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Hi Yujing, sure thing. Thanks for taking a look.
rawavg.mgz
Volume information for rawavg.mgz type: MGH dimensions: 208 x 300 x 320 voxel sizes: 0.800001, 0.800000, 0.800000 type: SHORT (4) fov: 256.000 dof: 1 xstart: -83.2, xend: 83.2 ystart: -120.0, yend: 120.0 zstart: -128.0, zend: 128.0 TR: 2500.00 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 = 0.9972, y_r = 0.0478, z_r = 0.0572, c_r = 4.2108 : x_a = -0.0268, y_a = 0.9456, z_a = -0.3241, c_a = 13.0358 : x_s = -0.0696, y_s = 0.3217, z_s = 0.9443, c_s = -19.3591
talairach xfm : Orientation : RAS Primary Slice Direction: axial
voxel to ras transform: 0.7978 0.0383 0.0457 -91.8157 -0.0214 0.7565 -0.2593 -56.7298 -0.0556 0.2573 0.7554 -173.0404 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant 0.512001
ras to voxel transform: 1.2465 -0.0335 -0.0869 97.5046 0.0598 1.1821 0.4021 142.1226 0.0714 -0.4051 1.1804 187.8310 0.0000 0.0000 0.0000 1.0000
orig.mgz
Volume information for rawavg.mgz type: MGH dimensions: 208 x 300 x 320 voxel sizes: 0.800001, 0.800000, 0.800000 type: SHORT (4) fov: 256.000 dof: 1 xstart: -83.2, xend: 83.2 ystart: -120.0, yend: 120.0 zstart: -128.0, zend: 128.0 TR: 2500.00 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 = 0.9972, y_r = 0.0478, z_r = 0.0572, c_r = 4.2108 : x_a = -0.0268, y_a = 0.9456, z_a = -0.3241, c_a = 13.0358 : x_s = -0.0696, y_s = 0.3217, z_s = 0.9443, c_s = -19.3591
talairach xfm : Orientation : RAS Primary Slice Direction: axial
voxel to ras transform: 0.7978 0.0383 0.0457 -91.8157 -0.0214 0.7565 -0.2593 -56.7298 -0.0556 0.2573 0.7554 -173.0404 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant 0.512001
ras to voxel transform: 1.2465 -0.0335 -0.0869 97.5046 0.0598 1.1821 0.4021 142.1226 0.0714 -0.4051 1.1804 187.8310 0.0000 0.0000 0.0000 1.0000
nu.mgz
Volume information for nu.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.000000, 1.000000, 1.000000 type: UCHAR (0) fov: 256.000 dof: 1 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 2500.00 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 = 4.2108 : x_a = 0.0000, y_a = -0.0000, z_a = 1.0000, c_a = 13.0358 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = -19.3591
talairach xfm : /autofs/space/yoda_002/users/datasets/HCA/data/derivatives/FreeSurfer_failed/HCA6429272_V1_MR/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: -1.0000 -0.0000 0.0000 132.2108 0.0000 -0.0000 1.0000 -114.9642 0.0000 -1.0000 0.0000 108.6409 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -1.0000 0.0000 0.0000 132.2108 0.0000 0.0000 -1.0000 108.6409 0.0000 1.0000 -0.0000 114.9643 -0.0000 -0.0000 -0.0000 1.0000
T1.mgz?
Volume information for T1.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.000000, 1.000000, 1.000000 type: UCHAR (0) fov: 256.000 dof: 1 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 2500.00 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 = 4.2108 : x_a = 0.0000, y_a = -0.0000, z_a = 1.0000, c_a = 13.0358 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = -19.3591
talairach xfm : /autofs/space/yoda_002/users/datasets/HCA/data/derivatives/FreeSurfer_failed/HCA6429272_V1_MR/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: -1.0000 -0.0000 0.0000 132.2108 0.0000 -0.0000 1.0000 -114.9642 0.0000 -1.0000 0.0000 108.6409 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -1.0000 0.0000 0.0000 132.2108 0.0000 0.0000 -1.0000 108.6409 0.0000 1.0000 -0.0000 114.9643 -0.0000 -0.0000 -0.0000 1.0000
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of freesurfer-request@nmr.mgh.harvard.edu freesurfer-request@nmr.mgh.harvard.edu Sent: Wednesday, July 12, 2023 12:16 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 233, Issue 12
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Today's Topics:
1. Re: FreeSurfer 6 Error On Macbook M2 (fsbuild) 2. Issue with FS7.4.1 (Ruifeng Dong) 3. Matrix setup to examine group effect between three groups, one covariate (age) as nuisance variable (Gavette, Levi William) 4. Re: Matrix setup to examine group effect between three groups, one covariate (age) as nuisance variable (Huang, Yujing) 5. Re: Issue with FS7.4.1 (Huang, Yujing) 6. Re: Indices out of bounds error during mri_watershed (Huang, Yujing)
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Message: 1 Date: Wed, 12 Jul 2023 15:57:21 +0200 From: fsbuild fsbuild@contbay.com Subject: Re: [Freesurfer] FreeSurfer 6 Error On Macbook M2 To: freesurfer@nmr.mgh.harvard.edu Cc: thuvaragan.prathifkumar@sri.utoronto.ca Message-ID: c47171311e8871740213347438567e50@trashmail.com Content-Type: text/plain; charset="utf-8"
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The graphics packages used in Freeview have changed since the Freesurfer 6 release, and also how they and the other Intel binaries are compiled for current versions of MacOS. So a run time error, e.g., segfault, could occur when running under Rosetta on a silicon Mac.
Please try one of the current MacOS Freesurfer 7 releases from the download page, surfer.nmr.mgh.harvard.edu/fswiki/rel7downloads
- R.
On 7/12/23 08:35, Prathifkumar, Thuvaragan (thuvaragan.prathifkumar@sri.utoronto.ca) wrote:
External Email - Use Caution
Hello,
I recently installed Free Surfer 6, and was following this guide: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1NRP4tsM45lW3UFB3Jf_X6qXB5GUcDVNjcJDXPLcS2Shw2L...
I got till Example 3, and Example 3 works perfectly. As attached as an image in this email.
For some reason, in Example 4, to open the GUI (freeview) based on the fully recon-ed subject bert in Example 3, I get an error and I'm not sure why. Why does that happen? Is it due to compatibility issues with the apple silicon chip? The error message is attached as an image in this email as well.
Any help is appreciated. Thank you.
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