOYoRiTfIEggOUJXH89tWGq0z0KNUQBi9yrVfyeVSHvMK15ho5H1195UbWADJTxrcVEsgtYoTT4EK6-fcJZwDvueVO2NnQTrjUIyIO4b87BZZ7Vx3K5SNdI94t9aJQwXKh-AB077QLdb4LranOpQCBBr7/https%3A%2F%2Fdocs.neuroinfodb.org%2Fnidb%2Fcontribute%2Fsquirrel-data-sharing-format%2Fsquirrel-utilities
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Re: [Freesurfer] Problem running recon-all

[Gregory Book]

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I did not see that message, which is why I posted again. Sorry about that!
I will try using the package installer. We're using the .tar.gz method
because it is located on a shared drive, but maybe we'll just need to
install it locally if that works.

On Tue, Apr 23, 2024 at 11:23 AM fsbuild  wrote:

>
> Did you try the instructions  you were sent yesterday to run the actual
> installer and not use the tar file (which is not an installer) ?
>
> - R.
>
> I would try downloading and running the actual package installer,
>
>
> https://secure-web.cisco.com/1HKiItqb5Mbre7Zh9wBla2EeSBdrUlDXryrzl69LkLYWblBErmMFIQQrfAMG0IRSf5qYRXiqLgAvxJ7hiHx31g3l5g8FV2BkFnHs3RGzcu7zuuOC7I8pJBrfxRyYIv5iKV-gp6sds9DH_hHTpLBP0gBFEUSc2NLLNO5Ouh-l2ZwyxNIyZ7D49U0pu0Vp_Jk1wARFlwU08uGKnDp_fQEy65AtwuZAvhzTmxwbFhVqjikdZGvH06c-6dboQip0HbcHfOykTHHyFgVTKOrNun21Hj-dmU-SZLt8xKCUfS84tJvSzHKAW5YjEOR98r64hu_z-l7zVRRqA76SrlukfJD_hew/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer_ubuntu22-7.4.1_amd64.deb
>
>
> on to the target system..  Then change directories to where you downloaded
> the package and try,
>
> $ sudo apt install ./freesurfer_ubuntu22-7.4.1_amd64.deb
>
> I cannot guarantee the installer will work as the Debian linux packaging
> tools may find requirements in the Ubuntu package they cannot
> resolve/satisfy on your Debian system.  We don’t test on debian linux.  But
> the installer should notify you if it fails and why that is.
>
>
>
> On 4/23/24 09:21, Gregory Book (gregory.a.b...@gmail.com) wrote:
>
> External Email - Use Caution
> I recently installed freesurfer 7.4.1 on a Debian 12 system (using the
> Ubuntu 22 .tar.gz). When running recon-all, I get the following error:
>
> -bash: /opt/freesurfer/freesurfer-7.4.1/bin/recon-all: cannot execute:
> required file not found
>
> Paths are all set, and all scripts and executables have execute
> permissions.
> What might be happening?
>
> ___
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Re: [Freesurfer] Problem running recon-all

[Gregory Book]

External Email - Use Caution

I also see this error which is sent to stderr:
/usr/bin/time: cannot run recon-all: No such file or directory
It seems to be something related to the time command (or bash keyword)


Is your Freesurfer Environment sourced correctly?  Here is the wiki
help 
https://secure-web.cisco.com/1ijMGNvsZHBy0jgsTYEFevQx_e5Y2oKLcFa7pDhxI5jfNgMM75HegbbUkTZoxL85vJjghWDwtg3Jjv4lsG0VZCTZ7YlhPuRczAQuIz8jePrWEIPQwVyAzcYv98U1CgmMpRUs3NZobucvYycgHFiqQk2sbCWslDa4-IfTbm2n-MTOjXS2Ej1uEpNgZ9lfvkJzcnj7SR5NRRe89nzPhY3jV3X1RPryu31aaVnBfDV7xeQ-b5WO6aR70li-RGAhVttoiUOo_E_Pj4-motaxaqZfNAhXYFAezM4dVSZlRAPrkwuMJG-Op02Vd54RwqKG-0U9qMFpYXqv7SLkSpIzyjUtjEw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FSetupConfiguration_Linux

Best,

Yujing
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Re: [Freesurfer] Problem running recon-all

[Gregory Book]

External Email - Use Caution

Yes, it's all sourced correctly. The output after sourcing:


bash:/opt/freesurfer/freesurfer-7.4.1$ source
$FREESURFER_HOME/SetUpFreeSurfer.sh
 freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /opt/freesurfer/freesurfer-7.4.1
FSFAST_HOME   /opt/freesurfer/freesurfer-7.4.1/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /opt/freesurfer/freesurfer-7.4.1/subjects
MNI_DIR   /opt/freesurfer/freesurfer-7.4.1/mni




