External Email - Use Caution
Hi Yujing,
Sure.
the results of applying mri_info are attached below
Bests,
Yazdan.
On Fri, 6 Oct 2023 at 23:19, Huang, Yujing <yhuan...@mgh.harvard.edu> wrote:
> External Email - Use Caution
>
> Hi Yazdan,
>
>
>
> Thank you for the detailed explanation.
>
>
>
> I’m wondering if you could send output of mri_info for Image.nii,
> fsl_resampled.nii.gz, fslregistered.nii.gz, freesurfer.nii, and output from
> ANTs.
>
>
>
> Best,
>
>
>
> Yujing
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Yazdan Rezaee
> Jouryabi
> *Sent:* Friday, September 29, 2023 12:19 PM
> *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> *Subject:* Re: [Freesurfer] lta_convert issue with ants Registration
> Matrix
>
>
>
> * External Email - Use Caution *
>
> Hi Yujing,
>
> I'll try to explain it more explicitly, I rerun my Code and show the
> results beyond attaching the Registration files too.
>
>
>
> Consider a 3D-Nifti image called "Image.nii" the steps bellow executed in
> order:
>
> 0- Every time we Will generate a random Registration Matrix and Save it
> under the name "fsl.mat" which is the desired Registration matrix.
>
>
> ==============================================================================
>
> fsl.mat :=
>
> [[ 0.95509431, -0.28438761, 0.08317783, -5. ]
>
> [ 0.2961434, 0.90701597, -0.29936787, -5. ]
>
> [ 0.00969289, 0.31055712, 0.9505053, -2. ]
>
> [ 0., 0., 0., 1. ]]
>
>
> ==============================================================================
>
>
>
> 1- using a known registration matrice (called and attached in the first
> message and this message as "fsl.mat") resample the "Image.nii" to second
> Image called "fsl_resampled.nii"
>
> Command : flirt -ref ./Image.nii -in ./Image.nii -applyxfm -init
> ./fsl.mat -out ./fsl_resampled.nii -interp spline
>
> 2- find out the registration matrices using Registration Methods, here we
> will use FSL, FreesSurefer, ANTs:
>
> 2.1. FSL Commands:
>
>
> ===============================================================================
>
> Command : flirt -in ./Image.nii -out ./fslregistered.nii.gz -ref
> ./fsl_resampled.nii.gz -cost normmi -dof 6 -omat ./fslregistered.mat
> -interp spline
>
>
> ===============================================================================
>
> fslregistered :
>
> 0.9551458402 -0.2842262621 0.08313877187 -5.029802253
>
> 0.2959789517 0.9070999982 -0.2992758021 -5.014360215
>
> 0.009646861275 0.3104593324 0.9505376886 -1.971170444
>
> 0 0 0 1
> =======================================================
>
> The Registration Matrice in this Case Called "fslregistered.mat", using
> lta_convert we will make "fslregistered.lta"
>
> Command : lta_convert --infsl ./fsl/fslregistered.mat --outlta
> ./fsl/fslregistered.lta --src ./Image.nii --trg ./fsl/fslregistered.nii.gz
> --ltavox2vox
>
>
> ===============================================================================
>
> fslregistered.lta :
>
> 9.551459550857544e-01 -2.368552237749100e-01 6.928230822086334e-02
> -4.191513061523438e+00
>
> 3.551747798919678e-01 9.071001410484314e-01 -2.992758452892303e-01
> -5.014381408691406e+00
>
> 1.157622877508402e-02 3.104593753814697e-01 9.505378007888794e-01
> -1.971183776855469e+00
>
> 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
> 1.000000000000000e+00
>
> 2.2. FreeSurfer Commands:
>
>
> ===============================================================================
>
> Command : mri_robust_register --mov ./Image.nii --dst
> ./fsl_resampled.nii.gz --mapmov ./freesurfer.nii --lta freesurfer.lta
> --halfmov half-mov.nii --halfdst halfdst.nii --halfmovlta h1.lta
> --halfdstlta h2.lta --iscale --satit
>
> ===============================================================================
> freesurfer.lta :
> type = 0 # LINEAR_VOX_TO_VOX
>
> nxforms = 1
>
> mean = 87.0000 129.0000 106.0000
>
> sigma = 10000.0000
>
> 1 4 4
>
