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help > CONN preprocessing :normalization error
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Jul 19, 2017 03:07 PM | njoud aldusary
CONN preprocessing :normalization error
Hi all
I did the pre-processing in may for my data and the process wen so fine , bur now I need to re do it but I got new error that:
** The images do not all have same orientation and/or voxel sizes. **
The function assumes that a voxel in one image corresponds exactly
with the same voxel in another. This is not a safe assumption if
the orientation information in the headers or .mat files says that
the images are oriented differently. Please ensure that you process
all data correctly. For example, you may have realigned the images,
but not actually resliced them to be in voxel-wise alignment.
Here are the orientation matrices of the image volumes. This list
can be used to determine which file(s) are causing the problem.
[-1.49725 0.0437924 -0.0795128 95.8085; 0.0433495 1.49934 0.00949192 -121.927; -0.0797552 -0.00717663 1.49786 -66.8717] C:\spm12\tpm\TPM.nii
[-1.5 0 0 91.5; 0 1.5 0 -127.5; 0 0 1.5 -73.5] C:\spm12\tpm\TPM.nii
[-1.5 0 0 91.5; 0 1.5 0 -127.5; 0 0 1.5 -73.5] C:\spm12\tpm\TPM.nii
[-1.5 0 0 91.5; 0 1.5 0 -127.5; 0 0 1.5 -73.5] C:\spm12\tpm\TPM.nii
[-1.5 0 0 91.5; 0 1.5 0 -127.5; 0 0 1.5 -73.5] C:\spm12\tpm\TPM.nii
[-1.5 0 0 91.5; 0 1.5 0 -127.5; 0 0 1.5 -73.5] C:\spm12\tpm\TPM.nii
Failed 'Normalise: Estimate & Write'
Error using spm_check_orientations (line 65)
The orientations etc must be identical for this procedure.
In file "C:\spm12\spm_check_orientations.m" (v5097), function "spm_check_orientations" at line 65.
In file "C:\spm12\spm_load_priors8.m" (v5962), function "spm_load_priors8" at line 22.
In file "C:\spm12\spm_preproc_run.m" (v6365), function "run_job" at line 61.
In file "C:\spm12\spm_preproc_run.m" (v6365), function "spm_preproc_run" at line 41.
In file "C:\spm12\config\spm_run_norm.m" (v6578), function "normalise" at line 72.
In file "C:\spm12\config\spm_run_norm.m" (v6578), function "spm_run_norm" at line 23.
The following modules did not run:
Failed: Normalise: Estimate & Write
any solution suggestion .....
Thank you
Njoud
I did the pre-processing in may for my data and the process wen so fine , bur now I need to re do it but I got new error that:
** The images do not all have same orientation and/or voxel sizes. **
The function assumes that a voxel in one image corresponds exactly
with the same voxel in another. This is not a safe assumption if
the orientation information in the headers or .mat files says that
the images are oriented differently. Please ensure that you process
all data correctly. For example, you may have realigned the images,
but not actually resliced them to be in voxel-wise alignment.
Here are the orientation matrices of the image volumes. This list
can be used to determine which file(s) are causing the problem.
[-1.49725 0.0437924 -0.0795128 95.8085; 0.0433495 1.49934 0.00949192 -121.927; -0.0797552 -0.00717663 1.49786 -66.8717] C:\spm12\tpm\TPM.nii
[-1.5 0 0 91.5; 0 1.5 0 -127.5; 0 0 1.5 -73.5] C:\spm12\tpm\TPM.nii
[-1.5 0 0 91.5; 0 1.5 0 -127.5; 0 0 1.5 -73.5] C:\spm12\tpm\TPM.nii
[-1.5 0 0 91.5; 0 1.5 0 -127.5; 0 0 1.5 -73.5] C:\spm12\tpm\TPM.nii
[-1.5 0 0 91.5; 0 1.5 0 -127.5; 0 0 1.5 -73.5] C:\spm12\tpm\TPM.nii
[-1.5 0 0 91.5; 0 1.5 0 -127.5; 0 0 1.5 -73.5] C:\spm12\tpm\TPM.nii
Failed 'Normalise: Estimate & Write'
Error using spm_check_orientations (line 65)
The orientations etc must be identical for this procedure.
In file "C:\spm12\spm_check_orientations.m" (v5097), function "spm_check_orientations" at line 65.
In file "C:\spm12\spm_load_priors8.m" (v5962), function "spm_load_priors8" at line 22.
In file "C:\spm12\spm_preproc_run.m" (v6365), function "run_job" at line 61.
In file "C:\spm12\spm_preproc_run.m" (v6365), function "spm_preproc_run" at line 41.
In file "C:\spm12\config\spm_run_norm.m" (v6578), function "normalise" at line 72.
In file "C:\spm12\config\spm_run_norm.m" (v6578), function "spm_run_norm" at line 23.
The following modules did not run:
Failed: Normalise: Estimate & Write
any solution suggestion .....
Thank you
Njoud
Jul 20, 2017 12:07 AM | Alfonso Nieto-Castanon - Boston University
RE: CONN preprocessing :normalization error
Hi Njoud,
My guess is that this reflects an earlier attempt to either coregister or realign the first image in your TPM.nii file (which caused the 6 tissue maps inside the TPM.nii file to be out of registration). If my guess is correct there will be a file named TPM.mat in the spm12/tpm folder, and simply deleting this file should fix this issue.