Is your Freesurfer Environment sourced correctly?  Here is the wiki
help 
https://secure-web.cisco.com/1ijMGNvsZHBy0jgsTYEFevQx_e5Y2oKLcFa7pDhxI5jfNgMM75HegbbUkTZoxL85vJjghWDwtg3Jjv4lsG0VZCTZ7YlhPuRczAQuIz8jePrWEIPQwVyAzcYv98U1CgmMpRUs3NZobucvYycgHFiqQk2sbCWslDa4-IfTbm2n-MTOjXS2Ej1uEpNgZ9lfvkJzcnj7SR5NRRe89nzPhY3jV3X1RPryu31aaVnBfDV7xeQ-b5WO6aR70li-RGAhVttoiUOo_E_Pj4-motaxaqZfNAhXYFAezM4dVSZlRAPrkwuMJG-Op02Vd54RwqKG-0U9qMFpYXqv7SLkSpIzyjUtjEw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FSetupConfiguration_Linux

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu
 On Behalf Of Gregory Book
Sent: Tuesday, April 23, 2024 9:21 AM
To: freesurfer 
Subject: [Freesurfer] Problem running recon-all


External Email - Use Caution
I recently installed freesurfer 7.4.1 on a Debian 12 system (using the Ubuntu
22 .tar.gz). When running recon-all, I get the following error:

-bash: /opt/freesurfer/freesurfer-7.4.1/bin/recon-all: cannot execute: required
file not found

Paths are all set, and all scripts and executables have execute permissions.
What might be happening?

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[Freesurfer] Problem running recon-all

[Gregory Book]

External Email - Use Caution

I recently installed freesurfer 7.4.1 on a Debian 12 system (using the
Ubuntu 22 .tar.gz). When running recon-all, I get the following error:

-bash: /opt/freesurfer/freesurfer-7.4.1/bin/recon-all: cannot execute:
required file not found

Paths are all set, and all scripts and executables have execute permissions.
What might be happening?
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[Freesurfer] recon-all error

[Gregory Book]

External Email - Use Caution

I installed freesurfer 7.4.1 on Debian 12 (using the Ubuntu 22 .tar.gz).
Some programs run fine, but some do not.

When running recon-all, I get the following error:
-bash: /opt/freesurfer/freesurfer-7.4.1/bin/recon-all: cannot execute:
required file not found

It does have execute permissions.

What might be happening?
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[Freesurfer] Options to decrease computation time

[Gregory Book]

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I'm curious if there are options to decrease computation time, even at the
expense of quality?
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[Freesurfer] RA/programmer job posting - neuroinformatics, big data {Disarmed} {Disarmed}

[Gregory Book]

The Olin Neuropsychiatry Research Center (http://nrc-iol.org
)
located in Hartford, CT USA is looking for a research assistant II/data
manager (or post-doc, depending on candidate) to assist with data
management, neuroinformatics development, and big-data analyses. The Olin
Center is a 40 person department, opened in 2003 at the Institute of
Living. We have a Siemens Skyra 3T whole-body MRI, EEG, and TMS suites. The
Olin Center's database of 30,000 imaging sessions also provides an
internally accessible source of data for the candidate's own analyses, and
a 350 node compute cluster with 0.5PB storage is available to use. We are
looking for an RA or post-doc to help develop the Neuroinformatics Database
(http://github.com/gbook/nidb

), manage neuroimaging data, and assist with the programming of automated
neuroimaging processing systems. The primary focus and approximately half
of the position will be developing and maintaining imaging and non-imaging
databases, but duties will also include responding to support requests,
training, documentation, and bug fixing. The other half of the position
will be analyzing data and contributing to manuscripts. Candidate is
expected to have a bachelor’s degree (PhD for post-doc) and experience with
at least 1 programming language. Attention to detail and database
experience are very desirable. Experience programming PHP, Perl, HTML, SQL,
in a Linux environment is strongly preferred. Neuroimaging experience is
also preferred, but not necessary. Contact Greg at
gregory.b...@hhchealth.org

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[Freesurfer] Longitudinal study concept question

[Gregory Book]

In writing a paper of longitudinal changes in a large heterogeneous
population with no group comparisons, what would be considered "more
important" to include: absolute ROI volumes, or volumes corrected for ICV?

Using ICV corrected volumes makes sense when comparing groups, but when
just describing population changes over time, for example a cross section
of a population over a lifespan, is it better to use absolute volumes,
corrected volumes, or both?
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dispose of the e-mail.

[Freesurfer] Job postings: Post-doc & Data manager/programmer

[Gregory Book]

The Olin Neuropsychiatry Research Center, located in Hartford CT, USA is
looking to fill 2 open positions.