> 9.550938606262207e-01 -2.369909435510635e-01 6.931482255458832e-02
> -4.167178630828857e+00
>
> 3.553738296031952e-01 9.070160388946533e-01 -2.993661761283875e-01
> -4.999662876129150e+00
>
> 1.163147203624249e-02 3.105554580688477e-01 9.505058526992798e-01
> -2.000635147094727e+00
>
> 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
> 1.000000000000000e+00
>
>
> ================================================================================
>
> The Registration Matrice in this Case Called "freesurfer.lta", using
> lta_convert we will do the conversion and build the FSL-Space
> "freesurfer.mat"
>
> Command : lta_convert --inlta ./freesurfer/freesurfer.lta --outfsl
> ./freesurfer/freesurfer.mat --src ./Image.nii --trg ./fsl_resampled.nii.gz
>
> ========================================================
> freesurfer.mat :
> 0.95509410 -0.28438917 0.08317780 -5.00063801
>
> 0.29614490 0.90701610 -0.29936624 -4.99965954
>
> 0.00969290 0.31055552 0.95050597 -2.00067019
>
> 0.00000000 0.00000000 0.00000000 1.00000000
>
>
> ================================================================================
>
> 2.3. ANTs Commands:
>
>
> ================================================================================
>
> Commands : antsRegistrationSyNQuick.sh -d 3 -f ./fsl_resampled.nii.gz
> -m ./Image.nii -o ants_ -t r
>
> Using the ConvertTransform File we will make the "ants.txt"
>
> Command : ConvertTransformFile 3 ./ANTS/ants_0GenericAffine.mat
> ./ANTS/ants.txt
>
>
> ================================================================================
>
> ants.txt:
>
> #Insight Transform File V1.0
>
> #Transform 0
>
> Transform: AffineTransform_double_3_3
>
> Parameters: 0.9996357319973235 -0.01682948721742278 -0.021099091785527296
> 0.015864886388920783 0.9988573896699559 -0.045080156184165145
> 0.02183365965755943 0.04472900023162478 0.9987605357863502 -2.215029749904149
> 1.2122977228542815 -6.0667455324006445
>
> FixedParameters: 5.195914900051355 -10.250280974097581 -6.670270481513606
>
>
> ================================================================================
>
> Using lta_convert we first make "ants.lta"
>
> Command: lta_convert --initk ./ANTS/ants.txt --outlta ./ANTS/ants.lta
> --src ./Image.nii --trg ./fsl_resampled.nii.gz --ltavox2vox
>
>
> ================================================================================
>
> type = 0 # LINEAR_VOX_TO_VOX
>
> nxforms = 1
>
> mean = 0.0000 0.0000 0.0000
>
> sigma = 1.0000
>
> 1 4 4
>
> 9.996357560157776e-01 -1.322073861956596e-02 1.819471642374992e-02
> 1.924201965332031e+00
>
> 2.019538544118404e-02 9.988574385643005e-01 -4.472899809479713e-02
> 3.623344421386719e+00
>
> -2.531890943646431e-02 4.508015885949135e-02 9.987605214118958e-01
> 2.642463684082031e+00
>
> 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
> 1.000000000000000e+00
> =================================================================================
> Using the lta_convert we make the "ants.mat", the FSL-Spaced Registration
> matrix for ANTs
> Command: lta_convert --inlta ./ANTS/ants.lta --outfsl ./ANTS/ants.mat
> --src ./Image.nii --trg ./fsl_resampled.nii.gz
> =================================================================================
> 0.99963582 -0.01586489 0.02183366 2.30903101
>
> 0.01682949 0.99885744 -0.04472899 3.62335658
>
> -0.02109909 0.04508016 0.99876052 2.64244890
>
> 0.00000000 0.00000000 0.00000000 1.00000000
>
>
> As we could see there are problems in 'ants.lta' and 'ants.mat', I'm not sure
> Yet but I Suspect that the "PSR" Orientation of the Image Which is a
> Left-handed coordination System may cause that because in Another Experiment
> with "LAS" these problem had been occured but in another "RAS" Image the
> lta_convertor worked precisely with no problem.
>
> The Registration Files are attached for More Information about Image's
> Geometry Sform's and Other ...
