[Freesurfer] DPABI V8.0, DPABISurfSlurm and DPABI Harmonization module were released!

YAN Chao-Gan Mon, 06 Nov 2023 22:30:29 -0800

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Dear colleagues,

We are pleased to announce the release of DPABI V8.0, DPABISurfSlurm and
DPABI Harmonization module.

New features of DPABI_V8.0_231111 (download at
http://secure-web.cisco.com/1iu1Tns8hOQhPl_19d90nC0eQexs39Tq6UxLJzJ-WyJoYklczI2yb7komDIE1RFHf40sUpvc9Bd2_crp8uXmEx96JWCsYjDkif2HHL-LGOTUg9-5cTBmu0PAQ_62_Gp17lIWDBDzjKZ2YUyxCjjPBY6BU5bG6-7eyO7du7rac2o3SIl8qXTmMos1IfJbjoTZ22iJ7kPjr6BH5yNs_0Ycn7Nx294fCunIa1kWobyHfph3i8JesCEtY6gk54kEd7QOU7_qobooO6wh0ytBZ23OrRhxiR4ElY5dzFZvi7LKB1WkpduuBB65oKIIoFOczNwj0kU1qLmyV_mx07-jBXtaCVg/http%3A%2F%2Frfmri.org%2Fdpabi,
please also update the docker file by: docker pull cgyan/dpabi and docker
pull cgyan/dpabifiber):
1. DPABI Harmonization module was released.
This module could be used to harmonizing the brain images
(.nii/.nii.gz/.gii/.mat) to remove site effects for big data in statistical
analysis. Please read our latest Reference: Wang, Y.W., Chen, X., Yan, C.G.
(2023). Comprehensive evaluation of harmonization on functional brain
imaging for multisite data-fusion. Neuroimage, 274, 120089,
doi:10.1016/j.neuroimage.2023.120089.
2. DPABISurf 3.0.
2.1. DPABISurfSlurm: High Performance Computing Version of DPABISurf was
released. Please read here for how to use it:
http://secure-web.cisco.com/1-s7rUQYmnIYW5KNs2c_2Ua6A5hfNaBoITZqssWTtvVB7Vlg1k5SXxEtRAHsWF6T-mdmU2tg3E73cBbcfZyX9BJKMjj6etaGqAzs7Lr9LafWJABEwJ23c9PXmJGR2cj6aMlscJSMm6_vVbIhK6a8rUUpZeAUXLUhEVcZjpgzOmEBuL3kocyMMRFmcdk_qT80hnv8l1SV1To0f3cob-EFWinY7dmh7y_PiR3w5817xjz0Sb14HCaoToa6yIKIneL9RgTYgDvjDuOGC94hrtFBL8qJjI0xhjhRkk03970Z4Sld3JA-EyV4W_ow-9SMBaqOBLw3pGYUIRpIUtJc38_N_eQ/http%3A%2F%2Frfmri.org%2FDPABISurfSlurm
2.2. Back engine updated to fMRIPrep V23.1.4, thus using FreeSurfer 7.3.2.
2.3. Segment subregions (Thalamus, Hippocampus, Amygdala and Brainstem)
with FreeSurfer 7.3.2 was set to the default option now.
2.4. Added freesurfer atlases:
{DPABISurf}/SurfTemplates/fsaverage5_lh_aparc_a2009s_annot.label.gii and
fsaverage5_lh_aparc_annot.label.gii.
2.5. Could make use of DPABI Harmonization module.
3. DPABIFiber 1.1.
3.1. Back engine updated to QSIPrep V0.19.1.
3.2. Could make use of DPABI Harmonization module.
4. DPABINet 1.3.
4.1. Could make use of DPABI Harmonization module.
5. Fixed a bug in handling surface correlation analysis in
y_Correlation_Image.m.
6. Fixed a bug of "Brace indexing is not supported for variables of this
type" in DPABI_TDA.

Appendix: DPABISurfSlurm

DPABISurfSlurm is a high performance computing version of DPABISurf! You
can use it on High Performance Computing (HPC, or supercomputing) center.
The only requirement is Singularity!

1. Download the DPABISurfSlurm scripts to ${DPABISurfSlurmDIR}:
https://secure-web.cisco.com/1ZkUL0iquwMSl08IjP7ZjP5AJFpFNw60h7dS6F4Wh0mxJHU5Tp8ToH83G93HGmqB5e3QTeZ8CiXz8N0BJor4K9jRR0zN0eKcbK_p0S004oskQ5PevrQWADGzy6WestgLQShyotXPnmNptOrVXN6WzZZKZLJb8sGcpMtwFBNPn4ywFPRfqbHgP37KZKvR22EbUvOE5jxmNCg4gLujaC7hcClyLK474bNEIMzcbh3h4j65f6v5_UrOFyIC86pRBrMEy1t6IB3KWE41NOAxMdoWd175Ym3NwtrGyyxIKbZYIibwXdmgjO94RRmufuB73CQh-MWR14HqezdJKiGAAxgDWbw/https%3A%2F%2Fgithub.com%2FChaogan-Yan%2FDPABI%2Ftree%2Fmaster%2FDPABISurf%2FDPABISurfSlurm

