Hi everybody,
I'm trying to create my own atlas with the rebuild_gca_atlas script. I obtain the "Input TR, TE, FlipAngle for each subjects must match" error in the # TRAIN FROM SEGMENTED_SUBJECTS USING M3D_ONE step (using mri_ca_train for all subjects). TR, TE and FlipAngle are the same for all patients.
What can be the problem?
The log is:
mri_ca_train -prior_spacing 2 -node_spacing 4 -mask brain.mgz -parc_dir seg_edited.mgz -xform talairach_one.m3z -T1 norm.mgz -check 4163 4168 /Applications/freesurfer/subjects/average/RB_all_2013-03-07.gca reading input 0: /Applications/freesurfer/subjects/4163/mri/norm.mgz spacing priors every 2.0 mm spacing nodes every 4.0 mm using MR volume brain.mgz to mask input volume... reading segmentation from subject's mri/seg_edited.mgz directory reading xform from talairach_one.m3z reading T1 data from subject's mri/norm.mgz directory will conduct sanity-check of labels... training on 2 subject and writing results to /Applications/freesurfer/subjects/average/RB_all_2013-03-07.gca gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 4 *************************************************************************** processing subject 4163, 1 of 2... reading volume /Applications/freesurfer/subjects/4163/mri/brain.mgz for masking... gunzip -c /Applications/freesurfer/subjects/4163/mri/transforms/talairach_one.m3z checking labels in subject 4163... max_xtal_l_hippo = -12.6 max_xtal_l_caudate = -5.8 max_xtal_l_amygdala = -17.1 max_xtal_l_putamen = -12.7 max_xtal_l_pallidum = -11.4 min_xtal_r_hippo = 15.2 min_xtal_r_caudate = 6.4 min_xtal_r_amygdala = 16.4 min_xtal_r_putamen = 13.9 min_xtal_r_pallidum = 13.1 Input TR, TE, FlipAngle for each subjects must match.
23 prior holes filled *************************************************************************** processing subject 4168, 2 of 2... nn
Thank you in advance.
what version are you running? This should never happen on the first subject, so it's pretty puzzling. Bruce On Fri, 8 Mar 2013, alexandra.cristobal@urjc.es wrote:
Hi everybody,
I'm trying to create my own atlas with the rebuild_gca_atlas script. I obtain the "Input TR, TE, FlipAngle for each subjects must match" error in the # TRAIN FROM SEGMENTED_SUBJECTS USING M3D_ONE step (using mri_ca_train for all subjects). TR, TE and FlipAngle are the same for all patients.
What can be the problem?
The log is:
mri_ca_train -prior_spacing 2 -node_spacing 4 -mask brain.mgz -parc_dir seg_edited.mgz -xform talairach_one.m3z -T1 norm.mgz -check 4163 4168 /Applications/freesurfer/subjects/average/RB_all_2013-03-07.gca reading input 0: /Applications/freesurfer/subjects/4163/mri/norm.mgz spacing priors every 2.0 mm spacing nodes every 4.0 mm using MR volume brain.mgz to mask input volume... reading segmentation from subject's mri/seg_edited.mgz directory reading xform from talairach_one.m3z reading T1 data from subject's mri/norm.mgz directory will conduct sanity-check of labels... training on 2 subject and writing results to /Applications/freesurfer/subjects/average/RB_all_2013-03-07.gca gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 4
processing subject 4163, 1 of 2... reading volume /Applications/freesurfer/subjects/4163/mri/brain.mgz for masking... gunzip -c /Applications/freesurfer/subjects/4163/mri/transforms/talairach_one.m3z checking labels in subject 4163... max_xtal_l_hippo = -12.6 max_xtal_l_caudate = -5.8 max_xtal_l_amygdala = -17.1 max_xtal_l_putamen = -12.7 max_xtal_l_pallidum = -11.4 min_xtal_r_hippo = 15.2 min_xtal_r_caudate = 6.4 min_xtal_r_amygdala = 16.4 min_xtal_r_putamen = 13.9 min_xtal_r_pallidum = 13.1 Input TR, TE, FlipAngle for each subjects must match.
23 prior holes filled
processing subject 4168, 2 of 2... nn
Thank you in advance.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Bruce,
This is the information about my version:
freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0
As you can see, it runs in a iMac version 10.6.8
Thanks!
"Bruce Fischl" fischl@nmr.mgh.harvard.edu escribió:
what version are you running? This should never happen on the first subject, so it's pretty puzzling. Bruce On Fri, 8 Mar 2013, alexandra.cristobal@urjc.es wrote:
Hi everybody,
I'm trying to create my own atlas with the rebuild_gca_atlas script. I obtain the "Input TR, TE, FlipAngle for each subjects must match" error in the # TRAIN FROM SEGMENTED_SUBJECTS USING M3D_ONE step (using mri_ca_train for all subjects). TR, TE and FlipAngle are the same for all patients.