>
>
> Best,
>
> Yazdan
>
>
>
>
>
>
>
> On Mon, 25 Sept 2023 at 17:16, Huang, Yujing <yhuan...@mgh.harvard.edu>
> wrote:
>
> * External Email - Use Caution *
>
> Hi Yazdan,
>
>
>
> I’m trying to understand the issues.
>
>
>
> Can you specify the commands used to generate the matrices attached to
> your email? And give more details of the issues you are seeing?
>
>
>
> Best,
>
>
>
> Yujing
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Yazdan Rezaee
> Jouryabi
> *Sent:* Monday, September 25, 2023 1:49 AM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* [Freesurfer] lta_convert issue with ants Registration Matrix
>
>
>
> * External Email - Use Caution *
>
> Dear all, Hi
>
>
>
> for checking registration i used fsl applyxfm on an Image(1)(Called
> Image.nii ) with specific Registration Matrice (Which we suppose to receive
> when we apply registration Methods) and Generate the "fsl_resampled.nii.gz"
> (Note: Image Orientations were LAS and in one other Experiment with also
> the same problem PSR)
>
>
>
> for our case i will attach the "fsl.mat" (Desired Matrix)
>
>
>
> using, fsl, freesurfer, and ants i got the correct results (let's call
> them "fslregistered.mat" and "freesurfer.mat" the converted lta to
> fsl-liked Matrix) Everything is OK till now
>
>
>
> But the converted lta-like and fsl-like matrix for ANTs (Which are called
> ants.lta, and ants.mat) using the lines below:
>
> - ConvertTransformFile 3 ./ANTS/ants_0GenericAffine.mat ./ANTS/ants.txt
>
> - lta_convert --initk ./ANTS/ants.txt --outlta ./ANTS/ants.lta --src
> ./Image.nii --trg ./fsl_resampled.nii.gz --ltavox2vox
>
> - lta_convert --inlta ./ANTS/ants.lta --outfsl ./ANTS/ants.mat --src
> ./Image.nii --trg ./fsl_resampled.nii.gz
>
>
>
> As All Results Images (Registered Image of all Methods) are aligned
> perfectly i think that there might be some issues with lta_convert
>
>
>
>
>
> Best Regards
>
> Yazdan Rezaee J
>
>
>
>
>
>
> *P.S. *" I've checked the one similar mail on this topic and the
> conclusion on that was about (sform, qform) incompatibility but the affine
> matrices of S-form and q-form are equivalent in my case."
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> *MailScanner has detected a possible fraud attempt from
> "secure-web.cisco.com" claiming to be*
