Hi, I keep getting an error message after I run Create Surface. It is similar to questions found in the archive but those solutions did not work and this problem did not occur for the first 2 brains I reconstructed. I get an alert that the Images (filled): /subjectsdir/mri/filled/COR-001 not found. wmfill first. I thought the first step was to fill the wm so these files should have already been created. Thanks for any help, Margaret
Hi Margaret,
we need more information than that. Can you send us log files from trying to run mri_fill? Is it finding the cutting planes? Have you tried specifying them manually?
cheers, Bruce
On Tue, 30 Nov 2004, Margaret Duff wrote:
Hi, I keep getting an error message after I run Create Surface. It is similar to questions found in the archive but those solutions did not work and this problem did not occur for the first 2 brains I reconstructed. I get an alert that the Images (filled): /subjectsdir/mri/filled/COR-001 not found. wmfill first. I thought the first step was to fill the wm so these files should have already been created. Thanks for any help, Margaret
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The log file is below. And at the end it says command finished, not that something went wrong. I am not sure about the cutting planes or how to specify them manually. Thanks for your help. Margaret
/space/lyon/1/home/inverse/freesurfer_alpha/bin/Linux/mri_fill -lval 255 -rval 80 -ccmask -T 1 -L /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/tmp/ponscall.dat /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/wm /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/filled using 255 as fill val for left hemisphere. using 80 as fill val for right hemisphere. not using corpus callosum to mask possible location of pons. logging cutting plane coordinates to /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/tmp/ponscall.dat... voxel to talairach voxel transform 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; updating initial cc seed to Tal vol (121.00, 151.00, 77.00) TAL (15.27, 0.28, -12.82) Looking for area (min, max) = (350, 1400) area[0] = 365 (min = 350, max = 1400), aspect = 1.27 (min = 0.10, max = 0.75) need search nearby using +/- offset search region where offset is 3..... using +/- offset search region where offset is 6..... using +/- offset search region where offset is 9..... using +/- offset search region where offset is 12..... using +/- offset search region where offset is 15..... using +/- offset search region where offset is 18..... using +/- offset search region where offset is 21..... area[0] = 1210 (min = 350, max = 1400), aspect = 0.37 (min = 0.10, max = 0.75) corpus callosum seed point found at Tal vol: (121, 125, 162) TAL: (15.27, 85.28, 13.18) min_slice = -1, min_area = 65536 Looking for area (min, max) = (350, 1400) area[0] = 5435 (min = 350, max = 1400), aspect = 0.50 (min = 0.10, max = 0.75) need search nearby using +/- offset search region where offset is 3..... using +/- offset search region where offset is 6..... using +/- offset search region where offset is 9..... area[0] = 488 (min = 350, max = 1400), aspect = 0.26 (min = 0.10, max = 0.75) corpus callosum seed point found at Tal vol: (127, 97, 124) TAL: (9.27, 47.28, 41.18) min_slice = -1, min_area = 65536 /space/lyon/1/home/inverse/freesurfer_alpha/bin/Linux/mri_fill: could not find corpus callosum No such file or directory INFO: volume does not have linear_transform set nor lta is given by option.-xform. INFO: use identity matrix as the talairach transform. INFO: use src volume parameters for the talairach volume. INFO: Modifying dst c_(r,a,s), using the transform dst
Command Finished
On Tue, 30 Nov 2004, Bruce Fischl wrote:
Hi Margaret,
we need more information than that. Can you send us log files from trying to run mri_fill? Is it finding the cutting planes? Have you tried specifying them manually?
cheers, Bruce
On Tue, 30 Nov 2004, Margaret Duff wrote:
Hi, I keep getting an error message after I run Create Surface. It is similar to questions found in the archive but those solutions did not work and this problem did not occur for the first 2 brains I reconstructed. I get an alert that the Images (filled): /subjectsdir/mri/filled/COR-001 not found. wmfill first. I thought the first step was to fill the wm so these files should have already been created. Thanks for any help, Margaret
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi,
The log says that it could not find $subject/mri/transforms/talairach.xfm for this volume.
Tosa
Margaret Duff wrote:
The log file is below. And at the end it says command finished, not that something went wrong. I am not sure about the cutting planes or how to specify them manually. Thanks for your help. Margaret
/space/lyon/1/home/inverse/freesurfer_alpha/bin/Linux/mri_fill -lval 255 -rval 80 -ccmask -T 1 -L /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/tmp/ponscall.dat /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/wm /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/filled using 255 as fill val for left hemisphere. using 80 as fill val for right hemisphere. not using corpus callosum to mask possible location of pons. logging cutting plane coordinates to /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/tmp/ponscall.dat... voxel to talairach voxel transform 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; updating initial cc seed to Tal vol (121.00, 151.00, 77.00) TAL (15.27, 0.28, -12.82) Looking for area (min, max) = (350, 1400) area[0] = 365 (min = 350, max = 1400), aspect = 1.27 (min = 0.10, max = 0.75) need search nearby using +/- offset search region where offset is 3..... using +/- offset search region where offset is 6..... using +/- offset search region where offset is 9..... using +/- offset search region where offset is 12..... using +/- offset search region where offset is 15..... using +/- offset search region where offset is 18..... using +/- offset search region where offset is 21..... area[0] = 1210 (min = 350, max = 1400), aspect = 0.37 (min = 0.10, max = 0.75) corpus callosum seed point found at Tal vol: (121, 125, 162) TAL: (15.27, 85.28, 13.18) min_slice = -1, min_area = 65536 Looking for area (min, max) = (350, 1400) area[0] = 5435 (min = 350, max = 1400), aspect = 0.50 (min = 0.10, max = 0.75) need search nearby using +/- offset search region where offset is 3..... using +/- offset search region where offset is 6..... using +/- offset search region where offset is 9..... area[0] = 488 (min = 350, max = 1400), aspect = 0.26 (min = 0.10, max = 0.75) corpus callosum seed point found at Tal vol: (127, 97, 124) TAL: (9.27, 47.28, 41.18) min_slice = -1, min_area = 65536 /space/lyon/1/home/inverse/freesurfer_alpha/bin/Linux/mri_fill: could not find corpus callosum No such file or directory INFO: volume does not have linear_transform set nor lta is given by option.-xform. INFO: use identity matrix as the talairach transform. INFO: use src volume parameters for the talairach volume. INFO: Modifying dst c_(r,a,s), using the transform dst
Command Finished
On Tue, 30 Nov 2004, Bruce Fischl wrote:
Hi Margaret,
we need more information than that. Can you send us log files from trying to run mri_fill? Is it finding the cutting planes? Have you tried specifying them manually?
cheers, Bruce
On Tue, 30 Nov 2004, Margaret Duff wrote:
Hi, I keep getting an error message after I run Create Surface. It is similar to questions found in the archive but those solutions did not work and this problem did not occur for the first 2 brains I reconstructed. I get an alert that the Images (filled): /subjectsdir/mri/filled/COR-001 not found. wmfill first. I thought the first step was to fill the wm so these files should have already been created. Thanks for any help, Margaret
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
So, even though it says it will substitute the identity matrix for the transform, I still need a transform or it won't work? Is the only way to create a transform with that separate MNI software? Thanks, Margaret
On Wed, 1 Dec 2004, Yasunari Tosa wrote:
Hi,
The log says that it could not find $subject/mri/transforms/talairach.xfm for this volume.
