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."
Also if I try to avoid this step I get a new error
I don't know if this adds helpful insight!
fslswapdim /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/b0pha.nii.gz x -y z /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/b0pha.nii.gz
INFO: left-right orientation was flipped by fslswapdim
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
On Sat, Dec 3, 2016 at 2:42 PM, Katherine Damme katherine.damme@gmail.com wrote:
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."
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."
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."
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.
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.edumailto: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.commailto: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."
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.
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.ecclog /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 <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."
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 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, if you also send me the first file, /media/Data/Temple/Temple_Tracula/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_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.
On Wed, Dec 7, 2016 at 2:41 PM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Katherine Damme [katherine.damme@gmail.commailto: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.edumailto: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.commailto: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."
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.edumailto: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.
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_ Tracula/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_ 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.
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."
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 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 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.
Hi Katherine - Can you please use the attached version and tell me if it works? You'll have to copy it into $FREESURFER_HOME/bin, to overwrite the version of xfmrot that you have now. If it works, we'll include it in the next version. Thanks!
a.y
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Katherine Damme [katherine.damme@gmail.com] Sent: Tuesday, December 13, 2016 9:38 AM To: Freesurfer support list Subject: Re: [Freesurfer] Tracula Set: No Match
On Tue, Dec 13, 2016 at 8:34 AM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote: Ok, if you also send me the first file, /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi.ecclog, I'll see if I can replicate the error.
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Katherine Damme [katherine.damme@gmail.commailto:katherine.damme@gmail.com] Sent: Tuesday, December 13, 2016 9:21 AM
To: Freesurfer support list Subject: Re: [Freesurfer] Tracula Set: No Match
Yes. I immediately tried to enter the command in manually, checked the paths, and looked at the command manual for any format errors.
[ksd770@katelinux Temple_Tracula]$ xfmrot /media/Data/Temple/Temple_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.
On Wed, Dec 7, 2016 at 2:41 PM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Katherine Damme [katherine.damme@gmail.commailto: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.edumailto: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.commailto: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.echttp://dwi.ecclog /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.edumailto: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.edumailto: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.edumailto: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.
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.
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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.
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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.
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."
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 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 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 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.
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.damme@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.eduhttp://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.commailto: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.MRhttp://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.eduhttp://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.edumailto: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 $FREESURFER_HOME/bin, to overwrite the version of xfmrot that you have now. If it works, we'll include it in the next version. Thanks!
a.y
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Katherine Damme [katherine.damme@gmail.commailto:katherine.damme@gmail.com] Sent: Tuesday, December 13, 2016 9:38 AM
To: Freesurfer support list Subject: Re: [Freesurfer] Tracula Set: No Match
On Tue, Dec 13, 2016 at 8:34 AM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote: Ok, if you also send me the first file, /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi.echttp://dwi.ecclog, I'll see if I can replicate the error.
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Katherine Damme [katherine.damme@gmail.commailto:katherine.damme@gmail.com] Sent: Tuesday, December 13, 2016 9:21 AM
To: Freesurfer support list Subject: Re: [Freesurfer] Tracula Set: No Match
Yes. I immediately tried to enter the command in manually, checked the paths, and looked at the command manual for any format errors.
[ksd770@katelinux Temple_Tracula]$ xfmrot /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi.echttp://dwi.ecclog /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 <AYENDIKI@mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Katherine Damme [katherine.damme@gmail.commailto: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.edumailto: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.commailto: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.echttp://dwi.ecclog /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.edumailto: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.edumailto: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.edumailto: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.edumailto: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.
This is being generated by an earlier step in the trac-all -prep right?
On Fri, Dec 16, 2016 at 4:23 PM, Yendiki, Anastasia < AYENDIKI@mgh.harvard.edu> wrote:
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.damme@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 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_Trac ula/31313422_10128/dmri/b0pha.nii.gz
mri_probedicom --i //media/Data/Temple/Temple_Tra cula/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_Trac ula/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_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.
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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No, it's a separate scan that you provide.
________________________________ From: Katherine Damme [katherine.damme@gmail.com] Sent: Monday, December 19, 2016 1:43 PM To: Freesurfer support list; Anastasia Yendiki Subject: Re: [Freesurfer] Tracula Set: No Match
This is being generated by an earlier step in the trac-all -prep right?