What can be the problem?
The log is:
mri_ca_train -prior_spacing 2 -node_spacing 4 -mask brain.mgz -parc_dir seg_edited.mgz -xform talairach_one.m3z -T1 norm.mgz -check 4163 4168 /Applications/freesurfer/subjects/average/RB_all_2013-03-07.gca reading input 0: /Applications/freesurfer/subjects/4163/mri/norm.mgz spacing priors every 2.0 mm spacing nodes every 4.0 mm using MR volume brain.mgz to mask input volume... reading segmentation from subject's mri/seg_edited.mgz directory reading xform from talairach_one.m3z reading T1 data from subject's mri/norm.mgz directory will conduct sanity-check of labels... training on 2 subject and writing results to /Applications/freesurfer/subjects/average/RB_all_2013-03-07.gca gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 4
processing subject 4163, 1 of 2... reading volume /Applications/freesurfer/subjects/4163/mri/brain.mgz for masking... gunzip -c /Applications/freesurfer/subjects/4163/mri/transforms/talairach_one.m3z checking labels in subject 4163... max_xtal_l_hippo = -12.6 max_xtal_l_caudate = -5.8 max_xtal_l_amygdala = -17.1 max_xtal_l_putamen = -12.7 max_xtal_l_pallidum = -11.4 min_xtal_r_hippo = 15.2 min_xtal_r_caudate = 6.4 min_xtal_r_amygdala = 16.4 min_xtal_r_putamen = 13.9 min_xtal_r_pallidum = 13.1 Input TR, TE, FlipAngle for each subjects must match.
23 prior holes filled
processing subject 4168, 2 of 2... nn
Thank you in advance.
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
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi again,
Any suggestion? I haven't any idea about this error. Why does it happen?
Thank you.
alexandra.cristobal@urjc.es escribió:
Hi Bruce,
This is the information about my version:
freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0
As you can see, it runs in a iMac version 10.6.8
Thanks!
"Bruce Fischl" fischl@nmr.mgh.harvard.edu escribió:
what version are you running? This should never happen on the first subject, so it's pretty puzzling. Bruce On Fri, 8 Mar 2013, alexandra.cristobal@urjc.es wrote:
Hi everybody,
I'm trying to create my own atlas with the rebuild_gca_atlas script. I obtain the "Input TR, TE, FlipAngle for each subjects must match" error in the # TRAIN FROM SEGMENTED_SUBJECTS USING M3D_ONE step (using mri_ca_train for all subjects). TR, TE and FlipAngle are the same for all patients.
What can be the problem?
The log is:
mri_ca_train -prior_spacing 2 -node_spacing 4 -mask brain.mgz -parc_dir seg_edited.mgz -xform talairach_one.m3z -T1 norm.mgz -check 4163 4168 /Applications/freesurfer/subjects/average/RB_all_2013-03-07.gca reading input 0: /Applications/freesurfer/subjects/4163/mri/norm.mgz spacing priors every 2.0 mm spacing nodes every 4.0 mm using MR volume brain.mgz to mask input volume... reading segmentation from subject's mri/seg_edited.mgz directory reading xform from talairach_one.m3z reading T1 data from subject's mri/norm.mgz directory will conduct sanity-check of labels... training on 2 subject and writing results to /Applications/freesurfer/subjects/average/RB_all_2013-03-07.gca gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 4
processing subject 4163, 1 of 2... reading volume /Applications/freesurfer/subjects/4163/mri/brain.mgz for masking... gunzip -c /Applications/freesurfer/subjects/4163/mri/transforms/talairach_one.m3z checking labels in subject 4163... max_xtal_l_hippo = -12.6 max_xtal_l_caudate = -5.8 max_xtal_l_amygdala = -17.1 max_xtal_l_putamen = -12.7 max_xtal_l_pallidum = -11.4 min_xtal_r_hippo = 15.2 min_xtal_r_caudate = 6.4 min_xtal_r_amygdala = 16.4 min_xtal_r_putamen = 13.9 min_xtal_r_pallidum = 13.1 Input TR, TE, FlipAngle for each subjects must match.
23 prior holes filled
processing subject 4168, 2 of 2... nn
Thank you in advance.
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
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
it doesn't look like it's exiting, is it? That is, it keeps running after printing that message?
I would run mri_info on the input volumes (norm.mgz) and check their parameters
Bruce
On Tue, 12 Mar 2013, alexandra.cristobal@urjc.es wrote:
Hi again,
Any suggestion? I haven't any idea about this error. Why does it happen?
Thank you.
alexandra.cristobal@urjc.es escribió:
Hi Bruce,
This is the information about my version:
freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0
As you can see, it runs in a iMac version 10.6.8
Thanks!