Tosa
Margaret Duff wrote:
The log file is below. And at the end it says command finished, not that something went wrong. I am not sure about the cutting planes or how to specify them manually. Thanks for your help. Margaret
/space/lyon/1/home/inverse/freesurfer_alpha/bin/Linux/mri_fill -lval 255 -rval 80 -ccmask -T 1 -L /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/tmp/ponscall.dat /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/wm /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/filled using 255 as fill val for left hemisphere. using 80 as fill val for right hemisphere. not using corpus callosum to mask possible location of pons. logging cutting plane coordinates to /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/tmp/ponscall.dat... voxel to talairach voxel transform 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; updating initial cc seed to Tal vol (121.00, 151.00, 77.00) TAL (15.27, 0.28, -12.82) Looking for area (min, max) = (350, 1400) area[0] = 365 (min = 350, max = 1400), aspect = 1.27 (min = 0.10, max = 0.75) need search nearby using +/- offset search region where offset is 3..... using +/- offset search region where offset is 6..... using +/- offset search region where offset is 9..... using +/- offset search region where offset is 12..... using +/- offset search region where offset is 15..... using +/- offset search region where offset is 18..... using +/- offset search region where offset is 21..... area[0] = 1210 (min = 350, max = 1400), aspect = 0.37 (min = 0.10, max = 0.75) corpus callosum seed point found at Tal vol: (121, 125, 162) TAL: (15.27, 85.28, 13.18) min_slice = -1, min_area = 65536 Looking for area (min, max) = (350, 1400) area[0] = 5435 (min = 350, max = 1400), aspect = 0.50 (min = 0.10, max = 0.75) need search nearby using +/- offset search region where offset is 3..... using +/- offset search region where offset is 6..... using +/- offset search region where offset is 9..... area[0] = 488 (min = 350, max = 1400), aspect = 0.26 (min = 0.10, max = 0.75) corpus callosum seed point found at Tal vol: (127, 97, 124) TAL: (9.27, 47.28, 41.18) min_slice = -1, min_area = 65536 /space/lyon/1/home/inverse/freesurfer_alpha/bin/Linux/mri_fill: could not find corpus callosum No such file or directory INFO: volume does not have linear_transform set nor lta is given by option.-xform. INFO: use identity matrix as the talairach transform. INFO: use src volume parameters for the talairach volume. INFO: Modifying dst c_(r,a,s), using the transform dst
Command Finished
On Tue, 30 Nov 2004, Bruce Fischl wrote:
Hi Margaret,
we need more information than that. Can you send us log files from trying to run mri_fill? Is it finding the cutting planes? Have you tried specifying them manually?
cheers, Bruce
On Tue, 30 Nov 2004, Margaret Duff wrote:
Hi, I keep getting an error message after I run Create Surface. It is similar to questions found in the archive but those solutions did not work and this problem did not occur for the first 2 brains I reconstructed. I get an alert that the Images (filled): /subjectsdir/mri/filled/COR-001 not found. wmfill first. I thought the first step was to fill the wm so these files should have already been created. Thanks for any help, Margaret
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi,
The identity matrix did not work as you found. If you have a good talairach.xfm, it should work better.
You can try specifying the seed corpus callosum position:
Seed point options in Talairach coordinates (RAS): -C <x> <y> <z> - the Talairach coords of the seed for the corpus callosum
Alternative seed point options in voxel coordinates: -CV <x> <y> <z> - the voxel coords of the seed for the corpus callosum
Tosa
Margaret Duff wrote:
So, even though it says it will substitute the identity matrix for the transform, I still need a transform or it won't work? Is the only way to create a transform with that separate MNI software? Thanks, Margaret
On Wed, 1 Dec 2004, Yasunari Tosa wrote:
Hi,
The log says that it could not find $subject/mri/transforms/talairach.xfm for this volume.
Tosa
Margaret Duff wrote:
The log file is below. And at the end it says command finished, not that something went wrong. I am not sure about the cutting planes or how to specify them manually. Thanks for your help. Margaret
/space/lyon/1/home/inverse/freesurfer_alpha/bin/Linux/mri_fill -lval 255 -rval 80 -ccmask -T 1 -L /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/tmp/ponscall.dat /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/wm /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/filled using 255 as fill val for left hemisphere. using 80 as fill val for right hemisphere. not using corpus callosum to mask possible location of pons. logging cutting plane coordinates to /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/tmp/ponscall.dat... voxel to talairach voxel transform 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; updating initial cc seed to Tal vol (121.00, 151.00, 77.00) TAL (15.27, 0.28, -12.82) Looking for area (min, max) = (350, 1400) area[0] = 365 (min = 350, max = 1400), aspect = 1.27 (min = 0.10, max = 0.75) need search nearby using +/- offset search region where offset is 3..... using +/- offset search region where offset is 6..... using +/- offset search region where offset is 9..... using +/- offset search region where offset is 12..... using +/- offset search region where offset is 15..... using +/- offset search region where offset is 18..... using +/- offset search region where offset is 21..... area[0] = 1210 (min = 350, max = 1400), aspect = 0.37 (min = 0.10, max = 0.75) corpus callosum seed point found at Tal vol: (121, 125, 162) TAL: (15.27, 85.28, 13.18) min_slice = -1, min_area = 65536 Looking for area (min, max) = (350, 1400) area[0] = 5435 (min = 350, max = 1400), aspect = 0.50 (min = 0.10, max = 0.75) need search nearby using +/- offset search region where offset is 3..... using +/- offset search region where offset is 6..... using +/- offset search region where offset is 9..... area[0] = 488 (min = 350, max = 1400), aspect = 0.26 (min = 0.10, max = 0.75) corpus callosum seed point found at Tal vol: (127, 97, 124) TAL: (9.27, 47.28, 41.18) min_slice = -1, min_area = 65536 /space/lyon/1/home/inverse/freesurfer_alpha/bin/Linux/mri_fill: could not find corpus callosum No such file or directory INFO: volume does not have linear_transform set nor lta is given by option.-xform. INFO: use identity matrix as the talairach transform. INFO: use src volume parameters for the talairach volume. INFO: Modifying dst c_(r,a,s), using the transform dst
Command Finished
On Tue, 30 Nov 2004, Bruce Fischl wrote:
Hi Margaret,
we need more information than that. Can you send us log files from trying to run mri_fill? Is it finding the cutting planes? Have you tried specifying them manually?