The Olin Neuropsychiatry Research Center has an opening for a post-doc
specializing in neuroinformatics, big-data analysis, and machine learning.
The Olin Center is the psychiatric research center within Hartford
Hospital’s Institute of Living campus, in Hartford, CT. We house a Siemens
Skyra 3T whole-body MRI, multiple EEG, TMS, and eye tracking systems, an
internal historical database of nearly 13,000 MRI sessions, and a 400-core
Linux compute cluster. The candidate will pursue their own research with a
focus on neuroinformatics and big-data analysis and assist multiple
principle investigators with large scale analyses. The candidate will
contribute to the development of the open-source Neuroinformatics Database (
http://github.com/gbook/nidb) and publish journal articles on their own
research and software development. MS degree in engineering, science,
neuroscience, or psychology is required, PhD preferred. Candidate is
expected to have experience in SQL programming and at least one other
programming language. Proficiency in multiple programming languages such as
Perl, C, C++, JavaScript, PHP, Matlab, and Python is highly desirable.
Contact Greg Book at gregory.b...@hhchealth.org

The Olin Neuropsychiatry Research Center is seeking a data
manager/programmer to help maintain neuroimaging databases in support of
multiple NIH funded projects. The Olin Center is a neuropsychiatric
research center within Hartford Hospital’s Institute of Living campus. We
house a 3T MRI, multiple EEG, TMS, and eye tracking systems, an internal
database of nearly 13,000 MRI sessions, and a 400-core compute cluster. The
primary responsibilities of the data manager will be to maintain internal
and public imaging databases by performing the following tasks: remove
personally identifiable information, perform uploads to NIH repositories,
identify missing data, organize identifiers, support remote sites with data
importing/uploading, and ensure data redundancy and backups. Additionally,
the data manager may contribute to the development of the Neuroinformatics
Database (http://github.com/gbook/nidb) using SQL, PHP, Perl, C++ and other
programming languages for the purpose of making data management more
efficient and robust. The data manager also will have the opportunity to
participate in research projects and contribute to manuscripts. Bachelor’s
degree in engineering, science, neuroscience, or psychology is required,
Masters or higher is preferred. Candidate is expected to have experience in
SQL programming. Proficiency in multiple programming languages is highly
desirable. Contact Greg Book at gregory.b...@hhchealth.org
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[Freesurfer] Post-doc opening in Neuroinformatics

[Gregory Book]

The Olin Neuropsychiatry Research Center has an opening for a post-doc
specializing in neuroinformatics, big-data analysis, and machine learning.
The Olin Center is the neuropsychiatric research center within Hartford
Hospital’s Institute of Living campus, in Hartford, CT. We house a Siemens
Skyra 3T whole-body MRI, multiple EEG, TMS, and eye tracking systems, an
internal historical database of nearly 13,000 MRI sessions, and a 400-core
Linux compute cluster. The candidate will contribute to the development of
neuroimaging databases in support of multiple NIH funded projects and with
several primary investigators on large scale analyses. The candidate will
contribute to the development of the Neuroinformatics Database (
http://github.com/gbook/nidb) to archive data, automate data analysis using
new and existing pipelines, and publish journal articles on their own
research. MS degree in engineering, science, neuroscience, or psychology is
required, PhD preferred. Candidate is expected to have experience in SQL
programming and at least one programming language. Proficiency in multiple
programming languages such as Perl, C, C++, Javascript, PHP, Matlab, and
Python is highly desirable. Contact Greg Book at gregory.b...@hhchealth.org
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[Freesurfer] Data manager/programmer position

[Gregory Book]

The Olin Neuropsychiatry Research Center is seeking a data
manager/programmer to help maintain neuroimaging databases in support of
multiple NIH funded projects. The Olin Center is a neuropsychiatric
research center within Hartford Hospital’s Institute of Living campus. We
house a 3T MRI, multiple EEG, TMS, and eye tracking systems, an internal
database of nearly 13,000 MRI sessions, and a 400-core compute cluster. The
primary responsibilities of the data manager will be to maintain internal
and public imaging databases by performing the following tasks: remove
personally identifiable information, perform uploads to NIH repositories,
identify missing data, organize identifiers, support remote sites with data
importing/uploading, and ensure data redundancy and backups. Additionally,
the data manager may contribute to the development of the Neuroinformatics
Database (http://github.com/gbook/nidb) using SQL, PHP, Perl, C++ and other
programming languages for the purpose of making data management more
efficient and robust. The data manager also will have the opportunity to
participate in research projects and contribute to manuscripts. Bachelor’s
degree in engineering, science, neuroscience, or psychology is required,
Masters or higher is preferred. Candidate is expected to have experience in
SQL programming and at least one programming language. Proficiency in
multiple programming languages is highly desirable. Contact Greg Book at
gregory.b...@hhchealth.org
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[Freesurfer] Labeled Nifti atlases

[Gregory Book]

Are there any labeled nifti atlases that correspond to the freesurfer
parcellation atlases output from recon-all?
I'm basically interested in visualization of group results.
-Greg
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