> https://secure-web.cisco.com/1BStSAxLh5BeN2L3rU2frK5cGS07arbjFgCFDCXjer8mI9E6QhC8axsTzJmtNHA0f1DD52gOLn7V-0bXwHcjGpMgOvj5Ej9o0ngUReq4erjdQzvYap5kCRZ7e1R0AlzG3ItDCyzjDBFs1Hwuf_QGSCA0SbXehYcVoataMjv341ofR-qoXsG8G2K8Q2d1z1G3CluiFixSCjME4890bumFvO47QQG0nNCEDOPpFNuPHYPbFtpXrvY-tFm2uqnoNPMEp5d-TAX_caWLaTC52xtF8vU_f4PLeM-ImIm6-4ZiPLVGGJ6bU0ZNKXVhnhIG9oCdTp1_UXPx1xKVwGkz_KsQhyQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
> <https://secure-web.cisco.com/1CVysUaKA0QPJhHH2wwhYBipzUhFEaeL8kkwOtuATULgzm-ARVtRifTqrnuMch9mPrhoX5WsrgJCZI4n6LV0QrBOiwz8JOJSZcKXl0-srjhHE7Ez1eAdpgDrWIqslv1yZuu9lDDu4UrcCR_1k8-OHZM1lX5im7TD25ziCO5ibM6spWh-yZJ_pdgSrOWg3COhe2JLUiyCL3VPWaa-l3gJ-VY8E3fKgFi47mdINsuywYT2Z2bpFzMA0qVMOcxBZP6V2Jz-SpyfFbeS55S0r_f_lNm2JigMyuajjviAgHw-npf_6HYFs541IzQp4hzn0kOTN/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
> 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*
> https://secure-web.cisco.com/1Cw0A3cVjhHcWsRIekyy6Q8-imKvdraduISNe4Ov9uMpCll4kaZi6vRqNSbeXf5oHAJOWU0yc9x101MlugaGXfg393-hK7jLPlwskqaX9jghAgPYPl83J2yX_uUlZiB13Lx7ktR0rhXhZh2ecEYt7MW37SAI36Uj5Ulne7g4z3Out8L-iEezNr37SOf3T_y5FjcgdnZb1hXacCNjUZEKacAykR8sKRTyhhAG_E8ctWpyW8lzYotL3wx2NnOBnVKaFTjqHmusxL7PADZchaGiJLDHbflArXF6id4bAHVBYXAqA_lly_--W2-vdqYHLzapz3rtUitsPr_P065wxJ_b1Ig/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline
> <https://secure-web.cisco.com/1iXmC6GDGT_irmtwnhqZdBKSxywaeJC3Q1wdvh_a0KY5o7X2IMOclXP4f0k-GqI_PRroMRHLYU-2PytqXKGTg6_fWW1KVDHATy0ENxJF3psR7lP7a-RRfcFNfBEjlwcIVKlvbWPxlCCMyKVbMe6U5Fh-MyOLPX0g_j4lWjXAjcWLJkRG0g4PBTK_xzSz904-Aq-5yTIzIoulIOOVdRa03bD2RdUbEfx4x44oD3QmrEeVyAQcHQXg97yGoNqncOG-pa601HCmc65kmd9kIqklmkjAhm1NA5O-PbF2zqMYfQYmUWbVziolYCOD5tYgNE9wx/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>
> <*MailScanner has detected a possible fraud attempt from
> "secure-web.cisco.com" claiming to be*
> https://secure-web.cisco.com/1Cw0A3cVjhHcWsRIekyy6Q8-imKvdraduISNe4Ov9uMpCll4kaZi6vRqNSbeXf5oHAJOWU0yc9x101MlugaGXfg393-hK7jLPlwskqaX9jghAgPYPl83J2yX_uUlZiB13Lx7ktR0rhXhZh2ecEYt7MW37SAI36Uj5Ulne7g4z3Out8L-iEezNr37SOf3T_y5FjcgdnZb1hXacCNjUZEKacAykR8sKRTyhhAG_E8ctWpyW8lzYotL3wx2NnOBnVKaFTjqHmusxL7PADZchaGiJLDHbflArXF6id4bAHVBYXAqA_lly_--W2-vdqYHLzapz3rtUitsPr_P065wxJ_b1Ig/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline
> <https://secure-web.cisco.com/1iXmC6GDGT_irmtwnhqZdBKSxywaeJC3Q1wdvh_a0KY5o7X2IMOclXP4f0k-GqI_PRroMRHLYU-2PytqXKGTg6_fWW1KVDHATy0ENxJF3psR7lP7a-RRfcFNfBEjlwcIVKlvbWPxlCCMyKVbMe6U5Fh-MyOLPX0g_j4lWjXAjcWLJkRG0g4PBTK_xzSz904-Aq-5yTIzIoulIOOVdRa03bD2RdUbEfx4x44oD3QmrEeVyAQcHQXg97yGoNqncOG-pa601HCmc65kmd9kIqklmkjAhm1NA5O-PbF2zqMYfQYmUWbVziolYCOD5tYgNE9wx/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>>
> .