cheers, Bruce
On Tue, 30 Nov 2004, Margaret Duff wrote:
Hi, I keep getting an error message after I run Create Surface. It is similar to questions found in the archive but those solutions did not work and this problem did not occur for the first 2 brains I reconstructed. I get an alert that the Images (filled): /subjectsdir/mri/filled/COR-001 not found. wmfill first. I thought the first step was to fill the wm so these files should have already been created. Thanks for any help, Margaret
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Margaret,
if no talairach.xfm exists, then the fill may still find the cc and pons, but it might not. You can always specify them manually be finding a sagittal slice in which the cc is disconnected and a horizontal slice above the cerebellar peduncles where the pons is disconnected.
cheers, Bruce
On Wed, 1 Dec 2004, Margaret Duff wrote:
The log file is below. And at the end it says command finished, not that something went wrong. I am not sure about the cutting planes or how to specify them manually. Thanks for your help. Margaret
/space/lyon/1/home/inverse/freesurfer_alpha/bin/Linux/mri_fill -lval 255 -rval 80 -ccmask -T 1 -L /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/tmp/ponscall.dat /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/wm /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/filled using 255 as fill val for left hemisphere. using 80 as fill val for right hemisphere. not using corpus callosum to mask possible location of pons. logging cutting plane coordinates to /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/tmp/ponscall.dat... voxel to talairach voxel transform 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; updating initial cc seed to Tal vol (121.00, 151.00, 77.00) TAL (15.27, 0.28, -12.82) Looking for area (min, max) = (350, 1400) area[0] = 365 (min = 350, max = 1400), aspect = 1.27 (min = 0.10, max = 0.75) need search nearby using +/- offset search region where offset is 3..... using +/- offset search region where offset is 6..... using +/- offset search region where offset is 9..... using +/- offset search region where offset is 12..... using +/- offset search region where offset is 15..... using +/- offset search region where offset is 18..... using +/- offset search region where offset is 21..... area[0] = 1210 (min = 350, max = 1400), aspect = 0.37 (min = 0.10, max = 0.75) corpus callosum seed point found at Tal vol: (121, 125, 162) TAL: (15.27, 85.28, 13.18) min_slice = -1, min_area = 65536 Looking for area (min, max) = (350, 1400) area[0] = 5435 (min = 350, max = 1400), aspect = 0.50 (min = 0.10, max = 0.75) need search nearby using +/- offset search region where offset is 3..... using +/- offset search region where offset is 6..... using +/- offset search region where offset is 9..... area[0] = 488 (min = 350, max = 1400), aspect = 0.26 (min = 0.10, max = 0.75) corpus callosum seed point found at Tal vol: (127, 97, 124) TAL: (9.27, 47.28, 41.18) min_slice = -1, min_area = 65536 /space/lyon/1/home/inverse/freesurfer_alpha/bin/Linux/mri_fill: could not find corpus callosum No such file or directory INFO: volume does not have linear_transform set nor lta is given by option.-xform. INFO: use identity matrix as the talairach transform. INFO: use src volume parameters for the talairach volume. INFO: Modifying dst c_(r,a,s), using the transform dst
Command Finished
On Tue, 30 Nov 2004, Bruce Fischl wrote:
Hi Margaret,
we need more information than that. Can you send us log files from trying to run mri_fill? Is it finding the cutting planes? Have you tried specifying them manually?
cheers, Bruce
On Tue, 30 Nov 2004, Margaret Duff wrote:
Hi, I keep getting an error message after I run Create Surface. It is similar to questions found in the archive but those solutions did not work and this problem did not occur for the first 2 brains I reconstructed. I get an alert that the Images (filled): /subjectsdir/mri/filled/COR-001 not found. wmfill first. I thought the first step was to fill the wm so these files should have already been created. Thanks for any help, Margaret
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi, I tried to manually set the cutting planes, but I was unable to get the create surface to run. My subjects info is at /space/troy/1/users/FREESURFER/SM2S4_freesurfer and I tried to specify coordinates (121 90 139) for the CC and (131 159 118) for the pons. I used the manuals troubleshooting to guide me, but is still cannot find them. The logfile I got is below. Could something besides specifying these coordinates be going wrong? Thanks, Margaret
/space/lyon/1/home/inverse/freesurfer_alpha/bin/Linux/mri_fill -lval 255 -rval 80 -P 131 159 118 -C 121 90 139 -ccmask -T 1 -L /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/tmp/ponscall.dat /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/wm /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/filled using 255 as fill val for left hemisphere. using 80 as fill val for right hemisphere. using Talairach position (131, 159, 118) as pons seed point using Talairach position (121, 90, 139) as corpus callosum seed point not using corpus callosum to mask possible location of pons. logging cutting plane coordinates to /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/tmp/ponscall.dat... voxel to talairach voxel transform 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; The seed point (121.00, 90.00, 139.00) is mapped to a voxel (15.27, -0.82. 166.72). Make sure that the seed point is given in talaraich position or use -CV option INFO: volume does not have linear_transform set nor lta is given by option.-xform. INFO: use identity matrix as the talairach transform. INFO: use src volume parameters for the talairach volume. INFO: Modifying dst c_(r,a,s), using the transform dst Using the seed to calculate the cutting plane Verify whether the seed point is inside the volume first
Command Finished
On Wed, 1 Dec 2004, Bruce Fischl wrote:
Hi Margaret,
if no talairach.xfm exists, then the fill may still find the cc and pons, but it might not. You can always specify them manually be finding a sagittal slice in which the cc is disconnected and a horizontal slice above the cerebellar peduncles where the pons is disconnected.
cheers, Bruce
On Wed, 1 Dec 2004, Margaret Duff wrote:
The log file is below. And at the end it says command finished, not that something went wrong. I am not sure about the cutting planes or how to specify them manually. Thanks for your help. Margaret
/space/lyon/1/home/inverse/freesurfer_alpha/bin/Linux/mri_fill -lval 255 -rval 80 -ccmask -T 1 -L /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/tmp/ponscall.dat /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/wm /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/filled using 255 as fill val for left hemisphere. using 80 as fill val for right hemisphere. not using corpus callosum to mask possible location of pons. logging cutting plane coordinates to /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/tmp/ponscall.dat... voxel to talairach voxel transform 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; updating initial cc seed to Tal vol (121.00, 151.00, 77.00) TAL (15.27, 0.28, -12.82) Looking for area (min, max) = (350, 1400) area[0] = 365 (min = 350, max = 1400), aspect = 1.27 (min = 0.10, max = 0.75) need search nearby using +/- offset search region where offset is 3..... using +/- offset search region where offset is 6..... using +/- offset search region where offset is 9..... using +/- offset search region where offset is 12..... using +/- offset search region where offset is 15..... using +/- offset search region where offset is 18..... using +/- offset search region where offset is 21..... area[0] = 1210 (min = 350, max = 1400), aspect = 0.37 (min = 0.10, max = 0.75) corpus callosum seed point found at Tal vol: (121, 125, 162) TAL: (15.27, 85.28, 13.18) min_slice = -1, min_area = 65536 Looking for area (min, max) = (350, 1400) area[0] = 5435 (min = 350, max = 1400), aspect = 0.50 (min = 0.10, max = 0.75) need search nearby using +/- offset search region where offset is 3..... using +/- offset search region where offset is 6..... using +/- offset search region where offset is 9..... area[0] = 488 (min = 350, max = 1400), aspect = 0.26 (min = 0.10, max = 0.75) corpus callosum seed point found at Tal vol: (127, 97, 124) TAL: (9.27, 47.28, 41.18) min_slice = -1, min_area = 65536 /space/lyon/1/home/inverse/freesurfer_alpha/bin/Linux/mri_fill: could not find corpus callosum No such file or directory INFO: volume does not have linear_transform set nor lta is given by option.-xform. INFO: use identity matrix as the talairach transform. INFO: use src volume parameters for the talairach volume. INFO: Modifying dst c_(r,a,s), using the transform dst
Command Finished
On Tue, 30 Nov 2004, Bruce Fischl wrote:
Hi Margaret,
we need more information than that. Can you send us log files from trying to run mri_fill? Is it finding the cutting planes? Have you tried specifying them manually?