"Bruce Fischl" fischl@nmr.mgh.harvard.edu escribió:
what version are you running? This should never happen on the first subject, so it's pretty puzzling. Bruce On Fri, 8 Mar 2013, alexandra.cristobal@urjc.es wrote:
Hi everybody,
I'm trying to create my own atlas with the rebuild_gca_atlas script. I obtain the "Input TR, TE, FlipAngle for each subjects must match" error in the # TRAIN FROM SEGMENTED_SUBJECTS USING M3D_ONE step (using mri_ca_train for all subjects). TR, TE and FlipAngle are the same for all patients.
What can be the problem?
The log is:
mri_ca_train -prior_spacing 2 -node_spacing 4 -mask brain.mgz -parc_dir seg_edited.mgz -xform talairach_one.m3z -T1 norm.mgz -check 4163 4168 /Applications/freesurfer/subjects/average/RB_all_2013-03-07.gca reading input 0: /Applications/freesurfer/subjects/4163/mri/norm.mgz spacing priors every 2.0 mm spacing nodes every 4.0 mm using MR volume brain.mgz to mask input volume... reading segmentation from subject's mri/seg_edited.mgz directory reading xform from talairach_one.m3z reading T1 data from subject's mri/norm.mgz directory will conduct sanity-check of labels... training on 2 subject and writing results to /Applications/freesurfer/subjects/average/RB_all_2013-03-07.gca gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 4
processing subject 4163, 1 of 2... reading volume /Applications/freesurfer/subjects/4163/mri/brain.mgz for masking... gunzip -c /Applications/freesurfer/subjects/4163/mri/transforms/talairach_one.m3z checking labels in subject 4163... max_xtal_l_hippo = -12.6 max_xtal_l_caudate = -5.8 max_xtal_l_amygdala = -17.1 max_xtal_l_putamen = -12.7 max_xtal_l_pallidum = -11.4 min_xtal_r_hippo = 15.2 min_xtal_r_caudate = 6.4 min_xtal_r_amygdala = 16.4 min_xtal_r_putamen = 13.9 min_xtal_r_pallidum = 13.1 Input TR, TE, FlipAngle for each subjects must match.
23 prior holes filled
processing subject 4168, 2 of 2... nn
Thank you in advance.
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
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi again,
The script doesn't keep running after that. I've run mri_info for my two subject, and there is a little difference between them. In the dicom header this parameters have, for example, the value for echo time as 4.568 and 4.56. Could it be the reason?
iAlba-2:mri Alexandra$ mri_info norm.mgz Volume information for norm.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.0000, 1.0000, 1.0000 type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 10.04 msec, TE: 4.57 msec, TI: 600.00 msec, flip angle: 12.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = -1.8417 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 27.9162 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 33.6772
talairach xfm : /Applications/freesurfer/subjects/4163/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: -1.0000 0.0000 0.0000 126.1583 0.0000 0.0000 1.0000 -100.0838 0.0000 -1.0000 0.0000 161.6772 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -1.0000 0.0000 0.0000 126.1583 -0.0000 -0.0000 -1.0000 161.6772 -0.0000 1.0000 -0.0000 100.0838 0.0000 0.0000 0.0000 1.0000
---------------------------------------------------------------------------------------------- iAlba-2:mri Alexandra$ mri_info norm.mgz Volume information for norm.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.0000, 1.0000, 1.0000 type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 10.05 msec, TE: 4.56 msec, TI: 600.00 msec, flip angle: 12.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 1.0851 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 41.0452 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 23.7262
talairach xfm : /Applications/freesurfer/subjects/4168/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: -1.0000 0.0000 0.0000 129.0851 0.0000 0.0000 1.0000 -86.9548 0.0000 -1.0000 0.0000 151.7262 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -1.0000 0.0000 0.0000 129.0851 -0.0000 -0.0000 -1.0000 151.7262 -0.0000 1.0000 -0.0000 86.9548 0.0000 0.0000 0.0000 1.0000
"Bruce Fischl" fischl@nmr.mgh.harvard.edu escribió:
it doesn't look like it's exiting, is it? That is, it keeps running after printing that message?
I would run mri_info on the input volumes (norm.mgz) and check their parameters
Bruce
On Tue, 12 Mar 2013, alexandra.cristobal@urjc.es wrote:
Hi again,
Any suggestion? I haven't any idea about this error. Why does it happen?
Thank you.
alexandra.cristobal@urjc.es escribió:
Hi Bruce,
This is the information about my version:
freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0
As you can see, it runs in a iMac version 10.6.8
Thanks!
"Bruce Fischl" fischl@nmr.mgh.harvard.edu escribió:
what version are you running? This should never happen on the first subject, so it's pretty puzzling. Bruce On Fri, 8 Mar 2013, alexandra.cristobal@urjc.es wrote:
Hi everybody,
I'm trying to create my own atlas with the rebuild_gca_atlas script. I obtain the "Input TR, TE, FlipAngle for each subjects must match" error in the # TRAIN FROM SEGMENTED_SUBJECTS USING M3D_ONE step (using mri_ca_train for all subjects). TR, TE and FlipAngle are the same for all patients.
