Hi all -- I have edited an anatomical volume (using AFNI's 3dcalc and 3dLRflip commands), and the final volume looks good. My reading is that mri_convert should not have trouble recognizing an afni BRIK file. However, the error is: unknown file type for file ... (The original Volume+orig.BRIK file went through the mri_convert step with no problem.) Is there another way to convert the final merged+orig file below into an 001.mgz file? Or should I be using a flagged option that I'm unaware of? Help appreciated. Joan
For anyone interested in the steps I took in AFNI to make the transformed brain, they are:
History of inputs to 3dcalc === [joan@cronus: Sat Feb 3 16:35:56 2007] === Input a: [joan@cronus: Sat Feb 3 16:35:56 2007] [joan@cronus: Fri Dec 22 16:18:07 2006] to3d -spgr -prefix Volume -session Results -view orig -xFOV 120.003A-119.997P -yFOV 120.0S-120.0I -zSLAB 88.733L-89.767R '3D:0:8432:256:256:1:Volume/I*' [joan@cronus: Sat Feb 3 16:20:52 2007] Dataset Copy {Input: Dataset=005/Results/Volume+orig.HEAD} {Output: Prefix=rotated} {Data Fill: Method=Data [All]} [joan@cronus: Sat Feb 3 16:24:43 2007] plug_nudge: -rotate 0.00I 0.00R -6.00A -ashift 0.31S -2.98L 0.00P [joan@cronus: Sat Feb 3 16:35:56 2007] === Input b: [joan@cronus: Sat Feb 3 16:35:56 2007] [joan@cronus: Fri Dec 22 16:18:07 2006] to3d -spgr -prefix Volume -session Results -view orig -xFOV 120.003A-119.997P -yFOV 120.0S-120.0I -zSLAB 88.733L-89.767R '3D:0:8432:256:256:1:Volume/I*' [joan@cronus: Sat Feb 3 16:20:52 2007] Dataset Copy {Input: Dataset=005/Results/Volume+orig.HEAD} {Output: Prefix=rotated} {Data Fill: Method=Data [All]} [joan@cronus: Sat Feb 3 16:24:43 2007] plug_nudge: -rotate 0.00I 0.00R -6.00A -ashift 0.31S -2.98L 0.00P [joan@cronus: Sat Feb 3 16:31:05 2007] 3dLRflip -prefix flip rotated+orig. [joan@cronus: Sat Feb 3 16:35:56 2007] === Input c: [joan@cronus: Sat Feb 3 16:35:56 2007] [joan@cronus: Fri Dec 22 16:18:07 2006] to3d -spgr -prefix Volume -session Results -view orig -xFOV 120.003A-119.997P -yFOV 120.0S-120.0I -zSLAB 88.733L-89.767R '3D:0:8432:256:256:1:Volume/I*' [joan@cronus: Sun Jan 14 20:52:47 2007] Dataset Copy {Input: Dataset=005/Results/Volume+orig.HEAD} {Output: Prefix=Lesion} {Data Fill: Method=Zero [One]} [joan@cronus: Sat Feb 3 16:25:29 2007] Dataset Copy {Input: Dataset=005/Results/Lesion+orig.HEAD} {Output: Prefix=lesion_rot} {Data Fill: Method=Data [All]} [joan@cronus: Sat Feb 3 16:26:25 2007] plug_nudge: -rotate 0.00I 0.00R -6.00A -ashift 0.00S -3.00L 0.00P [joan@cronus: Sat Feb 3 16:35:56 2007] =================================== [joan@cronus: Sat Feb 3 16:35:56 2007] 3dcalc -a rotated+orig. -b flip+orig. -c lesion_rot+orig. -expr '(1-c)*a+c*b' -prefix merged
These steps created merged+orig.BRIK and merged+orig.HEAD that look fine in afni.
Joan,
Try using the flag "-it brik" or "-it afni".
The "--help" flag to mri_convert lists all its options.