cheers, Bruce
On Tue, 30 Nov 2004, Margaret Duff wrote:
Hi, I keep getting an error message after I run Create Surface. It is similar to questions found in the archive but those solutions did not work and this problem did not occur for the first 2 brains I reconstructed. I get an alert that the Images (filled): /subjectsdir/mri/filled/COR-001 not found. wmfill first. I thought the first step was to fill the wm so these files should have already been created. Thanks for any help, Margaret
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi, Margaret
The head is tilted almost 10 degrees. This makes it difficult to cut the brain into two. You really need the talairach transform or any other transform to straighten up the head to find the cutting planes.
I just copied your volume and ran recon-all -stage1 and "mri_fill" created a very clean filled volume.
Tosa
Margaret Duff wrote:
Hi, I tried to manually set the cutting planes, but I was unable to get the create surface to run. My subjects info is at /space/troy/1/users/FREESURFER/SM2S4_freesurfer and I tried to specify coordinates (121 90 139) for the CC and (131 159 118) for the pons. I used the manuals troubleshooting to guide me, but is still cannot find them. The logfile I got is below. Could something besides specifying these coordinates be going wrong? Thanks, Margaret
/space/lyon/1/home/inverse/freesurfer_alpha/bin/Linux/mri_fill -lval 255 -rval 80 -P 131 159 118 -C 121 90 139 -ccmask -T 1 -L /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/tmp/ponscall.dat /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/wm /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/filled using 255 as fill val for left hemisphere. using 80 as fill val for right hemisphere. using Talairach position (131, 159, 118) as pons seed point using Talairach position (121, 90, 139) as corpus callosum seed point not using corpus callosum to mask possible location of pons. logging cutting plane coordinates to /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/tmp/ponscall.dat... voxel to talairach voxel transform 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; The seed point (121.00, 90.00, 139.00) is mapped to a voxel (15.27, -0.82. 166.72). Make sure that the seed point is given in talaraich position or use -CV option INFO: volume does not have linear_transform set nor lta is given by option.-xform. INFO: use identity matrix as the talairach transform. INFO: use src volume parameters for the talairach volume. INFO: Modifying dst c_(r,a,s), using the transform dst Using the seed to calculate the cutting plane Verify whether the seed point is inside the volume first
Command Finished
On Wed, 1 Dec 2004, Bruce Fischl wrote:
Hi Margaret,
if no talairach.xfm exists, then the fill may still find the cc and pons, but it might not. You can always specify them manually be finding a sagittal slice in which the cc is disconnected and a horizontal slice above the cerebellar peduncles where the pons is disconnected.
cheers, Bruce
On Wed, 1 Dec 2004, Margaret Duff wrote:
The log file is below. And at the end it says command finished, not that something went wrong. I am not sure about the cutting planes or how to specify them manually. Thanks for your help. Margaret
/space/lyon/1/home/inverse/freesurfer_alpha/bin/Linux/mri_fill -lval 255 -rval 80 -ccmask -T 1 -L /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/tmp/ponscall.dat /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/wm /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/filled using 255 as fill val for left hemisphere. using 80 as fill val for right hemisphere. not using corpus callosum to mask possible location of pons. logging cutting plane coordinates to /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/tmp/ponscall.dat... voxel to talairach voxel transform 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; updating initial cc seed to Tal vol (121.00, 151.00, 77.00) TAL (15.27, 0.28, -12.82) Looking for area (min, max) = (350, 1400) area[0] = 365 (min = 350, max = 1400), aspect = 1.27 (min = 0.10, max = 0.75) need search nearby using +/- offset search region where offset is 3..... using +/- offset search region where offset is 6..... using +/- offset search region where offset is 9..... using +/- offset search region where offset is 12..... using +/- offset search region where offset is 15..... using +/- offset search region where offset is 18..... using +/- offset search region where offset is 21..... area[0] = 1210 (min = 350, max = 1400), aspect = 0.37 (min = 0.10, max = 0.75) corpus callosum seed point found at Tal vol: (121, 125, 162) TAL: (15.27, 85.28, 13.18) min_slice = -1, min_area = 65536 Looking for area (min, max) = (350, 1400) area[0] = 5435 (min = 350, max = 1400), aspect = 0.50 (min = 0.10, max = 0.75) need search nearby using +/- offset search region where offset is 3..... using +/- offset search region where offset is 6..... using +/- offset search region where offset is 9..... area[0] = 488 (min = 350, max = 1400), aspect = 0.26 (min = 0.10, max = 0.75) corpus callosum seed point found at Tal vol: (127, 97, 124) TAL: (9.27, 47.28, 41.18) min_slice = -1, min_area = 65536 /space/lyon/1/home/inverse/freesurfer_alpha/bin/Linux/mri_fill: could not find corpus callosum No such file or directory INFO: volume does not have linear_transform set nor lta is given by option.-xform. INFO: use identity matrix as the talairach transform. INFO: use src volume parameters for the talairach volume. INFO: Modifying dst c_(r,a,s), using the transform dst
Command Finished
On Tue, 30 Nov 2004, Bruce Fischl wrote:
Hi Margaret,
we need more information than that. Can you send us log files from trying to run mri_fill? Is it finding the cutting planes? Have you tried specifying them manually?
cheers, Bruce
On Tue, 30 Nov 2004, Margaret Duff wrote:
Hi, I keep getting an error message after I run Create Surface. It is similar to questions found in the archive but those solutions did not work and this problem did not occur for the first 2 brains I reconstructed. I get an alert that the Images (filled): /subjectsdir/mri/filled/COR-001 not found. wmfill first. I thought the first step was to fill the wm so these files should have already been created. Thanks for any help, Margaret
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
hi, just to clarify, running this from the command line will create talairach coordinates or do you need to download the additional mni software? and, is this step included in the process volume command when using the csurf interface? thanks, margaret
On Mon, 6 Dec 2004, Yasunari Tosa wrote:
Hi, Margaret
The head is tilted almost 10 degrees. This makes it difficult to cut the brain into two. You really need the talairach transform or any other transform to straighten up the head to find the cutting planes.
