Hi, mri_ca_normalize failed for a subject. Here is the CA normalize portion of recon-all.log: =========================================== CA Normalize Thu Nov 17 17:02:05 PST 2005 $SUBJECTS_DIR/<subjid>/mri mri_ca_normalize -mask brain.mgz nu.mgz /space/monkeys/1/pubsw/packages/freesurfer/RH4-x86_64/average/RB40_talairach_2005-07-20.gca transforms/talairach.lta norm.mgz using MR volume brain.mgz to mask input volume... reading 1 input volumes reading atlas from '/space/monkeys/1/pubsw/packages/freesurfer/RH4-x86_64/average/RB40_talairach_2005-07-20.gca'... setting gca type = Normal gca type Direction cosines read: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000 x_a = 0.0000, y_a = 0.0000, z_a = 1.0000 x_s = 0.0000, y_s = -1.0000, z_s = 0.0000 c_r = 0.0000, c_a = 0.0000, c_s = 0.0000 reading transform from 'transforms/talairach.lta'... mghRead: encountered error executing: 'zcat $SUBJECTS_DIR/<subjid>/mri/nu.mgz',frame -1 mri_ca_normalize: could not read input MR volume from nu.mgz reading input volume from nu.mgz... ERROR: mri_ca_normalize with non-zero status =======================================================
$SUBJECTS_DIR/<subjid>/mri contains nu.mgz and the talairach looks normal. How do I fix this?
Michele
sounds like un.mgz doesn't exist (or you don't have read permission)
On Mon, 28 Nov 2005, Michele Perry wrote:
Hi, mri_ca_normalize failed for a subject. Here is the CA normalize portion of recon-all.log: =========================================== CA Normalize Thu Nov 17 17:02:05 PST 2005 $SUBJECTS_DIR/<subjid>/mri mri_ca_normalize -mask brain.mgz nu.mgz /space/monkeys/1/pubsw/packages/freesurfer/RH4-x86_64/average/RB40_talairach_2005-07-20.gca transforms/talairach.lta norm.mgz using MR volume brain.mgz to mask input volume... reading 1 input volumes reading atlas from '/space/monkeys/1/pubsw/packages/freesurfer/RH4-x86_64/average/RB40_talairach_2005-07-20.gca'... setting gca type = Normal gca type Direction cosines read: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000 x_a = 0.0000, y_a = 0.0000, z_a = 1.0000 x_s = 0.0000, y_s = -1.0000, z_s = 0.0000 c_r = 0.0000, c_a = 0.0000, c_s = 0.0000 reading transform from 'transforms/talairach.lta'... mghRead: encountered error executing: 'zcat $SUBJECTS_DIR/<subjid>/mri/nu.mgz',frame -1 mri_ca_normalize: could not read input MR volume from nu.mgz reading input volume from nu.mgz... ERROR: mri_ca_normalize with non-zero status =======================================================
$SUBJECTS_DIR/<subjid>/mri contains nu.mgz and the talairach looks normal. How do I fix this?
Michele
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
could also be something wrong with running zcat
Bruce Fischl wrote:
sounds like un.mgz doesn't exist (or you don't have read permission)
On Mon, 28 Nov 2005, Michele Perry wrote:
Hi, mri_ca_normalize failed for a subject. Here is the CA normalize portion of recon-all.log: =========================================== CA Normalize Thu Nov 17 17:02:05 PST 2005 $SUBJECTS_DIR/<subjid>/mri mri_ca_normalize -mask brain.mgz nu.mgz /space/monkeys/1/pubsw/packages/freesurfer/RH4-x86_64/average/RB40_talairach_2005-07-20.gca
transforms/talairach.lta norm.mgz using MR volume brain.mgz to mask input volume... reading 1 input volumes reading atlas from '/space/monkeys/1/pubsw/packages/freesurfer/RH4-x86_64/average/RB40_talairach_2005-07-20.gca'...
setting gca type = Normal gca type Direction cosines read: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000 x_a = 0.0000, y_a = 0.0000, z_a = 1.0000 x_s = 0.0000, y_s = -1.0000, z_s = 0.0000 c_r = 0.0000, c_a = 0.0000, c_s = 0.0000 reading transform from 'transforms/talairach.lta'... mghRead: encountered error executing: 'zcat $SUBJECTS_DIR/<subjid>/mri/nu.mgz',frame -1 mri_ca_normalize: could not read input MR volume from nu.mgz reading input volume from nu.mgz... ERROR: mri_ca_normalize with non-zero status =======================================================
$SUBJECTS_DIR/<subjid>/mri contains nu.mgz and the talairach looks normal. How do I fix this?
Michele
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
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Doug Greve -
Michele Perry