Thank you for your interest in the infantFreesurfer pipeline. The version below is our new beta distribution (Jan 2021). Please, continue giving me feedback and asking a lot of questions

along the way so that we can improve upon the user-friendliness of its use.

After downloading the package, you should run the below four commands:

source YOUR_FREESURFER_ENVIRONMENT

setenv SUBJECTS_DIR your_data_path  or  export SUBJECTS_DIR=your_data_path

infant_recon_all --s SUBJ --age age_in_months

SUBJ is the subjectID of the subjects's whose data you are processing. The script will expect the input file to be located at $SUBJECTS_DIR/$subj/mprage.nii.gz or $SUBJECTS_DIR/

$subj/mprage.mgz by default. Unless otherwise specified, the output of this process will be

saved to $SUBJECTS_DIR/$SUBJ using a FreeSurfer type directory structure. If the --masked flag is used, we recommend also running intensity normalization, for example by using:

mri_nu_correct.mni --i $infile --o $nufile --n 2

Note, you can use both tcsh and bash for this distribution.

Before execution, you will also need install FSL [MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation]. Note, we have changed our default nonlinear registration tool. We rely on

niftyreg which ships directly with this release. If you would like to use DRAMMS you will need to install it separately and use the corresponding flag.

Other useful flags:

--outdir (redirecting output)

--kneigh (number of training examples to use)

See infant_recon_all --help for more information or visit

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* Skullstripping

The current release ships with our new skullstripping tool so you will not need to

skullstrip your data before running infantFS. Note, the new tool requires about 23GB

of memory! At present, the error messages related to lack of sufficient memory are

pretty vague, so please, check whether you have enough if you rely on this tool.

Also "Your CPU supports instructions that this TensorFlow binary was not compiled to

use" is just a warning not an error. It indicates that the process could be faster

if you built with a more modern tensorflow, but the computations should be working

even with this version.

* Citation:

Cite the below papers if you use our work and publish yourself:

 

Zöllei, L, Iglesias, JE, Ou, Y, Grant, PR, Fischl,B. Infant FreeSurfer: An automated segmentation and surface extraction

pipeline for T1-weighted neuroimaging data of infants 0-2 years, NeuroImage, Volume 218, September 2020, 116946

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://doi.org/10.1016/j.neuroimage.2020.116946.

(MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://www.sciencedirect.com/science/article/pii/S1053811920304328)

de Macedo Rodrigues, K., et al., A FreeSurfer-compliant consistent

manual segmentation of infant brains spanning the 0–2 year age range.

Front. Hum. Neurosci., 2015. 9(21).

* Download:

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Lilla

NOTE: Currently, the parcellation information (aparc) is provided only for the sake of completeness but has not been fully validated. It is a projected version of the adult atlas, so it

does not originate from the infant training data set directly!

---

From: webmaster@nmr.mgh.harvard.edu <webmaster@nmr.mgh.harvard.edu> on behalf of MGH/HST Martinos Center for Biomedical Imaging via MGH/HST Martinos Center for Biomedical Imaging <webmaster@nmr.mgh.harvard.edu>
Sent: Thursday, January 7, 2021 10:12 AM
To: lzollei@nmr.mgh.harvard.edu <lzollei@nmr.mgh.harvard.edu>
Subject: Form submission from: Infant Freesurfer Download Request

 

Submitted on Thursday, January 7, 2021 - 10:12
Submitted by anonymous user: 189.128.48.80
Submitted values are:

Name: Carlos Sair Flores Bautista
Email Address: sairfb@inb.unam.mx
Institution: UNAM-México
Operating System Used: Debian
Intended use of the Pipeline: analyze the neurodevelopment between perinatal
brain damage subject dataset and control subject data set during 0-8 years in
a longitudinal analysis


The results of this submission may be viewed at:
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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 Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://www.massgeneralbrigham.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.