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://secure-web.cisco.com/1BStSAxLh5BeN2L3rU2frK5cGS07arbjFgCFDCXjer8mI9E6QhC8axsTzJmtNHA0f1DD52gOLn7V-0bXwHcjGpMgOvj5Ej9o0ngUReq4erjdQzvYap5kCRZ7e1R0AlzG3ItDCyzjDBFs1Hwuf_QGSCA0SbXehYcVoataMjv341ofR-qoXsG8G2K8Q2d1z1G3CluiFixSCjME4890bumFvO47QQG0nNCEDOPpFNuPHYPbFtpXrvY-tFm2uqnoNPMEp5d-TAX_caWLaTC52xtF8vU_f4PLeM-ImIm6-4ZiPLVGGJ6bU0ZNKXVhnhIG9oCdTp1_UXPx1xKVwGkz_KsQhyQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
> 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
> https://secure-web.cisco.com/1Cw0A3cVjhHcWsRIekyy6Q8-imKvdraduISNe4Ov9uMpCll4kaZi6vRqNSbeXf5oHAJOWU0yc9x101MlugaGXfg393-hK7jLPlwskqaX9jghAgPYPl83J2yX_uUlZiB13Lx7ktR0rhXhZh2ecEYt7MW37SAI36Uj5Ulne7g4z3Out8L-iEezNr37SOf3T_y5FjcgdnZb1hXacCNjUZEKacAykR8sKRTyhhAG_E8ctWpyW8lzYotL3wx2NnOBnVKaFTjqHmusxL7PADZchaGiJLDHbflArXF6id4bAHVBYXAqA_lly_--W2-vdqYHLzapz3rtUitsPr_P065wxJ_b1Ig/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline
> <
> https://secure-web.cisco.com/1Cw0A3cVjhHcWsRIekyy6Q8-imKvdraduISNe4Ov9uMpCll4kaZi6vRqNSbeXf5oHAJOWU0yc9x101MlugaGXfg393-hK7jLPlwskqaX9jghAgPYPl83J2yX_uUlZiB13Lx7ktR0rhXhZh2ecEYt7MW37SAI36Uj5Ulne7g4z3Out8L-iEezNr37SOf3T_y5FjcgdnZb1hXacCNjUZEKacAykR8sKRTyhhAG_E8ctWpyW8lzYotL3wx2NnOBnVKaFTjqHmusxL7PADZchaGiJLDHbflArXF6id4bAHVBYXAqA_lly_--W2-vdqYHLzapz3rtUitsPr_P065wxJ_b1Ig/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>
> .
>
Volume information for Image.nii
type: nii
dimensions: 170 x 256 x 256
voxel sizes: 1.200000, 1.000000, 1.000000
type: SHORT (4)
fov: 204.000
dof: 1
xstart: -102.0, xend: 102.0
ystart: -128.0, yend: 128.0
zstart: -128.0, zend: 128.0
TR: 6.81 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
degrees
nframes: 1
PhEncDir: UNKNOWN
FieldStrength: 0.000000
ras xform present
xform info: x_r = -1.0000, y_r = -0.0000, z_r = -0.0000, c_r = -0.6003
: x_a = 0.0000, y_a = 1.0000, z_a = 0.0000, c_a = 17.5182
: x_s = -0.0000, y_s = -0.0000, z_s = 1.0000, c_s = 16.7755
Orientation : LAS
Primary Slice Direction: axial
voxel to ras transform:
-1.2000 -0.0000 -0.0000 101.3997
0.0000 1.0000 0.0000 -110.4818
-0.0000 -0.0000 1.0000 -111.2245
0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1.2
ras to voxel transform:
-0.8333 -0.0000 -0.0000 84.4998
-0.0000 1.0000 -0.0000 110.4818
-0.0000 -0.0000 1.0000 111.2245
-0.0000 -0.0000 -0.0000 1.0000
Volume information for fsl_resampled.nii.gz
type: nii
dimensions: 170 x 256 x 256
voxel sizes: 1.200000, 1.000000, 1.000000
type: SHORT (4)
fov: 204.000
dof: 1
xstart: -102.0, xend: 102.0
ystart: -128.0, yend: 128.0
zstart: -128.0, zend: 128.0
TR: 6.81 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
degrees
nframes: 1
PhEncDir: UNKNOWN
FieldStrength: 0.000000
ras xform present
xform info: x_r = -1.0000, y_r = -0.0000, z_r = -0.0000, c_r = -0.6003
: x_a = 0.0000, y_a = 1.0000, z_a = 0.0000, c_a = 17.5182
: x_s = -0.0000, y_s = -0.0000, z_s = 1.0000, c_s = 16.7755
Orientation : LAS
Primary Slice Direction: axial
voxel to ras transform:
-1.2000 -0.0000 -0.0000 101.3997
0.0000 1.0000 0.0000 -110.4818
-0.0000 -0.0000 1.0000 -111.2245
0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1.2
ras to voxel transform:
-0.8333 -0.0000 -0.0000 84.4998
-0.0000 1.0000 -0.0000 110.4818
-0.0000 -0.0000 1.0000 111.2245
-0.0000 -0.0000 -0.0000 1.0000