What can be the problem?
The log is:
mri_ca_train -prior_spacing 2 -node_spacing 4 -mask brain.mgz -parc_dir seg_edited.mgz -xform talairach_one.m3z -T1 norm.mgz -check 4163 4168 /Applications/freesurfer/subjects/average/RB_all_2013-03-07.gca reading input 0: /Applications/freesurfer/subjects/4163/mri/norm.mgz spacing priors every 2.0 mm spacing nodes every 4.0 mm using MR volume brain.mgz to mask input volume... reading segmentation from subject's mri/seg_edited.mgz directory reading xform from talairach_one.m3z reading T1 data from subject's mri/norm.mgz directory will conduct sanity-check of labels... training on 2 subject and writing results to /Applications/freesurfer/subjects/average/RB_all_2013-03-07.gca gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 4
processing subject 4163, 1 of 2... reading volume /Applications/freesurfer/subjects/4163/mri/brain.mgz for masking... gunzip -c /Applications/freesurfer/subjects/4163/mri/transforms/talairach_one.m3z checking labels in subject 4163... max_xtal_l_hippo = -12.6 max_xtal_l_caudate = -5.8 max_xtal_l_amygdala = -17.1 max_xtal_l_putamen = -12.7 max_xtal_l_pallidum = -11.4 min_xtal_r_hippo = 15.2 min_xtal_r_caudate = 6.4 min_xtal_r_amygdala = 16.4 min_xtal_r_putamen = 13.9 min_xtal_r_pallidum = 13.1 Input TR, TE, FlipAngle for each subjects must match.
23 prior holes filled
processing subject 4168, 2 of 2... nn
Thank you in advance.
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
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
yes, that is definitely the reason. Can you remind me what version you are running? I think the current one doesn't do this check. If it's not current, can you grab a new mri_ca_train and see if it fixes your problem?
Bruce
On Tue, 12 Mar 2013, alexandra.cristobal@urjc.es wrote:
Hi again,
The script doesn't keep running after that. I've run mri_info for my two subject, and there is a little difference between them. In the dicom header this parameters have, for example, the value for echo time as 4.568 and 4.56. Could it be the reason?
iAlba-2:mri Alexandra$ mri_info norm.mgz Volume information for norm.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.0000, 1.0000, 1.0000 type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 10.04 msec, TE: 4.57 msec, TI: 600.00 msec, flip angle: 12.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = -1.8417 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 27.9162 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 33.6772
talairach xfm : /Applications/freesurfer/subjects/4163/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: -1.0000 0.0000 0.0000 126.1583 0.0000 0.0000 1.0000 -100.0838 0.0000 -1.0000 0.0000 161.6772 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -1.0000 0.0000 0.0000 126.1583 -0.0000 -0.0000 -1.0000 161.6772 -0.0000 1.0000 -0.0000 100.0838 0.0000 0.0000 0.0000 1.0000
iAlba-2:mri Alexandra$ mri_info norm.mgz Volume information for norm.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.0000, 1.0000, 1.0000 type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 10.05 msec, TE: 4.56 msec, TI: 600.00 msec, flip angle: 12.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 1.0851 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 41.0452 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 23.7262
talairach xfm : /Applications/freesurfer/subjects/4168/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: -1.0000 0.0000 0.0000 129.0851 0.0000 0.0000 1.0000 -86.9548 0.0000 -1.0000 0.0000 151.7262 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -1.0000 0.0000 0.0000 129.0851 -0.0000 -0.0000 -1.0000 151.7262 -0.0000 1.0000 -0.0000 86.9548 0.0000 0.0000 0.0000 1.0000
"Bruce Fischl" fischl@nmr.mgh.harvard.edu escribió:
it doesn't look like it's exiting, is it? That is, it keeps running after printing that message?
I would run mri_info on the input volumes (norm.mgz) and check their parameters
Bruce
On Tue, 12 Mar 2013, alexandra.cristobal@urjc.es wrote:
Hi again,
Any suggestion? I haven't any idea about this error. Why does it happen?
Thank you.
alexandra.cristobal@urjc.es escribió:
Hi Bruce,
This is the information about my version:
freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0
As you can see, it runs in a iMac version 10.6.8
Thanks!
"Bruce Fischl" fischl@nmr.mgh.harvard.edu escribió:
what version are you running? This should never happen on the first subject, so it's pretty puzzling. Bruce On Fri, 8 Mar 2013, alexandra.cristobal@urjc.es wrote:
Hi everybody,
I'm trying to create my own atlas with the rebuild_gca_atlas script. I obtain the "Input TR, TE, FlipAngle for each subjects must match" error in the # TRAIN FROM SEGMENTED_SUBJECTS USING M3D_ONE step (using mri_ca_train for all subjects). TR, TE and FlipAngle are the same for all patients.
