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Hi Bruce,
Yes, the brains were registered in fsaverage space. The issue I am facing is my sig.mgh output from GLM will not convert into a .nii file using mri_convert.
I am trying to load them both as overlays not view them directly. The sig.mgh file loads fine, it is the .nii file that sees the problem.
Similarly, if I do GLM directly with a .nii output, I see the same issues.
You asked me to run mri_info on both the .mgh and .nii.gz files, which I gave in my previous email.
Please let me know how to proceed from here!
Best wishes,
Bruce Fischlhttps://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Bruce+Fischl%22 Mon, 04 Feb 2019 06:31:00 -0800https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20190204
Hi Emma
the dimensions (163842 x 1 x 1) mean that these are overlays on the fsaverage surface. Can you remind me what issue you are trying to solve?
cheers
Bruce
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Hi Bruce,
I ran the mri_info command on the sig.mgh and the sig.lh.nii.gz files for
participant 124 and got these outputs...
For sig.mgh:
Volume information for sig.mgh
type: MGH
dimensions: 163842 x 1 x 1
voxel sizes: 1.000000, 1.000000, 1.000000
type: FLOAT (3)
fov: 163842.000
dof: 0
xstart: -81921.0, xend: 81921.0
ystart: -0.5, yend: 0.5
zstart: -0.5, zend: 0.5
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 = 0.0000
: x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 0.0000
: x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 0.0000
talairach xfm :
Orientation : LIA
Primary Slice Direction: coronal
voxel to ras transform:
-1.0000 0.0000 0.0000 81921.0000
0.0000 0.0000 1.0000 -0.5000
0.0000 -1.0000 0.0000 0.5000
0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform:
-1.0000 -0.0000 -0.0000 81921.0000
-0.0000 -0.0000 -1.0000 0.5000
-0.0000 1.0000 -0.0000 0.5000
-0.0000 -0.0000 -0.0000 1.0000
For sig.lh.nii.gz:
Volume information for sig.lh.nii.gz
type: nii
dimensions: 163842 x 1 x 1
voxel sizes: 1.000000, 1.000000, 1.000000
type: FLOAT (3)
fov: 163842.000
dof: 0
xstart: -81921.0, xend: 81921.0
ystart: -0.5, yend: 0.5
zstart: -0.5, zend: 0.5
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 =
-68267.5000
: x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = -2.5000
: x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 0.0000
Orientation : LIA
Primary Slice Direction: coronal
voxel to ras transform:
-1.0000 0.0000 0.0000 13653.5000
0.0000 0.0000 1.0000 -3.0000
0.0000 -1.0000 0.0000 0.5000
0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform:
-1.0000 -0.0000 -0.0000 13653.5000
-0.0000 -0.0000 -1.0000 0.5000
-0.0000 1.0000 -0.0000 3.0000
-0.0000 -0.0000 -0.0000 1.0000
Please let me know if you need any other information in order to help with our
problem,
Best wishes,
Emma
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________________________________ 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: Monday, February 4, 2019 5:00:09 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 180, Issue 5
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1. gray matter volume of the entorhinal cortex (Laboratorio de Neurociencia Funcional) 2. Re: problem using recon-all (Shachar Gal) 3. Re: problem using recon-all (Glasser, Matthew) 4. Re: Surface to Volume conversion (Bunting, Emma) 5. Re: gray matter volume of the entorhinal cortex (Bruce Fischl) 6. Re: Surface to Volume conversion (Bruce Fischl) 7. Re: gray matter volume of the entorhinal cortex (Laboratorio de Neurociencia Funcional) 8. free surfer install issues (Jordan Fowler) 9. Re: free surfer install issues (Greve, Douglas N.,Ph.D.) 10. (no subject) (Jordan Fowler)
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Message: 1 Date: Mon, 4 Feb 2019 10:08:06 +0100 From: Laboratorio de Neurociencia Funcional neuroaginglnf@gmail.com Subject: [Freesurfer] gray matter volume of the entorhinal cortex To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: CABUYonO85t9vP8NBw9HtWuET2n4i-9s-Q_LevCxZ_rK3U4YAew@mail.gmail.com Content-Type: text/plain; charset="utf-8"
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Dear Freesurfers,
gray matter volume of the entorhinal cortex (EC) can be obtained either in the ?h.aparc.stats or ?h.BA_exvivo.stats/?h.BA_exvivo.thresh.stats files. Considering that all our T1 images were manually edited on a slice-by-slice basis to correct pial surface misplacements and erroneous white matter segmentation, which volume measure of the EC would be more precise?
I assume that gray matter volume contained in ?h.BA_exvivo.thresh.stats were thresholded at a specific probability value (% of case overlapping). Which probability value was used? Is there a reference paper explaining how probabilistic maps of EC were built based on ex vivo MRI contrast?
Thank you in advance.
Best, Jose L. Cantero