Volume information for fslregistered.nii.gz
type: nii
dimensions: 170 x 256 x 256
voxel sizes: 1.200000, 1.000000, 1.000000
type: SHORT (4)
fov: 204.000
dof: 1
xstart: -102.0, xend: 102.0
ystart: -128.0, yend: 128.0
zstart: -128.0, zend: 128.0
TR: 6.81 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
degrees
nframes: 1
PhEncDir: UNKNOWN
FieldStrength: 0.000000
ras xform present
xform info: x_r = -1.0000, y_r = -0.0000, z_r = -0.0000, c_r = -0.6003
: x_a = 0.0000, y_a = 1.0000, z_a = 0.0000, c_a = 17.5182
: x_s = -0.0000, y_s = -0.0000, z_s = 1.0000, c_s = 16.7755
Orientation : LAS
Primary Slice Direction: axial
voxel to ras transform:
-1.2000 -0.0000 -0.0000 101.3997
0.0000 1.0000 0.0000 -110.4818
-0.0000 -0.0000 1.0000 -111.2245
0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1.2
ras to voxel transform:
-0.8333 -0.0000 -0.0000 84.4998
-0.0000 1.0000 -0.0000 110.4818
-0.0000 -0.0000 1.0000 111.2245
-0.0000 -0.0000 -0.0000 1.0000
Volume information for freesurfer.nii
type: nii
dimensions: 170 x 256 x 256
voxel sizes: 1.200000, 1.000000, 1.000000
type: SHORT (4)
fov: 204.000
dof: 1
xstart: -102.0, xend: 102.0
ystart: -128.0, yend: 128.0
zstart: -128.0, zend: 128.0
TR: 6.81 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
degrees
nframes: 1
PhEncDir: UNKNOWN
FieldStrength: 0.000000
ras xform present
xform info: x_r = -1.0000, y_r = -0.0000, z_r = -0.0000, c_r = -0.6003
: x_a = 0.0000, y_a = 1.0000, z_a = 0.0000, c_a = 17.5182
: x_s = -0.0000, y_s = -0.0000, z_s = 1.0000, c_s = 16.7755
Orientation : LAS
Primary Slice Direction: axial
voxel to ras transform:
-1.2000 -0.0000 -0.0000 101.3997
0.0000 1.0000 0.0000 -110.4818
-0.0000 -0.0000 1.0000 -111.2245
0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1.2
ras to voxel transform:
-0.8333 -0.0000 -0.0000 84.4998
-0.0000 1.0000 -0.0000 110.4818
-0.0000 -0.0000 1.0000 111.2245
-0.0000 -0.0000 -0.0000 1.0000
niiRead(): detected input as 64 bit double, reading in as 32 bit float
Volume information for ants_Warped.nii.gz
type: nii
dimensions: 170 x 256 x 256
voxel sizes: 1.200000, 1.000000, 1.000000
type: FLOAT (3)
fov: 204.000
dof: 1
xstart: -102.0, xend: 102.0
ystart: -128.0, yend: 128.0
zstart: -128.0, zend: 128.0
TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
degrees
nframes: 1
PhEncDir: UNKNOWN
FieldStrength: 0.000000
ras xform present
xform info: x_r = -1.0000, y_r = -0.0000, z_r = 0.0000, c_r = -0.6003
: x_a = -0.0000, y_a = 1.0000, z_a = -0.0000, c_a = 17.5182
: x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = 16.7755
Orientation : LAS
Primary Slice Direction: axial
voxel to ras transform:
-1.2000 -0.0000 0.0000 101.3997
-0.0000 1.0000 -0.0000 -110.4818
0.0000 0.0000 1.0000 -111.2245
0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1.2
ras to voxel transform:
-0.8333 -0.0000 -0.0000 84.4998
-0.0000 1.0000 -0.0000 110.4818
-0.0000 -0.0000 1.0000 111.2245
-0.0000 -0.0000 -0.0000 1.0000
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Please note that this e-mail is not secure (encrypted). If you do not wish to
continue communication over unencrypted e-mail, please notify the sender of
this message immediately. Continuing to send or respond to e-mail after
receiving this message means you understand and accept this risk and wish to
continue to communicate over unencrypted e-mail.