I just copied your volume and ran recon-all -stage1 and "mri_fill" created a very clean filled volume.
Tosa
Margaret Duff wrote:
Hi, I tried to manually set the cutting planes, but I was unable to get the create surface to run. My subjects info is at /space/troy/1/users/FREESURFER/SM2S4_freesurfer and I tried to specify coordinates (121 90 139) for the CC and (131 159 118) for the pons. I used the manuals troubleshooting to guide me, but is still cannot find them. The logfile I got is below. Could something besides specifying these coordinates be going wrong? Thanks, Margaret
/space/lyon/1/home/inverse/freesurfer_alpha/bin/Linux/mri_fill -lval 255 -rval 80 -P 131 159 118 -C 121 90 139 -ccmask -T 1 -L /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/tmp/ponscall.dat /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/wm /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/filled using 255 as fill val for left hemisphere. using 80 as fill val for right hemisphere. using Talairach position (131, 159, 118) as pons seed point using Talairach position (121, 90, 139) as corpus callosum seed point not using corpus callosum to mask possible location of pons. logging cutting plane coordinates to /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/tmp/ponscall.dat... voxel to talairach voxel transform 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; The seed point (121.00, 90.00, 139.00) is mapped to a voxel (15.27, -0.82. 166.72). Make sure that the seed point is given in talaraich position or use -CV option INFO: volume does not have linear_transform set nor lta is given by option.-xform. INFO: use identity matrix as the talairach transform. INFO: use src volume parameters for the talairach volume. INFO: Modifying dst c_(r,a,s), using the transform dst Using the seed to calculate the cutting plane Verify whether the seed point is inside the volume first
Command Finished
On Wed, 1 Dec 2004, Bruce Fischl wrote:
Hi Margaret,
if no talairach.xfm exists, then the fill may still find the cc and pons, but it might not. You can always specify them manually be finding a sagittal slice in which the cc is disconnected and a horizontal slice above the cerebellar peduncles where the pons is disconnected.
cheers, Bruce
On Wed, 1 Dec 2004, Margaret Duff wrote:
The log file is below. And at the end it says command finished, not that something went wrong. I am not sure about the cutting planes or how to specify them manually. Thanks for your help. Margaret
/space/lyon/1/home/inverse/freesurfer_alpha/bin/Linux/mri_fill -lval 255 -rval 80 -ccmask -T 1 -L /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/tmp/ponscall.dat /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/wm /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/filled using 255 as fill val for left hemisphere. using 80 as fill val for right hemisphere. not using corpus callosum to mask possible location of pons. logging cutting plane coordinates to /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/tmp/ponscall.dat... voxel to talairach voxel transform 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; updating initial cc seed to Tal vol (121.00, 151.00, 77.00) TAL (15.27, 0.28, -12.82) Looking for area (min, max) = (350, 1400) area[0] = 365 (min = 350, max = 1400), aspect = 1.27 (min = 0.10, max = 0.75) need search nearby using +/- offset search region where offset is 3..... using +/- offset search region where offset is 6..... using +/- offset search region where offset is 9..... using +/- offset search region where offset is 12..... using +/- offset search region where offset is 15..... using +/- offset search region where offset is 18..... using +/- offset search region where offset is 21..... area[0] = 1210 (min = 350, max = 1400), aspect = 0.37 (min = 0.10, max = 0.75) corpus callosum seed point found at Tal vol: (121, 125, 162) TAL: (15.27, 85.28, 13.18) min_slice = -1, min_area = 65536 Looking for area (min, max) = (350, 1400) area[0] = 5435 (min = 350, max = 1400), aspect = 0.50 (min = 0.10, max = 0.75) need search nearby using +/- offset search region where offset is 3..... using +/- offset search region where offset is 6..... using +/- offset search region where offset is 9..... area[0] = 488 (min = 350, max = 1400), aspect = 0.26 (min = 0.10, max = 0.75) corpus callosum seed point found at Tal vol: (127, 97, 124) TAL: (9.27, 47.28, 41.18) min_slice = -1, min_area = 65536 /space/lyon/1/home/inverse/freesurfer_alpha/bin/Linux/mri_fill: could not find corpus callosum No such file or directory INFO: volume does not have linear_transform set nor lta is given by option.-xform. INFO: use identity matrix as the talairach transform. INFO: use src volume parameters for the talairach volume. INFO: Modifying dst c_(r,a,s), using the transform dst
Command Finished
On Tue, 30 Nov 2004, Bruce Fischl wrote:
Hi Margaret,
we need more information than that. Can you send us log files from trying to run mri_fill? Is it finding the cutting planes? Have you tried specifying them manually?
cheers, Bruce
On Tue, 30 Nov 2004, Margaret Duff wrote:
Hi, I keep getting an error message after I run Create Surface. It is similar to questions found in the archive but those solutions did not work and this problem did not occur for the first 2 brains I reconstructed. I get an alert that the Images (filled): /subjectsdir/mri/filled/COR-001 not found. wmfill first. I thought the first step was to fill the wm so these files should have already been created. Thanks for any help, Margaret
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi, Margaret:
If you have downloaded the freesurfer release, everything should be included (including MNI software). I guess that the script "recon-all" is not written in the out-dated documentation.
You can do the talairach using the script "talairach2" or line-by-line as follows:
$ setenv LANG C $ cd $subject/mri $ mri_convert nu nu.mnc $ mritotal -protocol icbm nu.mnc transforms/talairach.xfm $ mri_add_xform_to_header transforms/talairach.xfm orig
Tosa
Margaret Duff wrote:
hi, just to clarify, running this from the command line will create talairach coordinates or do you need to download the additional mni software? and, is this step included in the process volume command when using the csurf interface? thanks, margaret
On Mon, 6 Dec 2004, Yasunari Tosa wrote:
Hi, Margaret
The head is tilted almost 10 degrees. This makes it difficult to cut the brain into two. You really need the talairach transform or any other transform to straighten up the head to find the cutting planes.
I just copied your volume and ran recon-all -stage1 and "mri_fill" created a very clean filled volume.