2. Download the singularity files: singularity pull dpabisurfslurm.sif
docker://cgyan/dpabisurfslurm:latest and singularity pull freesurfer.sif
docker://cgyan/freesurfer:latest. Or download from here
<https://secure-web.cisco.com/1pYMqkkakGcgkJdcGjMUIsEqDKg_pLi4R0SfGcrWlbO0E_g95zDxXz_5r0W4ru9KTNgqcvNNjrrCh0jwSlm7FOphkk8q2bGHY3z4cQ3Bjle5ZHZ1Xh7dg9eYi6zww1ZOydruzfwcgmH81i4G2L48ysLuJKMXz6bzYl-1iG73nool-r6jTeUfZ0x5NnFRB2_lN36ZjN3YpXgbrf427FjocjIZFqtubyOLGYT6A3T07mxBycpMXwbpn2OsBs5Cw9e6XPM8Yqjojswu2q55pUJReEZ2PCp4g4jEInE6rt2wK_0mW29WYQxALTnoC1zIcEf6UfDHyh-FmzdENJ7C8fPbtNA/https%3A%2F%2Fpan.baidu.com%2Fs%2F1V01NJsa-s3sDo1fv0v3kGA%3Fpwd%3Dndp8>.
Place them in
the directory under ${SingularityDIR}.

3. Prepare your data in BIDS format in the BIDS directory under
${DATADIR}. You should also have a subjects.txt under ${DATADIR}. E.g.,

BIDS

subjects.txt

sub-Sub001

sub-Sub002

sub-Sub003

4. In the *.slurm files under ${DPABISurfSlurmDIR}, you should revise
this line:

#SBATCH -p normal #指定分区名称

normal is the partition you will use by Slurm. Ask your HPC administrator
for the partition name you can use, and then revise “normal” to that
partition name.

You may also need to revise this line to correctly load the singularity
module, please confirm with your HPC administrator.

module load singularity/3.8.0

5. Copy DPABISurf_runSlurm.sh and SetEnv.sh from ${DPABISurfSlurmDIR}
to your ${DATADIR}.

6. In DPABISurf_runSlurm.sh, you should define:

export DPABISurfSlurmDIR="/work1/yancg/Scripts/DPABISurfSlurm"

# Should have the DPABISurfSlurm files

export SetEnvScriptDir="/work1/yancg/Data/Test/Test"

# Should have SetEnv.sh

# You should also go into SetEnv.sh to define your parameters!!!

export DATADIR="/work1/yancg/Data/Test/Test"

# Should have BIDS and subjects.txt

7. In SetEnv.sh, you should define:

export DATADIR="/work1/yancg/Data/Test/Test"

# Should have BIDS and subjects.txt

export SingularityDIR="/work1/yancg/Soft/Singularity"

# Should have dpabisurfslurm.sif. You can get it by singularity pull
dpabisurfslurm.sif docker://cgyan/dpabisurfslurm:latest

# Should have freesurfer.sif. You can get it by singularity pull
freesurfer.sif docker://cgyan/freesurfer:latest

export FreeSurferLicenseDIR="/work1/yancg/Soft/FreeSurferLicense"

# Should have license.txt from FreeSurfer

export RemoveFirstTimePoints="5"

# Set up Number of time points needs to be removed

export FunctionalSessionNumber="1"

# Set up Number of Functional Sessions

8. Make a directory to save the log files under ${DATADIR} and cd to
that directory.

9. source ../DPABISurf_runSlurm.sh. Submit your tasks! You can use
squeue to check the status of running.

10. You will have all you want at ${DATADIR}/ResultsOrganized.tar.gz.

Best,

Chao-Gan

--
Chao-Gan YAN, Ph.D.
Professor, Principal Investigator
Director, International Big-Data Center for Depression Research
Director, Magnetic Resonance Imaging Research Center
Institute of Psychology, Chinese Academy of Sciences
16 Lincui Road, Chaoyang District, Beijing 100101, China
-
Initiator
<http://secure-web.cisco.com/17VG5K3SI6ILdFFVqh0kzYbEF2O8UWDst5GyZx7oHeZTsvJGpv4LBNH2EzquAApjZBlqcbw0NU-SBiYaB93mN524LAb2A3FQycbfbKCjzUyc8yVPT6BXRFrVYlHkLWZqhBRHVMubSQHf6QnVfMZPkTc3Lq7MTvrUL6KgOt2A5XsC1bJbh_ed7FFTe7ULkuM20PVnMpDaSzrXnZrSvXiXXMNuq_9yEBUxPSFC1U_tMacSp6eOnAcNTbix7emT0JnplrPfbwGEeOai6RIKbwMTjI6MUCov2EoU4jJxqztCGahTw7sV9XoWadwbAYAzMPaNMqe_Qh4JSQm9SW_HjwX421g/http%3A%2F%2Frfmri.org%2FDPARSF>DPABI

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[Freesurfer] DPABI V8.0, DPABISurfSlurm and DPABI Harmonization module were released!

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