On Fri, Dec 16, 2016 at 4:23 PM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote: 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.damme@gmail.commailto:katherine.damme@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.eduhttp://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.commailto: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.MRhttp://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.eduhttp://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.edumailto: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 $FREESURFER_HOME/bin, to overwrite the version of xfmrot that you have now. If it works, we'll include it in the next version. Thanks!
a.y
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Katherine Damme [katherine.damme@gmail.commailto:katherine.damme@gmail.com] Sent: Tuesday, December 13, 2016 9:38 AM
To: Freesurfer support list Subject: Re: [Freesurfer] Tracula Set: No Match
On Tue, Dec 13, 2016 at 8:34 AM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote: Ok, if you also send me the first file, /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi.echttp://dwi.ecclog, I'll see if I can replicate the error.
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Katherine Damme [katherine.damme@gmail.commailto:katherine.damme@gmail.com] Sent: Tuesday, December 13, 2016 9:21 AM
To: Freesurfer support list Subject: Re: [Freesurfer] Tracula Set: No Match
Yes. I immediately tried to enter the command in manually, checked the paths, and looked at the command manual for any format errors.
[ksd770@katelinux Temple_Tracula]$ xfmrot /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi.echttp://dwi.ecclog /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 <AYENDIKI@mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Katherine Damme [katherine.damme@gmail.commailto: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.edumailto: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.commailto: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.echttp://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.
Is this meant to be calculated from the B0 dicoms?
On Mon, Dec 19, 2016 at 12:44 PM, Yendiki, Anastasia < AYENDIKI@mgh.harvard.edu> wrote:
No, it's a separate scan that you provide.
*From:* Katherine Damme [katherine.damme@gmail.com] *Sent:* Monday, December 19, 2016 1:43 PM
*To:* Freesurfer support list; Anastasia Yendiki *Subject:* Re: [Freesurfer] Tracula Set: No Match
This is being generated by an earlier step in the trac-all -prep right?
On Fri, Dec 16, 2016 at 4:23 PM, Yendiki, Anastasia < AYENDIKI@mgh.harvard.edu> wrote:
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.damme@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_Trac ula/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_Trac ula/31313422_10128/dmri/dwi_eddy.nii.gz /media/Data/Temple/Temple_Trac ula/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_Trac ula/31313422_10128/dmri/b0pha.nii.gz
mri_probedicom --i //media/Data/Temple/Temple_Tra cula/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_Trac ula/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_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.
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." > > _______________________________________________ > 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. > >
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No - there is no relation between B0 field inhomogeneities (measured by a field map) and b=0 volumes. The capital B refers to the magnetic field in the scanner, the small b is the b-value (diffusion weighting).
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Katherine Damme [katherine.damme@gmail.com] Sent: Monday, December 19, 2016 11:01 PM To: Freesurfer support list Subject: Re: [Freesurfer] Tracula Set: No Match
Is this meant to be calculated from the B0 dicoms?
On Mon, Dec 19, 2016 at 12:44 PM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote: No, it's a separate scan that you provide.
________________________________ From: Katherine Damme [katherine.damme@gmail.commailto:katherine.damme@gmail.com] Sent: Monday, December 19, 2016 1:43 PM
To: Freesurfer support list; Anastasia Yendiki Subject: Re: [Freesurfer] Tracula Set: No Match
This is being generated by an earlier step in the trac-all -prep right?
On Fri, Dec 16, 2016 at 4:23 PM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote: 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.damme@gmail.commailto:katherine.damme@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.eduhttp://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.commailto: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.MRhttp://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.eduhttp://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.edumailto: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 $FREESURFER_HOME/bin, to overwrite the version of xfmrot that you have now. If it works, we'll include it in the next version. Thanks!
a.y
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Katherine Damme [katherine.damme@gmail.commailto:katherine.damme@gmail.com] Sent: Tuesday, December 13, 2016 9:38 AM
To: Freesurfer support list Subject: Re: [Freesurfer] Tracula Set: No Match
On Tue, Dec 13, 2016 at 8:34 AM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote: Ok, if you also send me the first file, /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi.echttp://dwi.ecclog, I'll see if I can replicate the error.
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Katherine Damme [katherine.damme@gmail.commailto:katherine.damme@gmail.com] Sent: Tuesday, December 13, 2016 9:21 AM
To: Freesurfer support list Subject: Re: [Freesurfer] Tracula Set: No Match
Yes. I immediately tried to enter the command in manually, checked the paths, and looked at the command manual for any format errors.
[ksd770@katelinux Temple_Tracula]$ xfmrot /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi.echttp://dwi.ecclog /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 <AYENDIKI@mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Katherine Damme [katherine.damme@gmail.commailto: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.edumailto: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.commailto: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.echttp://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.
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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.
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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.
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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.
How do I generate a field map?
