External Email - Use Caution
Hi Anastasia, Thank you for answering! I think you are right and the problem is there, when checking the number of slices in the dwindling file I get: dimensions: 104 x 104 x 72
Although the original dwindling data has: 104 x 104 x 72 x 111
voxel sizes: 2.019231, 2.019231, 2.000000 type: SHORT (4) fov: 210.000 dof: 0 xstart: -105.0, xend: 105.0 ystart: -105.0, yend: 105.0 zstart: -72.0, zend: 72.0 TR: 3670.00 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 = -0.9897, y_r = 0.1290, z_r = -0.0618, c_r = -1.2731 : x_a = -0.1108, y_a = -0.9647, z_a = -0.2389, c_a = -22.2682 : x_s = -0.0904, y_s = -0.2296, z_s = 0.9691, c_s = 12.8890 Orientation : LPS Primary Slice Direction: axial
voxel to ras transform: -1.9985 0.2605 -0.1236 93.5531 -0.2238 -1.9480 -0.4778 107.8607 -0.1826 -0.4636 1.9382 -23.2834 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant 8.15459
ras to voxel transform: -0.4901 -0.0549 -0.0448 50.7312 0.0639 -0.4778 -0.1137 42.9079 -0.0309 -0.1194 0.4845 27.0558 0.0000 0.0000 0.0000 1.0000
I don't understand why, given those are outputs of recon-all ..
Do you think you know what's happening?
Thank you very much!?
Best, Cecilia
Cecilia Mazzetti - Ph.D. Researcher Donders Centre for Cognitive Neuroimaging, room 2.257 Kapittelweg 29 | 6525 EN Nijmegen
How many volumes does this file have? /myfolder/freesurfer/subject02_C/dmri/data.nii.gz
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Mazzetti, C. (Cecilia) C.Mazzetti@donders.ru.nl Sent: Sunday, October 6, 2019 5:56 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Errors running TRACULA (data attached) - valid frame numbers
External Email - Use Caution
Hi Anastasia, Thank you for answering! I think you are right and the problem is there, when checking the number of slices in the dwindling file I get: dimensions: 104 x 104 x 72
Although the original dwindling data has: 104 x 104 x 72 x 111
voxel sizes: 2.019231, 2.019231, 2.000000 type: SHORT (4) fov: 210.000 dof: 0 xstart: -105.0, xend: 105.0 ystart: -105.0, yend: 105.0 zstart: -72.0, zend: 72.0 TR: 3670.00 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 = -0.9897, y_r = 0.1290, z_r = -0.0618, c_r = -1.2731 : x_a = -0.1108, y_a = -0.9647, z_a = -0.2389, c_a = -22.2682 : x_s = -0.0904, y_s = -0.2296, z_s = 0.9691, c_s = 12.8890 Orientation : LPS Primary Slice Direction: axial
voxel to ras transform: -1.9985 0.2605 -0.1236 93.5531 -0.2238 -1.9480 -0.4778 107.8607 -0.1826 -0.4636 1.9382 -23.2834 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant 8.15459
ras to voxel transform: -0.4901 -0.0549 -0.0448 50.7312 0.0639 -0.4778 -0.1137 42.9079 -0.0309 -0.1194 0.4845 27.0558 0.0000 0.0000 0.0000 1.0000
I don’t understand why, given those are outputs of recon-all ..
Do you think you know what’s happening?
Thank you very much!
Best, Cecilia
Cecilia Mazzetti - Ph.D. Researcher Donders Centre for Cognitive Neuroimaging, room 2.257 Kapittelweg 29 | 6525 EN Nijmegen
freesurfer@nmr.mgh.harvard.edu
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Mazzetti, C. (Cecilia) -
Yendiki, Anastasia