Best
Alfonso
Originally posted by njoud aldusary:
My guess is that this reflects an earlier attempt to either coregister or realign the first image in your TPM.nii file (which caused the 6 tissue maps inside the TPM.nii file to be out of registration). If my guess is correct there will be a file named TPM.mat in the spm12/tpm folder, and simply deleting this file should fix this issue.
Best
Alfonso
Originally posted by njoud aldusary:
Hi all
I did the pre-processing in may for my data and the process wen so fine , bur now I need to re do it but I got new error that:
** The images do not all have same orientation and/or voxel sizes. **
The function assumes that a voxel in one image corresponds exactly
with the same voxel in another. This is not a safe assumption if
the orientation information in the headers or .mat files says that
the images are oriented differently. Please ensure that you process
all data correctly. For example, you may have realigned the images,
but not actually resliced them to be in voxel-wise alignment.
Here are the orientation matrices of the image volumes. This list
can be used to determine which file(s) are causing the problem.
[-1.49725 0.0437924 -0.0795128 95.8085; 0.0433495 1.49934 0.00949192 -121.927; -0.0797552 -0.00717663 1.49786 -66.8717] C:\spm12\tpm\TPM.nii
[-1.5 0 0 91.5; 0 1.5 0 -127.5; 0 0 1.5 -73.5] C:\spm12\tpm\TPM.nii
[-1.5 0 0 91.5; 0 1.5 0 -127.5; 0 0 1.5 -73.5] C:\spm12\tpm\TPM.nii
[-1.5 0 0 91.5; 0 1.5 0 -127.5; 0 0 1.5 -73.5] C:\spm12\tpm\TPM.nii
[-1.5 0 0 91.5; 0 1.5 0 -127.5; 0 0 1.5 -73.5] C:\spm12\tpm\TPM.nii
[-1.5 0 0 91.5; 0 1.5 0 -127.5; 0 0 1.5 -73.5] C:\spm12\tpm\TPM.nii
Failed 'Normalise: Estimate & Write'
Error using spm_check_orientations (line 65)
The orientations etc must be identical for this procedure.
In file "C:\spm12\spm_check_orientations.m" (v5097), function "spm_check_orientations" at line 65.
In file "C:\spm12\spm_load_priors8.m" (v5962), function "spm_load_priors8" at line 22.
In file "C:\spm12\spm_preproc_run.m" (v6365), function "run_job" at line 61.
In file "C:\spm12\spm_preproc_run.m" (v6365), function "spm_preproc_run" at line 41.
In file "C:\spm12\config\spm_run_norm.m" (v6578), function "normalise" at line 72.
In file "C:\spm12\config\spm_run_norm.m" (v6578), function "spm_run_norm" at line 23.
The following modules did not run:
Failed: Normalise: Estimate & Write
any solution suggestion .....
Thank you
Njoud
I did the pre-processing in may for my data and the process wen so fine , bur now I need to re do it but I got new error that:
** The images do not all have same orientation and/or voxel sizes. **
The function assumes that a voxel in one image corresponds exactly
with the same voxel in another. This is not a safe assumption if
the orientation information in the headers or .mat files says that
the images are oriented differently. Please ensure that you process
all data correctly. For example, you may have realigned the images,
but not actually resliced them to be in voxel-wise alignment.
Here are the orientation matrices of the image volumes. This list
can be used to determine which file(s) are causing the problem.
[-1.49725 0.0437924 -0.0795128 95.8085; 0.0433495 1.49934 0.00949192 -121.927; -0.0797552 -0.00717663 1.49786 -66.8717] C:\spm12\tpm\TPM.nii
[-1.5 0 0 91.5; 0 1.5 0 -127.5; 0 0 1.5 -73.5] C:\spm12\tpm\TPM.nii
[-1.5 0 0 91.5; 0 1.5 0 -127.5; 0 0 1.5 -73.5] C:\spm12\tpm\TPM.nii
[-1.5 0 0 91.5; 0 1.5 0 -127.5; 0 0 1.5 -73.5] C:\spm12\tpm\TPM.nii
[-1.5 0 0 91.5; 0 1.5 0 -127.5; 0 0 1.5 -73.5] C:\spm12\tpm\TPM.nii
[-1.5 0 0 91.5; 0 1.5 0 -127.5; 0 0 1.5 -73.5] C:\spm12\tpm\TPM.nii
Failed 'Normalise: Estimate & Write'
Error using spm_check_orientations (line 65)
The orientations etc must be identical for this procedure.
In file "C:\spm12\spm_check_orientations.m" (v5097), function "spm_check_orientations" at line 65.
In file "C:\spm12\spm_load_priors8.m" (v5962), function "spm_load_priors8" at line 22.
In file "C:\spm12\spm_preproc_run.m" (v6365), function "run_job" at line 61.
In file "C:\spm12\spm_preproc_run.m" (v6365), function "spm_preproc_run" at line 41.
In file "C:\spm12\config\spm_run_norm.m" (v6578), function "normalise" at line 72.
In file "C:\spm12\config\spm_run_norm.m" (v6578), function "spm_run_norm" at line 23.
The following modules did not run:
Failed: Normalise: Estimate & Write
any solution suggestion .....
Thank you
Njoud
Jul 27, 2017 02:07 PM | njoud aldusary
RE: CONN preprocessing :normalization error
Thank you very much it is worked very well ....