Tosa
Margaret Duff wrote:
Hi, I tried to manually set the cutting planes, but I was unable to get the create surface to run. My subjects info is at /space/troy/1/users/FREESURFER/SM2S4_freesurfer and I tried to specify coordinates (121 90 139) for the CC and (131 159 118) for the pons. I used the manuals troubleshooting to guide me, but is still cannot find them. The logfile I got is below. Could something besides specifying these coordinates be going wrong? Thanks, Margaret
/space/lyon/1/home/inverse/freesurfer_alpha/bin/Linux/mri_fill -lval 255 -rval 80 -P 131 159 118 -C 121 90 139 -ccmask -T 1 -L /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/tmp/ponscall.dat /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/wm /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/filled using 255 as fill val for left hemisphere. using 80 as fill val for right hemisphere. using Talairach position (131, 159, 118) as pons seed point using Talairach position (121, 90, 139) as corpus callosum seed point not using corpus callosum to mask possible location of pons. logging cutting plane coordinates to /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/tmp/ponscall.dat... voxel to talairach voxel transform 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; The seed point (121.00, 90.00, 139.00) is mapped to a voxel (15.27, -0.82. 166.72). Make sure that the seed point is given in talaraich position or use -CV option INFO: volume does not have linear_transform set nor lta is given by option.-xform. INFO: use identity matrix as the talairach transform. INFO: use src volume parameters for the talairach volume. INFO: Modifying dst c_(r,a,s), using the transform dst Using the seed to calculate the cutting plane Verify whether the seed point is inside the volume first
Command Finished
On Wed, 1 Dec 2004, Bruce Fischl wrote:
Hi Margaret,
if no talairach.xfm exists, then the fill may still find the cc and pons, but it might not. You can always specify them manually be finding a sagittal slice in which the cc is disconnected and a horizontal slice above the cerebellar peduncles where the pons is disconnected.
cheers, Bruce
On Wed, 1 Dec 2004, Margaret Duff wrote:
The log file is below. And at the end it says command finished, not that something went wrong. I am not sure about the cutting planes or how to specify them manually. Thanks for your help. Margaret
/space/lyon/1/home/inverse/freesurfer_alpha/bin/Linux/mri_fill -lval 255 -rval 80 -ccmask -T 1 -L /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/tmp/ponscall.dat /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/wm /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/filled using 255 as fill val for left hemisphere. using 80 as fill val for right hemisphere. not using corpus callosum to mask possible location of pons. logging cutting plane coordinates to /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/tmp/ponscall.dat... voxel to talairach voxel transform 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; updating initial cc seed to Tal vol (121.00, 151.00, 77.00) TAL (15.27, 0.28, -12.82) Looking for area (min, max) = (350, 1400) area[0] = 365 (min = 350, max = 1400), aspect = 1.27 (min = 0.10, max = 0.75) need search nearby using +/- offset search region where offset is 3..... using +/- offset search region where offset is 6..... using +/- offset search region where offset is 9..... using +/- offset search region where offset is 12..... using +/- offset search region where offset is 15..... using +/- offset search region where offset is 18..... using +/- offset search region where offset is 21..... area[0] = 1210 (min = 350, max = 1400), aspect = 0.37 (min = 0.10, max = 0.75) corpus callosum seed point found at Tal vol: (121, 125, 162) TAL: (15.27, 85.28, 13.18) min_slice = -1, min_area = 65536 Looking for area (min, max) = (350, 1400) area[0] = 5435 (min = 350, max = 1400), aspect = 0.50 (min = 0.10, max = 0.75) need search nearby using +/- offset search region where offset is 3..... using +/- offset search region where offset is 6..... using +/- offset search region where offset is 9..... area[0] = 488 (min = 350, max = 1400), aspect = 0.26 (min = 0.10, max = 0.75) corpus callosum seed point found at Tal vol: (127, 97, 124) TAL: (9.27, 47.28, 41.18) min_slice = -1, min_area = 65536 /space/lyon/1/home/inverse/freesurfer_alpha/bin/Linux/mri_fill: could not find corpus callosum No such file or directory INFO: volume does not have linear_transform set nor lta is given by option.-xform. INFO: use identity matrix as the talairach transform. INFO: use src volume parameters for the talairach volume. INFO: Modifying dst c_(r,a,s), using the transform dst
Command Finished
On Tue, 30 Nov 2004, Bruce Fischl wrote:
Hi Margaret,
we need more information than that. Can you send us log files from trying to run mri_fill? Is it finding the cutting planes? Have you tried specifying them manually?
cheers, Bruce
On Tue, 30 Nov 2004, Margaret Duff wrote:
>Hi, I keep getting an error message after I run Create Surface. It is >similar to questions found in the archive but those solutions did not work >and this problem did not occur for the first 2 brains I reconstructed. I >get an alert that the Images (filled): /subjectsdir/mri/filled/COR-001 not >found. wmfill first. I thought the first step was to fill the wm so >these files should have already been created. Thanks for any help, >Margaret > >_______________________________________________ >Freesurfer mailing list >Freesurfer@nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > >
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Margaret,
the points need to be specified in talairach coords - it looks like you are using voxels coords.
Bruce
On Mon, 6 Dec 2004, Margaret Duff wrote:
Hi, I tried to manually set the cutting planes, but I was unable to get the create surface to run. My subjects info is at /space/troy/1/users/FREESURFER/SM2S4_freesurfer and I tried to specify coordinates (121 90 139) for the CC and (131 159 118) for the pons. I used the manuals troubleshooting to guide me, but is still cannot find them. The logfile I got is below. Could something besides specifying these coordinates be going wrong? Thanks, Margaret
/space/lyon/1/home/inverse/freesurfer_alpha/bin/Linux/mri_fill -lval 255 -rval 80 -P 131 159 118 -C 121 90 139 -ccmask -T 1 -L /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/tmp/ponscall.dat /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/wm /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/filled using 255 as fill val for left hemisphere. using 80 as fill val for right hemisphere. using Talairach position (131, 159, 118) as pons seed point using Talairach position (121, 90, 139) as corpus callosum seed point not using corpus callosum to mask possible location of pons. logging cutting plane coordinates to /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/tmp/ponscall.dat... voxel to talairach voxel transform 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; The seed point (121.00, 90.00, 139.00) is mapped to a voxel (15.27, -0.82. 166.72). Make sure that the seed point is given in talaraich position or use -CV option INFO: volume does not have linear_transform set nor lta is given by option.-xform. INFO: use identity matrix as the talairach transform. INFO: use src volume parameters for the talairach volume. INFO: Modifying dst c_(r,a,s), using the transform dst Using the seed to calculate the cutting plane Verify whether the seed point is inside the volume first
Command Finished
On Wed, 1 Dec 2004, Bruce Fischl wrote:
Hi Margaret,
if no talairach.xfm exists, then the fill may still find the cc and pons, but it might not. You can always specify them manually be finding a sagittal slice in which the cc is disconnected and a horizontal slice above the cerebellar peduncles where the pons is disconnected.
