You should not need to recompute this registration for HCP data. You can use ${StudyFolder}/${Subject}/MNINonLinear/xfms/standard2acpc_dc.nii.gz with applywarp to warp the masks.
Matt.
From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of "Tsolaki, Evangelia C." <[log in to unmask]>
Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
Date: Friday, June 5, 2020 at 12:18 PM
To: "[log in to unmask]" <[log in to unmask]>
Subject: Re: [FSL] Register ROI from MNI to T1 space - Human Connectome Project
Hi Paul,
Can I use FLIRT instead of FNIRT for the MNI to T1 registration with 12 dof?
flirt -in T1.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_2mm_brain -out str2standard -omat str2standard.mat -bins 256 -cost mutualinfo -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -dof 12 -interp trilinear
convert_xfm -omat standard2str.mat -inverse str2standard.mat
flirt -in mask_Standard.nii.gz -applyxfm -init standard2str.mat -out masks_str.nii.gz -paddingsize 0.0 -interp nearestneighbour -ref T1.nii.gz
Thank you,
Evie
Evangelia Tsolaki, MSc, PhD
Assistant Project Scientist
Neurosurgical Brain Mapping & Restoration Lab
University of California, Los Angeles
300 Stein Plaza, Suite 464
Los Angeles, CA 90095
________________________________
From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of paul mccarthy <[log in to unmask]>
Sent: Friday, June 5, 2020 7:40 AM
To: [log in to unmask] <[log in to unmask]>
Subject: Re: [FSL] Register ROI from MNI to T1 space - Human Connectome Project
CAUTION - EXTERNAL EMAIL:Do not click links or open attachments unless you recognize the sender.
Hi Evie,
Honestly, to me it looks like the transformation has worked quite well. What is it about the results that you are concerned about?
Paul
On Thu, 4 Jun 2020 at 19:30, Tsolaki, Evangelia C. <[log in to unmask]<mailto:[log in to unmask]>> wrote:
Hi Paul,
I just uploaded the requested files.
Thank you in advance,
Evie
Evangelia Tsolaki, MSc, PhD
Assistant Project Scientist
Neurosurgical Brain Mapping & Restoration Lab
University of California, Los Angeles
300 Stein Plaza, Suite 464
Los Angeles, CA 90095
________________________________
From: FSL - FMRIB's Software Library <[log in to unmask]<mailto:[log in to unmask]>> on behalf of paul mccarthy <[log in to unmask]<mailto:[log in to unmask]>>
Sent: Thursday, June 4, 2020 2:17 AM
To: [log in to unmask]<mailto:[log in to unmask]> <[log in to unmask]<mailto:[log in to unmask]>>
Subject: Re: [FSL] Register ROI from MNI to T1 space - Human Connectome Project
CAUTION - EXTERNAL EMAIL:Do not click links or open attachments unless you recognize the sender.
Hi Evie,
Can you share the following files with me, so I can try and reproduce the problem?
- T1w_acpc_dc_restore_brain.nii.gz
- T1w_acpc_dc_restore.nii.gz
- mask_MNI
You can use any file sharing service (e.g dropbox), or if you prefer, you can upload the files to:
https://oxfile.ox.ac.uk/oxfile/work/extBox?id=88602424802D9CEADD<https://urldefense.proofpoint.com/v2/url?u=https-3A__oxfile.ox.ac.uk_oxfile_work_extBox-3Fid-3D88602424802D9CEADD&d=DwMFaQ&c=UXmaowRpu5bLSLEQRunJ2z-YIUZuUoa9Rw_x449Hd_Y&r=sY6buNmt7QxVTnux8MqLS4knipQTw7Pek1QAbIgg_sI&m=MdDzc694Um91ZTkQ_7nU4-zm5oKJVhkF-ZhCPDM7OcU&s=a8sPSkl7OuzR8vny75_l-YYfWKxsg6FKPJlKtszw51E&e=>
Paul
On Wed, 3 Jun 2020 at 20:52, Evie Tsolaki <[log in to unmask]<mailto:[log in to unmask]>> wrote:
Hi all,
I do my analysis using the Human Connectome data and I want to register the masks that I create in MNI space to structural space. I use the following code but the resulted transformed mask does not look correct.
flirt -in T1w/T1w_acpc_dc_restore_brain.nii.gz -ref $FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz -dof 12 -out T1toMNIlin.nii.gz -omat T1toMNIlin.mat
fnirt --ref=MNI152_T1_2mm --in=T1w/T1w_acpc_dc_restore.nii.gz --aff=T1toMNIlin.mat --config=T1_2_MNI152_2mm.cnf --iout=T1toMNInonlin.nii.gz --cout=T1toMNI_coef.nii.gz --fout=T1toMNI_warp.nii.gz
invwarp --ref=T1w/T1w_acpc_dc_restore.nii.gz --warp=T1toMNI_warp.nii.gz --out=MNItoT1_warp.nii.gz
applywarp --ref=T1w/T1w_acpc_dc_restore.nii.gz --in=mask_MNI --warp=MNItoT1_warp.nii.gz --out=mask_T1 --interp=nn
Could you please tell me what might be wrong?
Thank you in advance,
Evie
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