What can be the problem?
The log is:
mri_ca_train -prior_spacing 2 -node_spacing 4 -mask brain.mgz -parc_dir seg_edited.mgz -xform talairach_one.m3z -T1 norm.mgz -check 4163 4168 /Applications/freesurfer/subjects/average/RB_all_2013-03-07.gca reading input 0: /Applications/freesurfer/subjects/4163/mri/norm.mgz spacing priors every 2.0 mm spacing nodes every 4.0 mm using MR volume brain.mgz to mask input volume... reading segmentation from subject's mri/seg_edited.mgz directory reading xform from talairach_one.m3z reading T1 data from subject's mri/norm.mgz directory will conduct sanity-check of labels... training on 2 subject and writing results to /Applications/freesurfer/subjects/average/RB_all_2013-03-07.gca gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 4
processing subject 4163, 1 of 2... reading volume /Applications/freesurfer/subjects/4163/mri/brain.mgz for masking... gunzip -c /Applications/freesurfer/subjects/4163/mri/transforms/talairach_one.m3z checking labels in subject 4163... max_xtal_l_hippo = -12.6 max_xtal_l_caudate = -5.8 max_xtal_l_amygdala = -17.1 max_xtal_l_putamen = -12.7 max_xtal_l_pallidum = -11.4 min_xtal_r_hippo = 15.2 min_xtal_r_caudate = 6.4 min_xtal_r_amygdala = 16.4 min_xtal_r_putamen = 13.9 min_xtal_r_pallidum = 13.1 Input TR, TE, FlipAngle for each subjects must match.
23 prior holes filled
processing subject 4168, 2 of 2... nn
Thank you in advance.
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
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The version is 5.1.0. I don't know how to fix it. I'm running the script with two subjects with the same values (to check if it is the problem). It's very strange, because we are acquiring all subjects with the same parameters, and I don't know why it has a different decimal value.
Thanks!
"Bruce Fischl" fischl@nmr.mgh.harvard.edu escribió:
yes, that is definitely the reason. Can you remind me what version you are running? I think the current one doesn't do this check. If it's not current, can you grab a new mri_ca_train and see if it fixes your problem?
Bruce
On Tue, 12 Mar 2013, alexandra.cristobal@urjc.es wrote:
Hi again,
The script doesn't keep running after that. I've run mri_info for my two subject, and there is a little difference between them. In the dicom header this parameters have, for example, the value for echo time as 4.568 and 4.56. Could it be the reason?
iAlba-2:mri Alexandra$ mri_info norm.mgz Volume information for norm.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.0000, 1.0000, 1.0000 type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 10.04 msec, TE: 4.57 msec, TI: 600.00 msec, flip angle: 12.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = -1.8417 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 27.9162 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 33.6772
talairach xfm : /Applications/freesurfer/subjects/4163/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: -1.0000 0.0000 0.0000 126.1583 0.0000 0.0000 1.0000 -100.0838 0.0000 -1.0000 0.0000 161.6772 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -1.0000 0.0000 0.0000 126.1583 -0.0000 -0.0000 -1.0000 161.6772 -0.0000 1.0000 -0.0000 100.0838 0.0000 0.0000 0.0000 1.0000
iAlba-2:mri Alexandra$ mri_info norm.mgz Volume information for norm.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.0000, 1.0000, 1.0000 type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 10.05 msec, TE: 4.56 msec, TI: 600.00 msec, flip angle: 12.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 1.0851 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 41.0452 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 23.7262
talairach xfm : /Applications/freesurfer/subjects/4168/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: -1.0000 0.0000 0.0000 129.0851 0.0000 0.0000 1.0000 -86.9548 0.0000 -1.0000 0.0000 151.7262 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -1.0000 0.0000 0.0000 129.0851 -0.0000 -0.0000 -1.0000 151.7262 -0.0000 1.0000 -0.0000 86.9548 0.0000 0.0000 0.0000 1.0000
"Bruce Fischl" fischl@nmr.mgh.harvard.edu escribió:
it doesn't look like it's exiting, is it? That is, it keeps running after printing that message?
I would run mri_info on the input volumes (norm.mgz) and check their parameters
Bruce
On Tue, 12 Mar 2013, alexandra.cristobal@urjc.es wrote:
Hi again,
Any suggestion? I haven't any idea about this error. Why does it happen?
Thank you.
alexandra.cristobal@urjc.es escribió:
Hi Bruce,
This is the information about my version:
freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0
As you can see, it runs in a iMac version 10.6.8
Thanks!
