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 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.damme@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.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 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 < AYENDIKI@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 $FREESURFER_HOME/bin, to overwrite the version of xfmrot that you have now. If it works, we'll include it in the next version. Thanks!
a.y
*From:* freesurfer-bounces@nmr.mgh.harvard.edu [ freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Katherine Damme [ katherine.damme@gmail.com] *Sent:* Tuesday, December 13, 2016 9:38 AM
*To:* Freesurfer support list *Subject:* Re: [Freesurfer] Tracula Set: No Match
On Tue, Dec 13, 2016 at 8:34 AM, Yendiki, Anastasia < AYENDIKI@mgh.harvard.edu> wrote:
Ok, if you also send me the first file, /media/Data/Temple/Temple_Trac ula/31313422_10128/dmri/dwi.ecclog, I'll see if I can replicate the error.
*From:* freesurfer-bounces@nmr.mgh.harvard.edu [ freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Katherine Damme [ katherine.damme@gmail.com] *Sent:* Tuesday, December 13, 2016 9:21 AM
*To:* Freesurfer support list *Subject:* Re: [Freesurfer] Tracula Set: No Match
Yes. I immediately tried to enter the command in manually, checked the paths, and looked at the command manual for any format errors.
[ksd770@katelinux Temple_Tracula]$ xfmrot /media/Data/Temple/Temple_Trac ula/31313422_10128/dmri/dwi.ecclog /media/Data/Temple/Temple_Trac ula/31313422_10128/dmri/bvecs.norot /media/Data/Temple/Temple_Trac ula/31313422_10128/dmri/bvecs
set: No match.
On Wed, Dec 7, 2016 at 2:41 PM, Yendiki, Anastasia < AYENDIKI@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-bounces@nmr.mgh.harvard.edu [ freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Katherine Damme [ katherine.damme@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 < AYENDIKI@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.damme@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.ecclog /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/bvecs.norot /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/bvecs set: No match."
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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.