cheers, Bruce
On Wed, 1 Dec 2004, Margaret Duff wrote:
The log file is below. And at the end it says command finished, not that something went wrong. I am not sure about the cutting planes or how to specify them manually. Thanks for your help. Margaret
/space/lyon/1/home/inverse/freesurfer_alpha/bin/Linux/mri_fill -lval 255 -rval 80 -ccmask -T 1 -L /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/tmp/ponscall.dat /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/wm /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/filled using 255 as fill val for left hemisphere. using 80 as fill val for right hemisphere. not using corpus callosum to mask possible location of pons. logging cutting plane coordinates to /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/tmp/ponscall.dat... voxel to talairach voxel transform 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; updating initial cc seed to Tal vol (121.00, 151.00, 77.00) TAL (15.27, 0.28, -12.82) Looking for area (min, max) = (350, 1400) area[0] = 365 (min = 350, max = 1400), aspect = 1.27 (min = 0.10, max = 0.75) need search nearby using +/- offset search region where offset is 3..... using +/- offset search region where offset is 6..... using +/- offset search region where offset is 9..... using +/- offset search region where offset is 12..... using +/- offset search region where offset is 15..... using +/- offset search region where offset is 18..... using +/- offset search region where offset is 21..... area[0] = 1210 (min = 350, max = 1400), aspect = 0.37 (min = 0.10, max = 0.75) corpus callosum seed point found at Tal vol: (121, 125, 162) TAL: (15.27, 85.28, 13.18) min_slice = -1, min_area = 65536 Looking for area (min, max) = (350, 1400) area[0] = 5435 (min = 350, max = 1400), aspect = 0.50 (min = 0.10, max = 0.75) need search nearby using +/- offset search region where offset is 3..... using +/- offset search region where offset is 6..... using +/- offset search region where offset is 9..... area[0] = 488 (min = 350, max = 1400), aspect = 0.26 (min = 0.10, max = 0.75) corpus callosum seed point found at Tal vol: (127, 97, 124) TAL: (9.27, 47.28, 41.18) min_slice = -1, min_area = 65536 /space/lyon/1/home/inverse/freesurfer_alpha/bin/Linux/mri_fill: could not find corpus callosum No such file or directory INFO: volume does not have linear_transform set nor lta is given by option.-xform. INFO: use identity matrix as the talairach transform. INFO: use src volume parameters for the talairach volume. INFO: Modifying dst c_(r,a,s), using the transform dst
Command Finished
On Tue, 30 Nov 2004, Bruce Fischl wrote:
Hi Margaret,
we need more information than that. Can you send us log files from trying to run mri_fill? Is it finding the cutting planes? Have you tried specifying them manually?
cheers, Bruce
On Tue, 30 Nov 2004, Margaret Duff wrote:
Hi, I keep getting an error message after I run Create Surface. It is similar to questions found in the archive but those solutions did not work and this problem did not occur for the first 2 brains I reconstructed. I get an alert that the Images (filled): /subjectsdir/mri/filled/COR-001 not found. wmfill first. I thought the first step was to fill the wm so these files should have already been created. Thanks for any help, Margaret
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
in the manual it says if the talairach coordinates are not available, enter the x,y,z locations from the volume index in the cursor area. is this not true anymore? thanks, margaret
On Mon, 6 Dec 2004, Bruce Fischl wrote:
Hi Margaret,
the points need to be specified in talairach coords - it looks like you are using voxels coords.
Bruce
On Mon, 6 Dec 2004, Margaret Duff wrote:
Hi, I tried to manually set the cutting planes, but I was unable to get the create surface to run. My subjects info is at /space/troy/1/users/FREESURFER/SM2S4_freesurfer and I tried to specify coordinates (121 90 139) for the CC and (131 159 118) for the pons. I used the manuals troubleshooting to guide me, but is still cannot find them. The logfile I got is below. Could something besides specifying these coordinates be going wrong? Thanks, Margaret
/space/lyon/1/home/inverse/freesurfer_alpha/bin/Linux/mri_fill -lval 255 -rval 80 -P 131 159 118 -C 121 90 139 -ccmask -T 1 -L /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/tmp/ponscall.dat /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/wm /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/filled using 255 as fill val for left hemisphere. using 80 as fill val for right hemisphere. using Talairach position (131, 159, 118) as pons seed point using Talairach position (121, 90, 139) as corpus callosum seed point not using corpus callosum to mask possible location of pons. logging cutting plane coordinates to /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/tmp/ponscall.dat... voxel to talairach voxel transform 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; The seed point (121.00, 90.00, 139.00) is mapped to a voxel (15.27, -0.82. 166.72). Make sure that the seed point is given in talaraich position or use -CV option INFO: volume does not have linear_transform set nor lta is given by option.-xform. INFO: use identity matrix as the talairach transform. INFO: use src volume parameters for the talairach volume. INFO: Modifying dst c_(r,a,s), using the transform dst Using the seed to calculate the cutting plane Verify whether the seed point is inside the volume first
Command Finished
On Wed, 1 Dec 2004, Bruce Fischl wrote:
Hi Margaret,
if no talairach.xfm exists, then the fill may still find the cc and pons, but it might not. You can always specify them manually be finding a sagittal slice in which the cc is disconnected and a horizontal slice above the cerebellar peduncles where the pons is disconnected.
cheers, Bruce
On Wed, 1 Dec 2004, Margaret Duff wrote:
The log file is below. And at the end it says command finished, not that something went wrong. I am not sure about the cutting planes or how to specify them manually. Thanks for your help. Margaret
/space/lyon/1/home/inverse/freesurfer_alpha/bin/Linux/mri_fill -lval 255 -rval 80 -ccmask -T 1 -L /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/tmp/ponscall.dat /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/wm /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/filled using 255 as fill val for left hemisphere. using 80 as fill val for right hemisphere. not using corpus callosum to mask possible location of pons. logging cutting plane coordinates to /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/tmp/ponscall.dat... voxel to talairach voxel transform 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; updating initial cc seed to Tal vol (121.00, 151.00, 77.00) TAL (15.27, 0.28, -12.82) Looking for area (min, max) = (350, 1400) area[0] = 365 (min = 350, max = 1400), aspect = 1.27 (min = 0.10, max = 0.75) need search nearby using +/- offset search region where offset is 3..... using +/- offset search region where offset is 6..... using +/- offset search region where offset is 9..... using +/- offset search region where offset is 12..... using +/- offset search region where offset is 15..... using +/- offset search region where offset is 18..... using +/- offset search region where offset is 21..... area[0] = 1210 (min = 350, max = 1400), aspect = 0.37 (min = 0.10, max = 0.75) corpus callosum seed point found at Tal vol: (121, 125, 162) TAL: (15.27, 85.28, 13.18) min_slice = -1, min_area = 65536 Looking for area (min, max) = (350, 1400) area[0] = 5435 (min = 350, max = 1400), aspect = 0.50 (min = 0.10, max = 0.75) need search nearby using +/- offset search region where offset is 3..... using +/- offset search region where offset is 6..... using +/- offset search region where offset is 9..... area[0] = 488 (min = 350, max = 1400), aspect = 0.26 (min = 0.10, max = 0.75) corpus callosum seed point found at Tal vol: (127, 97, 124) TAL: (9.27, 47.28, 41.18) min_slice = -1, min_area = 65536 /space/lyon/1/home/inverse/freesurfer_alpha/bin/Linux/mri_fill: could not find corpus callosum No such file or directory INFO: volume does not have linear_transform set nor lta is given by option.-xform. INFO: use identity matrix as the talairach transform. INFO: use src volume parameters for the talairach volume. INFO: Modifying dst c_(r,a,s), using the transform dst
Command Finished
On Tue, 30 Nov 2004, Bruce Fischl wrote:
Hi Margaret,
we need more information than that. Can you send us log files from trying to run mri_fill? Is it finding the cutting planes? Have you tried specifying them manually?
