Re: [Freesurfer] trac-all -bedp ERROR: Could not read - merged_ph1samples.nii.gz
Good to know, thanks for sharing this trick! On Sat, 3 Sep 2016, Chung, Yoonho wrote: I found out why it didn't work. One of the script that bedpostx_postproc.sh calls is written in python2. I set my default to python3 and therefore caused the error in the last step. After I loaded python2 environment, i got the merged files and finished properly. Thanks for your help as always! Yoon ___ 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.
Re: [Freesurfer] trac-all -bedp ERROR: Could not read - merged_ph1samples.nii.gz
I found out why it didn't work. One of the script that bedpostx_postproc.sh calls is written in python2. I set my default to python3 and therefore caused the error in the last step. After I loaded python2 environment, i got the merged files and finished properly. Thanks for your help as always! Yoon ___ 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.
Re: [Freesurfer] trac-all -bedp ERROR: Could not read - merged_ph1samples.nii.gz
Hi Yoon - It sounds like FSL's bedpostx postprocessing script failed. You can run it like this: bedpostx_postproc.sh /path/to/your/subject/dmri This script merges the results from all the slices. It's possible that something went wrong with the slices (you ran out disk space for example). If the slice results are ok, this'll do it. Best, a.y On Fri, 2 Sep 2016, Chung, Yoonho wrote: Hi Anastasia, trac-all -prep completed without error. I thought trac-all -bedp starts and ends without any error but trac-all path failed with these messages. Loading BEDPOST parameter samples from */dmri.bedpostX niiRead(): error opening file*/dmri.bedpostX/merged_ph1samples.nii.gz ERROR: Could not read */dmri.bedpostX/merged_ph1samples.nii.gz I looked at the dmri.bedpostX directory and all slices exist in the dmri.bedpostX/diff_slices directory but realized the trac-all -bedp phase did not create the merged samples in this directory. I am currently runnning with FSL/5.0.6 Program versions: $Id: trac-all,v 1.56 2014/05/26 08:28:32 ayendiki Exp $ and freesurfer version 5.3 I looked through the mailing list to see if someone ran into a similar problem but could not find a good solution. Do you have what may have caused this? Any other files I would like to look into? Thank you Yoon ___ 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] trac-all -bedp ERROR: Could not read - merged_ph1samples.nii.gz
Hi Anastasia, trac-all -prep completed without error. I thought trac-all -bedp starts and ends without any error but trac-all path failed with these messages. Loading BEDPOST parameter samples from */dmri.bedpostX niiRead(): error opening file*/dmri.bedpostX/merged_ph1samples.nii.gz ERROR: Could not read */dmri.bedpostX/merged_ph1samples.nii.gz I looked at the dmri.bedpostX directory and all slices exist in the dmri.bedpostX/diff_slices directory but realized the trac-all -bedp phase did not create the merged samples in this directory. I am currently runnning with FSL/5.0.6 Program versions: $Id: trac-all,v 1.56 2014/05/26 08:28:32 ayendiki Exp $ and freesurfer version 5.3 I looked through the mailing list to see if someone ran into a similar problem but could not find a good solution. Do you have what may have caused this? Any other files I would like to look into? Thank you Yoon ___ 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.