Nick
On Sun, 2007-02-04 at 14:07 -0600, Joan Fisher wrote:
Hi all -- I have edited an anatomical volume (using AFNI's 3dcalc and 3dLRflip commands), and the final volume looks good. My reading is that mri_convert should not have trouble recognizing an afni BRIK file. However, the error is: unknown file type for file ... (The original Volume+orig.BRIK file went through the mri_convert step with no problem.) Is there another way to convert the final merged+orig file below into an 001.mgz file? Or should I be using a flagged option that I'm unaware of? Help appreciated. Joan
For anyone interested in the steps I took in AFNI to make the transformed brain, they are:
History of inputs to 3dcalc === [joan@cronus: Sat Feb 3 16:35:56 2007] === Input a: [joan@cronus: Sat Feb 3 16:35:56 2007] [joan@cronus: Fri Dec 22 16:18:07 2006] to3d -spgr -prefix Volume -session Results -view orig -xFOV 120.003A-119.997P -yFOV 120.0S-120.0I -zSLAB 88.733L-89.767R '3D:0:8432:256:256:1:Volume/I*' [joan@cronus: Sat Feb 3 16:20:52 2007] Dataset Copy {Input: Dataset=005/Results/Volume+orig.HEAD} {Output: Prefix=rotated} {Data Fill: Method=Data [All]} [joan@cronus: Sat Feb 3 16:24:43 2007] plug_nudge: -rotate 0.00I 0.00R -6.00A -ashift 0.31S -2.98L 0.00P [joan@cronus: Sat Feb 3 16:35:56 2007] === Input b: [joan@cronus: Sat Feb 3 16:35:56 2007] [joan@cronus: Fri Dec 22 16:18:07 2006] to3d -spgr -prefix Volume -session Results -view orig -xFOV 120.003A-119.997P -yFOV 120.0S-120.0I -zSLAB 88.733L-89.767R '3D:0:8432:256:256:1:Volume/I*' [joan@cronus: Sat Feb 3 16:20:52 2007] Dataset Copy {Input: Dataset=005/Results/Volume+orig.HEAD} {Output: Prefix=rotated} {Data Fill: Method=Data [All]} [joan@cronus: Sat Feb 3 16:24:43 2007] plug_nudge: -rotate 0.00I 0.00R -6.00A -ashift 0.31S -2.98L 0.00P [joan@cronus: Sat Feb 3 16:31:05 2007] 3dLRflip -prefix flip rotated+orig. [joan@cronus: Sat Feb 3 16:35:56 2007] === Input c: [joan@cronus: Sat Feb 3 16:35:56 2007] [joan@cronus: Fri Dec 22 16:18:07 2006] to3d -spgr -prefix Volume -session Results -view orig -xFOV 120.003A-119.997P -yFOV 120.0S-120.0I -zSLAB 88.733L-89.767R '3D:0:8432:256:256:1:Volume/I*' [joan@cronus: Sun Jan 14 20:52:47 2007] Dataset Copy {Input: Dataset=005/Results/Volume+orig.HEAD} {Output: Prefix=Lesion} {Data Fill: Method=Zero [One]} [joan@cronus: Sat Feb 3 16:25:29 2007] Dataset Copy {Input: Dataset=005/Results/Lesion+orig.HEAD} {Output: Prefix=lesion_rot} {Data Fill: Method=Data [All]} [joan@cronus: Sat Feb 3 16:26:25 2007] plug_nudge: -rotate 0.00I 0.00R -6.00A -ashift 0.00S -3.00L 0.00P [joan@cronus: Sat Feb 3 16:35:56 2007] =================================== [joan@cronus: Sat Feb 3 16:35:56 2007] 3dcalc -a rotated+orig. -b flip+orig. -c lesion_rot+orig. -expr '(1-c)*a+c*b' -prefix merged
These steps created merged+orig.BRIK and merged+orig.HEAD that look fine in afni.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Joan,
what exactly are you trying to do? You should be able to specify the cc, wm and pons points to mri_fill without having to synthesize another hemi.