cheers, Bruce
On Tue, 30 Nov 2004, Margaret Duff wrote:
Hi, I keep getting an error message after I run Create Surface. It is similar to questions found in the archive but those solutions did not work and this problem did not occur for the first 2 brains I reconstructed. I get an alert that the Images (filled): /subjectsdir/mri/filled/COR-001 not found. wmfill first. I thought the first step was to fill the wm so these files should have already been created. Thanks for any help, Margaret
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
yes, that is incorrect. If there is no talalairach you need to enter the "volume scanner" coords from tkmedit (you can turn them on under view->information).
cheers, Bruce
On Mon, 6 Dec 2004, Margaret Duff wrote:
in the manual it says if the talairach coordinates are not available, enter the x,y,z locations from the volume index in the cursor area. is this not true anymore? thanks, margaret
On Mon, 6 Dec 2004, Bruce Fischl wrote:
Hi Margaret,
the points need to be specified in talairach coords - it looks like you are using voxels coords.
Bruce
On Mon, 6 Dec 2004, Margaret Duff wrote:
Hi, I tried to manually set the cutting planes, but I was unable to get the create surface to run. My subjects info is at /space/troy/1/users/FREESURFER/SM2S4_freesurfer and I tried to specify coordinates (121 90 139) for the CC and (131 159 118) for the pons. I used the manuals troubleshooting to guide me, but is still cannot find them. The logfile I got is below. Could something besides specifying these coordinates be going wrong? Thanks, Margaret
/space/lyon/1/home/inverse/freesurfer_alpha/bin/Linux/mri_fill -lval 255 -rval 80 -P 131 159 118 -C 121 90 139 -ccmask -T 1 -L /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/tmp/ponscall.dat /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/wm /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/filled using 255 as fill val for left hemisphere. using 80 as fill val for right hemisphere. using Talairach position (131, 159, 118) as pons seed point using Talairach position (121, 90, 139) as corpus callosum seed point not using corpus callosum to mask possible location of pons. logging cutting plane coordinates to /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/tmp/ponscall.dat... voxel to talairach voxel transform 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; The seed point (121.00, 90.00, 139.00) is mapped to a voxel (15.27, -0.82. 166.72). Make sure that the seed point is given in talaraich position or use -CV option INFO: volume does not have linear_transform set nor lta is given by option.-xform. INFO: use identity matrix as the talairach transform. INFO: use src volume parameters for the talairach volume. INFO: Modifying dst c_(r,a,s), using the transform dst Using the seed to calculate the cutting plane Verify whether the seed point is inside the volume first
Command Finished
On Wed, 1 Dec 2004, Bruce Fischl wrote:
Hi Margaret,
if no talairach.xfm exists, then the fill may still find the cc and pons, but it might not. You can always specify them manually be finding a sagittal slice in which the cc is disconnected and a horizontal slice above the cerebellar peduncles where the pons is disconnected.
cheers, Bruce
On Wed, 1 Dec 2004, Margaret Duff wrote:
The log file is below. And at the end it says command finished, not that something went wrong. I am not sure about the cutting planes or how to specify them manually. Thanks for your help. Margaret
/space/lyon/1/home/inverse/freesurfer_alpha/bin/Linux/mri_fill -lval 255 -rval 80 -ccmask -T 1 -L /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/tmp/ponscall.dat /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/wm /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/filled using 255 as fill val for left hemisphere. using 80 as fill val for right hemisphere. not using corpus callosum to mask possible location of pons. logging cutting plane coordinates to /space/troy/1/users/FREESURFER/SM2S4_freesurfer/mri/tmp/ponscall.dat... voxel to talairach voxel transform 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; updating initial cc seed to Tal vol (121.00, 151.00, 77.00) TAL (15.27, 0.28, -12.82) Looking for area (min, max) = (350, 1400) area[0] = 365 (min = 350, max = 1400), aspect = 1.27 (min = 0.10, max = 0.75) need search nearby using +/- offset search region where offset is 3..... using +/- offset search region where offset is 6..... using +/- offset search region where offset is 9..... using +/- offset search region where offset is 12..... using +/- offset search region where offset is 15..... using +/- offset search region where offset is 18..... using +/- offset search region where offset is 21..... area[0] = 1210 (min = 350, max = 1400), aspect = 0.37 (min = 0.10, max = 0.75) corpus callosum seed point found at Tal vol: (121, 125, 162) TAL: (15.27, 85.28, 13.18) min_slice = -1, min_area = 65536 Looking for area (min, max) = (350, 1400) area[0] = 5435 (min = 350, max = 1400), aspect = 0.50 (min = 0.10, max = 0.75) need search nearby using +/- offset search region where offset is 3..... using +/- offset search region where offset is 6..... using +/- offset search region where offset is 9..... area[0] = 488 (min = 350, max = 1400), aspect = 0.26 (min = 0.10, max = 0.75) corpus callosum seed point found at Tal vol: (127, 97, 124) TAL: (9.27, 47.28, 41.18) min_slice = -1, min_area = 65536 /space/lyon/1/home/inverse/freesurfer_alpha/bin/Linux/mri_fill: could not find corpus callosum No such file or directory INFO: volume does not have linear_transform set nor lta is given by option.-xform. INFO: use identity matrix as the talairach transform. INFO: use src volume parameters for the talairach volume. INFO: Modifying dst c_(r,a,s), using the transform dst
Command Finished
On Tue, 30 Nov 2004, Bruce Fischl wrote:
Hi Margaret,
we need more information than that. Can you send us log files from trying to run mri_fill? Is it finding the cutting planes? Have you tried specifying them manually?
cheers, Bruce
On Tue, 30 Nov 2004, Margaret Duff wrote:
> Hi, I keep getting an error message after I run Create Surface. It is > similar to questions found in the archive but those solutions did not work > and this problem did not occur for the first 2 brains I reconstructed. I > get an alert that the Images (filled): /subjectsdir/mri/filled/COR-001 not > found. wmfill first. I thought the first step was to fill the wm so > these files should have already been created. Thanks for any help, > Margaret > > _______________________________________________ > 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 -
Margaret Duff -
Yasunari Tosa