"Bruce Fischl" fischl@nmr.mgh.harvard.edu escribió:
what version are you running? This should never happen on the first subject, so it's pretty puzzling. Bruce On Fri, 8 Mar 2013, alexandra.cristobal@urjc.es wrote:
> Hi everybody, > > I'm trying to create my own atlas with the rebuild_gca_atlas script. I > obtain the "Input TR, TE, FlipAngle for each subjects must match" > error in the # TRAIN FROM SEGMENTED_SUBJECTS USING M3D_ONE step (using > mri_ca_train for all subjects). > TR, TE and FlipAngle are the same for all patients. > > What can be the problem? > > > The log is: > > mri_ca_train -prior_spacing 2 -node_spacing 4 -mask brain.mgz > -parc_dir seg_edited.mgz -xform talairach_one.m3z -T1 norm.mgz -check > 4163 4168 > /Applications/freesurfer/subjects/average/RB_all_2013-03-07.gca > reading input 0: /Applications/freesurfer/subjects/4163/mri/norm.mgz > spacing priors every 2.0 mm > spacing nodes every 4.0 mm > using MR volume brain.mgz to mask input volume... > reading segmentation from subject's mri/seg_edited.mgz directory > reading xform from talairach_one.m3z > reading T1 data from subject's mri/norm.mgz directory > will conduct sanity-check of labels... > training on 2 subject and writing results to > /Applications/freesurfer/subjects/average/RB_all_2013-03-07.gca > gcaAllocMax: node dims 64 64 64 > gcaAllocMax: prior dims 128 128 128 > gcaAllocMax: max_labels 4 > *************************************************************************** > processing subject 4163, 1 of 2... > reading volume /Applications/freesurfer/subjects/4163/mri/brain.mgz > for masking... > gunzip -c > /Applications/freesurfer/subjects/4163/mri/transforms/talairach_one.m3z > checking labels in subject 4163... > max_xtal_l_hippo = -12.6 > max_xtal_l_caudate = -5.8 > max_xtal_l_amygdala = -17.1 > max_xtal_l_putamen = -12.7 > max_xtal_l_pallidum = -11.4 > min_xtal_r_hippo = 15.2 > min_xtal_r_caudate = 6.4 > min_xtal_r_amygdala = 16.4 > min_xtal_r_putamen = 13.9 > min_xtal_r_pallidum = 13.1 > Input TR, TE, FlipAngle for each subjects must match. > > 23 prior holes filled > *************************************************************************** > processing subject 4168, 2 of 2... > nn > > > Thank you in advance. > > _______________________________________________ > 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
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
if you let us know the hardware/software environment you are using we'll get you a new version of mri_ca_train
On Tue, 12 Mar 2013, alexandra.cristobal@urjc.es wrote:
The version is 5.1.0. I don't know how to fix it. I'm running the script with two subjects with the same values (to check if it is the problem). It's very strange, because we are acquiring all subjects with the same parameters, and I don't know why it has a different decimal value.
Thanks!
"Bruce Fischl" fischl@nmr.mgh.harvard.edu escribió:
yes, that is definitely the reason. Can you remind me what version you are running? I think the current one doesn't do this check. If it's not current, can you grab a new mri_ca_train and see if it fixes your problem?
Bruce
On Tue, 12 Mar 2013, alexandra.cristobal@urjc.es wrote:
Hi again,
The script doesn't keep running after that. I've run mri_info for my two subject, and there is a little difference between them. In the dicom header this parameters have, for example, the value for echo time as 4.568 and 4.56. Could it be the reason?
iAlba-2:mri Alexandra$ mri_info norm.mgz Volume information for norm.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.0000, 1.0000, 1.0000 type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 10.04 msec, TE: 4.57 msec, TI: 600.00 msec, flip angle: 12.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = -1.8417 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 27.9162 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 33.6772
talairach xfm : /Applications/freesurfer/subjects/4163/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: -1.0000 0.0000 0.0000 126.1583 0.0000 0.0000 1.0000 -100.0838 0.0000 -1.0000 0.0000 161.6772 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -1.0000 0.0000 0.0000 126.1583 -0.0000 -0.0000 -1.0000 161.6772 -0.0000 1.0000 -0.0000 100.0838 0.0000 0.0000 0.0000 1.0000
iAlba-2:mri Alexandra$ mri_info norm.mgz Volume information for norm.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.0000, 1.0000, 1.0000 type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 10.05 msec, TE: 4.56 msec, TI: 600.00 msec, flip angle: 12.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 1.0851 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 41.0452 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 23.7262
talairach xfm : /Applications/freesurfer/subjects/4168/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: -1.0000 0.0000 0.0000 129.0851 0.0000 0.0000 1.0000 -86.9548 0.0000 -1.0000 0.0000 151.7262 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -1.0000 0.0000 0.0000 129.0851 -0.0000 -0.0000 -1.0000 151.7262 -0.0000 1.0000 -0.0000 86.9548 0.0000 0.0000 0.0000 1.0000
"Bruce Fischl" fischl@nmr.mgh.harvard.edu escribió:
it doesn't look like it's exiting, is it? That is, it keeps running after printing that message?
