It doesn't recognize the format of your field map. It assumes that the field map has either 2 frames (2 phase maps) or 1 frame (a phase difference map).
________________________________ From: Katherine Damme [katherine.da...@gmail.com] Sent: Friday, December 16, 2016 5:18 PM To: Freesurfer support list; Anastasia Yendiki Subject: Re: [Freesurfer] Tracula Set: No Match When I run this on the command line it seems to be completing the fslroi step fine: "fslroi /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi_eddy.nii.gz /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/lowb.nii.gz 0 1 ERROR: Unrecognized format of phase map /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/b0pha.nii.gz Linux katelinux.psych.northwestern.edu<http://katelinux.psych.northwestern.edu> 2.6.32-642.6.2.el6.x86_64 #1 SMP Mon Oct 24 10:22:33 EDT 2016 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Fri Dec 16 15:38:48 CST 2016 [ksd770@katelinux Temple_Tracula]# fslroi /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi_eddy.nii.gz /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/lowb.nii.gz 0 1 [ksd770@katelinux Temple_Tracula]# trac-all -prep -c dmrirc_10128.txt" What is the next step in the code where it is failing? On Wed, Dec 14, 2016 at 9:19 PM, Katherine Damme <katherine.da...@gmail.com<mailto:katherine.da...@gmail.com>> wrote: I am now getting this error. I am not sure if this is a new issue or related. fslorient -forceradiological /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/b0pha.nii.gz mri_probedicom --i //media/Data/Temple/Temple_Tracula/31313422_10128/dti_dicom/31313422_10128.MR<http://31313422_10128.MR>.Temple.9.1.20140806.182244.xfrp16.dcm > /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/b0info.dat TE: Subscript out of range. fslroi /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi_eddy.nii.gz /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/lowb.nii.gz 0 1 ERROR: Unrecognized format of phase map /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/b0pha.nii.gz Linux katelinux.psych.northwestern.edu<http://katelinux.psych.northwestern.edu> 2.6.32-642.6.2.el6.x86_64 #1 SMP Mon Oct 24 10:22:33 EDT 2016 x86_64 x86_64 x86_64 GNU/Linux I check all of these images and I can open them. On Tue, Dec 13, 2016 at 7:59 PM, Yendiki, Anastasia <ayend...@mgh.harvard.edu<mailto:ayend...@mgh.harvard.edu>> wrote: Hi Katherine - Can you please use the attached version and tell me if it works? You'll have to copy it into $FREESURFER_HOME/bin, to overwrite the version of xfmrot that you have now. If it works, we'll include it in the next version. Thanks! a.y ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> [freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of Katherine Damme [katherine.da...@gmail.com<mailto:katherine.da...@gmail.com>] Sent: Tuesday, December 13, 2016 9:38 AM To: Freesurfer support list Subject: Re: [Freesurfer] Tracula Set: No Match On Tue, Dec 13, 2016 at 8:34 AM, Yendiki, Anastasia <ayend...@mgh.harvard.edu<mailto:ayend...@mgh.harvard.edu>> wrote: Ok, if you also send me the first file, /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi.ec<http://dwi.ec>clog, I'll see if I can replicate the error. ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> [freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of Katherine Damme [katherine.da...@gmail.com<mailto:katherine.da...@gmail.com>] Sent: Tuesday, December 13, 2016 9:21 AM To: Freesurfer support list Subject: Re: [Freesurfer] Tracula Set: No Match Yes. I immediately tried to enter the command in manually, checked the paths, and looked at the command manual for any format errors. [ksd770@katelinux Temple_Tracula]$ xfmrot /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi.ec<http://dwi.ec>clog /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/bvecs.norot /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/bvecs set: No match. On Wed, Dec 7, 2016 at 2:41 PM, Yendiki, Anastasia <ayend...@mgh.harvard.edu<mailto:ayend...@mgh.harvard.edu>> wrote: Thanks. This looks fine. When you run that xfmrot command directly on the linux command line, do you get the same error? ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> [freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of Katherine Damme [katherine.da...@gmail.com<mailto:katherine.da...@gmail.com>] Sent: Wednesday, December 07, 2016 12:41 PM To: Freesurfer support list Subject: Re: [Freesurfer] Tracula Set: No Match On Mon, Dec 5, 2016 at 12:00 PM, Yendiki, Anastasia <ayend...@mgh.harvard.edu<mailto:ayend...@mgh.harvard.edu>> wrote: Hi Katherine - The error occurs when processing this file: /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/bvecs.norot Can you send this file? Thanks! a.y ________________________________ From: Katherine Damme [katherine.da...@gmail.com<mailto:katherine.da...@gmail.com>] Sent: Saturday, December 03, 2016 3:42 PM To: Freesurfer support list; Anastasia Yendiki Subject: Tracula Set: No Match Hello! I have been getting a "set: No match." error. I haven't been able to sort out what is causing it. Attached you will find the configuration file, command, and log files associated with this error. "mv -f /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/bvecs /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/bvecs.norot xfmrot /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi.ec<http://dwi.ec>clog /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/bvecs.norot /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/bvecs set: No match." _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto: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<mailto: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<mailto: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<mailto: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 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.