Bruce On Sun, 4 Feb 2007, Joan Fisher wrote:
Hi all -- I have edited an anatomical volume (using AFNI's 3dcalc and 3dLRflip commands), and the final volume looks good. My reading is that mri_convert should not have trouble recognizing an afni BRIK file. However, the error is: unknown file type for file ... (The original Volume+orig.BRIK file went through the mri_convert step with no problem.) Is there another way to convert the final merged+orig file below into an 001.mgz file? Or should I be using a flagged option that I'm unaware of? Help appreciated. Joan
For anyone interested in the steps I took in AFNI to make the transformed brain, they are:
History of inputs to 3dcalc === [joan@cronus: Sat Feb 3 16:35:56 2007] === Input a: [joan@cronus: Sat Feb 3 16:35:56 2007] [joan@cronus: Fri Dec 22 16:18:07 2006] to3d -spgr -prefix Volume -session Results -view orig -xFOV 120.003A-119.997P -yFOV 120.0S-120.0I -zSLAB 88.733L-89.767R '3D:0:8432:256:256:1:Volume/I*' [joan@cronus: Sat Feb 3 16:20:52 2007] Dataset Copy {Input: Dataset=005/Results/Volume+orig.HEAD} {Output: Prefix=rotated} {Data Fill: Method=Data [All]} [joan@cronus: Sat Feb 3 16:24:43 2007] plug_nudge: -rotate 0.00I 0.00R -6.00A -ashift 0.31S -2.98L 0.00P [joan@cronus: Sat Feb 3 16:35:56 2007] === Input b: [joan@cronus: Sat Feb 3 16:35:56 2007] [joan@cronus: Fri Dec 22 16:18:07 2006] to3d -spgr -prefix Volume -session Results -view orig -xFOV 120.003A-119.997P -yFOV 120.0S-120.0I -zSLAB 88.733L-89.767R '3D:0:8432:256:256:1:Volume/I*' [joan@cronus: Sat Feb 3 16:20:52 2007] Dataset Copy {Input: Dataset=005/Results/Volume+orig.HEAD} {Output: Prefix=rotated} {Data Fill: Method=Data [All]} [joan@cronus: Sat Feb 3 16:24:43 2007] plug_nudge: -rotate 0.00I 0.00R -6.00A -ashift 0.31S -2.98L 0.00P [joan@cronus: Sat Feb 3 16:31:05 2007] 3dLRflip -prefix flip rotated+orig. [joan@cronus: Sat Feb 3 16:35:56 2007] === Input c: [joan@cronus: Sat Feb 3 16:35:56 2007] [joan@cronus: Fri Dec 22 16:18:07 2006] to3d -spgr -prefix Volume -session Results -view orig -xFOV 120.003A-119.997P -yFOV 120.0S-120.0I -zSLAB 88.733L-89.767R '3D:0:8432:256:256:1:Volume/I*' [joan@cronus: Sun Jan 14 20:52:47 2007] Dataset Copy {Input: Dataset=005/Results/Volume+orig.HEAD} {Output: Prefix=Lesion} {Data Fill: Method=Zero [One]} [joan@cronus: Sat Feb 3 16:25:29 2007] Dataset Copy {Input: Dataset=005/Results/Lesion+orig.HEAD} {Output: Prefix=lesion_rot} {Data Fill: Method=Data [All]} [joan@cronus: Sat Feb 3 16:26:25 2007] plug_nudge: -rotate 0.00I 0.00R -6.00A -ashift 0.00S -3.00L 0.00P [joan@cronus: Sat Feb 3 16:35:56 2007] =================================== [joan@cronus: Sat Feb 3 16:35:56 2007] 3dcalc -a rotated+orig. -b flip+orig. -c lesion_rot+orig. -expr '(1-c)*a+c*b' -prefix merged
These steps created merged+orig.BRIK and merged+orig.HEAD that look fine in afni.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Joan Fisher -
Nick Schmansky