I would run mri_info on the input volumes (norm.mgz) and check their parameters
Bruce
On Tue, 12 Mar 2013, alexandra.cristobal@urjc.es wrote:
Hi again,
Any suggestion? I haven't any idea about this error. Why does it happen?
Thank you.
alexandra.cristobal@urjc.es escribió:
Hi Bruce,
This is the information about my version:
freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0
As you can see, it runs in a iMac version 10.6.8
Thanks!
"Bruce Fischl" fischl@nmr.mgh.harvard.edu escribió:
> what version are you running? This should never happen on the first > subject, so it's pretty puzzling. > Bruce > On Fri, 8 Mar 2013, > alexandra.cristobal@urjc.es wrote: > >> Hi everybody, >> >> I'm trying to create my own atlas with the rebuild_gca_atlas script. >> I >> obtain the "Input TR, TE, FlipAngle for each subjects must match" >> error in the # TRAIN FROM SEGMENTED_SUBJECTS USING M3D_ONE step >> (using >> mri_ca_train for all subjects). >> TR, TE and FlipAngle are the same for all patients. >> >> What can be the problem? >> >> >> The log is: >> >> mri_ca_train -prior_spacing 2 -node_spacing 4 -mask brain.mgz >> -parc_dir seg_edited.mgz -xform talairach_one.m3z -T1 norm.mgz -check >> 4163 4168 >> /Applications/freesurfer/subjects/average/RB_all_2013-03-07.gca >> reading input 0: /Applications/freesurfer/subjects/4163/mri/norm.mgz >> spacing priors every 2.0 mm >> spacing nodes every 4.0 mm >> using MR volume brain.mgz to mask input volume... >> reading segmentation from subject's mri/seg_edited.mgz directory >> reading xform from talairach_one.m3z >> reading T1 data from subject's mri/norm.mgz directory >> will conduct sanity-check of labels... >> training on 2 subject and writing results to >> /Applications/freesurfer/subjects/average/RB_all_2013-03-07.gca >> gcaAllocMax: node dims 64 64 64 >> gcaAllocMax: prior dims 128 128 128 >> gcaAllocMax: max_labels 4 >> *************************************************************************** >> processing subject 4163, 1 of 2... >> reading volume /Applications/freesurfer/subjects/4163/mri/brain.mgz >> for masking... >> gunzip -c >> /Applications/freesurfer/subjects/4163/mri/transforms/talairach_one.m3z >> checking labels in subject 4163... >> max_xtal_l_hippo = -12.6 >> max_xtal_l_caudate = -5.8 >> max_xtal_l_amygdala = -17.1 >> max_xtal_l_putamen = -12.7 >> max_xtal_l_pallidum = -11.4 >> min_xtal_r_hippo = 15.2 >> min_xtal_r_caudate = 6.4 >> min_xtal_r_amygdala = 16.4 >> min_xtal_r_putamen = 13.9 >> min_xtal_r_pallidum = 13.1 >> Input TR, TE, FlipAngle for each subjects must match. >> >> 23 prior holes filled >> *************************************************************************** >> processing subject 4168, 2 of 2... >> nn >> >> >> Thank you in advance. >> >> _______________________________________________ >> 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 > > > The information in this e-mail is intended only for the person to whom > it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to > you in error > but does not contain patient information, please contact the sender > and properly > dispose of the e-mail. > >
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
We have two enviroments:
- freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 - freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0
Thanks!
"Bruce Fischl" fischl@nmr.mgh.harvard.edu escribió:
if you let us know the hardware/software environment you are using we'll get you a new version of mri_ca_train
On Tue, 12 Mar 2013, alexandra.cristobal@urjc.es wrote:
The version is 5.1.0. I don't know how to fix it. I'm running the script with two subjects with the same values (to check if it is the problem). It's very strange, because we are acquiring all subjects with the same parameters, and I don't know why it has a different decimal value.
Thanks!
"Bruce Fischl" fischl@nmr.mgh.harvard.edu escribió:
yes, that is definitely the reason. Can you remind me what version you are running? I think the current one doesn't do this check. If it's not current, can you grab a new mri_ca_train and see if it fixes your problem?
Bruce
On Tue, 12 Mar 2013, alexandra.cristobal@urjc.es wrote:
Hi again,
The script doesn't keep running after that. I've run mri_info for my two subject, and there is a little difference between them. In the dicom header this parameters have, for example, the value for echo time as 4.568 and 4.56. Could it be the reason?
