Hi, I have received the following error message (copied from trac-all.log file).
fslstats -t /Volumes/RAID_4TB/futhink/nc331_recon/dmri/dwi.nii.gz -k /Volumes/RAID_4TB/futhink/nc331_recon/dlabel/diff/White-Matter++.bbr.nii.gz -m -s | awk '{print $1/$2}' > /Volumes/RAID_4TB/futhink/nc331_recon/dmri/dwi_snr.txt ** ERROR (nifti_image_read): failed to find header file for '-t' ** ERROR: nifti_image_open(-t): bad header info Error: failed to open file -t ERROR: Could not open image -t Image Exception : #22 :: Failed to read volume -t terminate called after throwing an instance of 'RBD_COMMON::BaseException'
The file (dwi.nii.gz) exists in the correct location, and appears to have the correct number of frames (60 directions + 10 b0). We scan on a Siemens 3T tim trio. I unpack the data using unpacksdcmdir and I specify the resulting .mgz file in the tracula config file. Running locally on mac os 10.6.8.
Any suggestions would be appreciated. Thanks, Scott
Hi Scott - Which version of FSL are you using? I cannot replicate this behavior of fslstats on our data.
Thanks, a.y
On Mon, 12 Dec 2011, Scott Hayes wrote:
Hi, I have received the following error message (copied from trac-all.log file).
fslstats -t /Volumes/RAID_4TB/futhink/nc331_recon/dmri/dwi.nii.gz -k /Volumes/RAID_4TB/futhink/nc331_recon/dlabel/diff/White-Matter++.bbr.nii.gz -m -s | awk '{print $1/$2}' > /Volumes/RAID_4TB/futhink/nc331_recon/dmri/dwi_snr.txt ** ERROR (nifti_image_read): failed to find header file for '-t' ** ERROR: nifti_image_open(-t): bad header info Error: failed to open file -t ERROR: Could not open image -t Image Exception : #22 :: Failed to read volume -t terminate called after throwing an instance of 'RBD_COMMON::BaseException'
The file (dwi.nii.gz) exists in the correct location, and appears to have the correct number of frames (60 directions + 10 b0). We scan on a Siemens 3T tim trio. I unpack the data using unpacksdcmdir and I specify the resulting .mgz file in the tracula config file. Running locally on mac os 10.6.8.
Any suggestions would be appreciated. Thanks, Scott _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi, I'm using FSL 4.1.4
On Mon, Dec 12, 2011 at 12:43 PM, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote:
Hi Scott - Which version of FSL are you using? I cannot replicate this behavior of fslstats on our data.
Thanks, a.y
On Mon, 12 Dec 2011, Scott Hayes wrote:
Hi, I have received the following error message (copied from trac-all.log file).
fslstats -t /Volumes/RAID_4TB/futhink/nc331_recon/dmri/dwi.nii.gz -k
/Volumes/RAID_4TB/futhink/nc331_recon/dlabel/diff/White-Matter++.bbr.nii.gz -m -s | awk '{print $1/$2}' > /Volumes/RAID_4TB/futhink/nc331_recon/dmri/dwi_snr.txt ** ERROR (nifti_image_read): failed to find header file for '-t' ** ERROR: nifti_image_open(-t): bad header info Error: failed to open file -t ERROR: Could not open image -t Image Exception : #22 :: Failed to read volume -t terminate called after throwing an instance of 'RBD_COMMON::BaseException'
The file (dwi.nii.gz) exists in the correct location, and appears to have the correct number of frames (60 directions + 10 b0). We scan on a Siemens 3T tim trio. I unpack the data using unpacksdcmdir and I specify the resulting .mgz file in the tracula config file. Running locally on mac os 10.6.8.
Any suggestions would be appreciated. Thanks, Scott _______________________________________________ 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.
Ok, I just checked the 4.1.4 version of fslstats, and indeed it doesn't have the -t option. We're using version 4.1.5.
On Mon, 12 Dec 2011, Scott Hayes wrote:
Hi, I'm using FSL 4.1.4
On Mon, Dec 12, 2011 at 12:43 PM, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote:
Hi Scott - Which version of FSL are you using? I cannot replicate this behavior of fslstats on our data.
Thanks, a.y
On Mon, 12 Dec 2011, Scott Hayes wrote:
Hi, I have received the following error message (copied from trac-all.log file).
fslstats -t /Volumes/RAID_4TB/futhink/nc331_recon/dmri/dwi.nii.gz -k
/Volumes/RAID_4TB/futhink/nc331_recon/dlabel/diff/White-Matter++.bbr.nii.gz -m -s | awk '{print $1/$2}' > /Volumes/RAID_4TB/futhink/nc331_recon/dmri/dwi_snr.txt ** ERROR (nifti_image_read): failed to find header file for '-t' ** ERROR: nifti_image_open(-t): bad header info Error: failed to open file -t ERROR: Could not open image -t Image Exception : #22 :: Failed to read volume -t terminate called after throwing an instance of 'RBD_COMMON::BaseException'
The file (dwi.nii.gz) exists in the correct location, and appears to have the correct number of frames (60 directions + 10 b0). We scan on a Siemens 3T tim trio. I unpack the data using unpacksdcmdir and I specify the resulting .mgz file in the tracula config file. Running locally on mac os 10.6.8.
Any suggestions would be appreciated. Thanks, Scott _______________________________________________ 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@nmr.mgh.harvard.edu
-
Anastasia Yendiki -
Scott Hayes