iAlba-2:mri Alexandra$ mri_info norm.mgz Volume information for norm.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.0000, 1.0000, 1.0000 type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 10.04 msec, TE: 4.57 msec, TI: 600.00 msec, flip angle: 12.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = -1.8417 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 27.9162 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 33.6772
talairach xfm : /Applications/freesurfer/subjects/4163/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: -1.0000 0.0000 0.0000 126.1583 0.0000 0.0000 1.0000 -100.0838 0.0000 -1.0000 0.0000 161.6772 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -1.0000 0.0000 0.0000 126.1583 -0.0000 -0.0000 -1.0000 161.6772 -0.0000 1.0000 -0.0000 100.0838 0.0000 0.0000 0.0000 1.0000
iAlba-2:mri Alexandra$ mri_info norm.mgz Volume information for norm.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.0000, 1.0000, 1.0000 type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 10.05 msec, TE: 4.56 msec, TI: 600.00 msec, flip angle: 12.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 1.0851 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 41.0452 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 23.7262
talairach xfm : /Applications/freesurfer/subjects/4168/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal
voxel to ras transform: -1.0000 0.0000 0.0000 129.0851 0.0000 0.0000 1.0000 -86.9548 0.0000 -1.0000 0.0000 151.7262 0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform: -1.0000 0.0000 0.0000 129.0851 -0.0000 -0.0000 -1.0000 151.7262 -0.0000 1.0000 -0.0000 86.9548 0.0000 0.0000 0.0000 1.0000
"Bruce Fischl" fischl@nmr.mgh.harvard.edu escribió:
it doesn't look like it's exiting, is it? That is, it keeps running after printing that message?
I would run mri_info on the input volumes (norm.mgz) and check their parameters
Bruce
On Tue, 12 Mar 2013, alexandra.cristobal@urjc.es wrote:
Hi again,
Any suggestion? I haven't any idea about this error. Why does it happen?
Thank you.
alexandra.cristobal@urjc.es escribió:
> Hi Bruce, > > This is the information about my version: > > freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 > > As you can see, it runs in a iMac version 10.6.8 > > Thanks! > > "Bruce Fischl" fischl@nmr.mgh.harvard.edu escribió: > >> what version are you running? This should never happen on the first >> subject, so it's pretty puzzling. >> Bruce >> On Fri, 8 Mar 2013, >> alexandra.cristobal@urjc.es wrote: >> >>> Hi everybody, >>> >>> I'm trying to create my own atlas with the rebuild_gca_atlas >>> script. I >>> obtain the "Input TR, TE, FlipAngle for each subjects must match" >>> error in the # TRAIN FROM SEGMENTED_SUBJECTS USING M3D_ONE >>> step (using >>> mri_ca_train for all subjects). >>> TR, TE and FlipAngle are the same for all patients. >>> >>> What can be the problem? >>> >>> >>> The log is: >>> >>> mri_ca_train -prior_spacing 2 -node_spacing 4 -mask brain.mgz >>> -parc_dir seg_edited.mgz -xform talairach_one.m3z -T1 norm.mgz -check >>> 4163 4168 >>> /Applications/freesurfer/subjects/average/RB_all_2013-03-07.gca >>> reading input 0: /Applications/freesurfer/subjects/4163/mri/norm.mgz >>> spacing priors every 2.0 mm >>> spacing nodes every 4.0 mm >>> using MR volume brain.mgz to mask input volume... >>> reading segmentation from subject's mri/seg_edited.mgz directory >>> reading xform from talairach_one.m3z >>> reading T1 data from subject's mri/norm.mgz directory >>> will conduct sanity-check of labels... >>> training on 2 subject and writing results to >>> /Applications/freesurfer/subjects/average/RB_all_2013-03-07.gca >>> gcaAllocMax: node dims 64 64 64 >>> gcaAllocMax: prior dims 128 128 128 >>> gcaAllocMax: max_labels 4 >>> *************************************************************************** >>> processing subject 4163, 1 of 2... >>> reading volume /Applications/freesurfer/subjects/4163/mri/brain.mgz >>> for masking... >>> gunzip -c >>> /Applications/freesurfer/subjects/4163/mri/transforms/talairach_one.m3z >>> checking labels in subject 4163... >>> max_xtal_l_hippo = -12.6 >>> max_xtal_l_caudate = -5.8 >>> max_xtal_l_amygdala = -17.1 >>> max_xtal_l_putamen = -12.7 >>> max_xtal_l_pallidum = -11.4 >>> min_xtal_r_hippo = 15.2 >>> min_xtal_r_caudate = 6.4 >>> min_xtal_r_amygdala = 16.4 >>> min_xtal_r_putamen = 13.9 >>> min_xtal_r_pallidum = 13.1 >>> Input TR, TE, FlipAngle for each subjects must match. >>> >>> 23 prior holes filled >>> *************************************************************************** >>> processing subject 4168, 2 of 2... >>> nn >>> >>> >>> Thank you in advance. >>> >>> _______________________________________________ >>> 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 >> >> >> The information in this e-mail is intended only for the >> person to whom it is >> addressed. If you believe this e-mail was sent to you in >> error and the e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to >> you in error >> but does not contain patient information, please contact the sender >> and properly >> dispose of the e-mail. >> >> > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >
freesurfer@nmr.mgh.harvard.edu
-
alexandra.cristobal＠urjc.es -
Bruce Fischl