On Mon, Dec 19, 2016 at 10:09 PM, Yendiki, Anastasia < AYENDIKI@mgh.harvard.edu> wrote:
No - there is no relation between B0 field inhomogeneities (measured by a field map) and b=0 volumes. The capital B refers to the magnetic field in the scanner, the small b is the b-value (diffusion weighting).
*From:* freesurfer-bounces@nmr.mgh.harvard.edu [ freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Katherine Damme [ katherine.damme@gmail.com] *Sent:* Monday, December 19, 2016 11:01 PM
*To:* Freesurfer support list *Subject:* Re: [Freesurfer] Tracula Set: No Match
Is this meant to be calculated from the B0 dicoms?
On Mon, Dec 19, 2016 at 12:44 PM, Yendiki, Anastasia < AYENDIKI@mgh.harvard.edu> wrote:
No, it's a separate scan that you provide.
*From:* Katherine Damme [katherine.damme@gmail.com] *Sent:* Monday, December 19, 2016 1:43 PM
*To:* Freesurfer support list; Anastasia Yendiki *Subject:* Re: [Freesurfer] Tracula Set: No Match
This is being generated by an earlier step in the trac-all -prep right?
On Fri, Dec 16, 2016 at 4:23 PM, Yendiki, Anastasia < AYENDIKI@mgh.harvard.edu> wrote:
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.damme@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_Trac ula/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_Trac ula/31313422_10128/dmri/dwi_eddy.nii.gz /media/Data/Temple/Temple_Trac ula/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_Trac ula/31313422_10128/dmri/b0pha.nii.gz
mri_probedicom --i //media/Data/Temple/Temple_Tra cula/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_Trac ula/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 $FREESURFER_HOME/bin, to overwrite the version of xfmrot that you have now. If it works, we'll include it in the next version. Thanks!
a.y
*From:* freesurfer-bounces@nmr.mgh.harvard.edu [ freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Katherine Damme [ katherine.damme@gmail.com] *Sent:* Tuesday, December 13, 2016 9:38 AM
*To:* Freesurfer support list *Subject:* Re: [Freesurfer] Tracula Set: No Match
On Tue, Dec 13, 2016 at 8:34 AM, Yendiki, Anastasia < AYENDIKI@mgh.harvard.edu> wrote:
Ok, if you also send me the first file, /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi.ecclog, I'll see if I can replicate the error.
*From:* freesurfer-bounces@nmr.mgh.harvard.edu [ freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Katherine Damme [katherine.damme@gmail.com] *Sent:* Tuesday, December 13, 2016 9:21 AM
*To:* Freesurfer support list *Subject:* Re: [Freesurfer] Tracula Set: No Match
Yes. I immediately tried to enter the command in manually, checked the paths, and looked at the command manual for any format errors.
[ksd770@katelinux Temple_Tracula]$ xfmrot /media/Data/Temple/Temple_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.
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." >> >> _______________________________________________ >> 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 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. > >
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Sorry the phase map. How do I generate an appropriately formatted phase map?
On Sun, Jan 1, 2017 at 4:15 PM, Katherine Damme katherine.damme@gmail.com wrote:
How do I generate a field map?
On Mon, Dec 19, 2016 at 10:09 PM, Yendiki, Anastasia < AYENDIKI@mgh.harvard.edu> wrote:
No - there is no relation between B0 field inhomogeneities (measured by a field map) and b=0 volumes. The capital B refers to the magnetic field in the scanner, the small b is the b-value (diffusion weighting).
*From:* freesurfer-bounces@nmr.mgh.harvard.edu [ freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Katherine Damme [ katherine.damme@gmail.com] *Sent:* Monday, December 19, 2016 11:01 PM
*To:* Freesurfer support list *Subject:* Re: [Freesurfer] Tracula Set: No Match
Is this meant to be calculated from the B0 dicoms?
On Mon, Dec 19, 2016 at 12:44 PM, Yendiki, Anastasia < AYENDIKI@mgh.harvard.edu> wrote:
No, it's a separate scan that you provide.
*From:* Katherine Damme [katherine.damme@gmail.com] *Sent:* Monday, December 19, 2016 1:43 PM
*To:* Freesurfer support list; Anastasia Yendiki *Subject:* Re: [Freesurfer] Tracula Set: No Match
This is being generated by an earlier step in the trac-all -prep right?
On Fri, Dec 16, 2016 at 4:23 PM, Yendiki, Anastasia < AYENDIKI@mgh.harvard.edu> wrote:
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.damme@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_Trac ula/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_Trac ula/31313422_10128/dmri/b0pha.nii.gz
mri_probedicom --i //media/Data/Temple/Temple_Tra cula/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_Trac ula/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 $FREESURFER_HOME/bin, to overwrite the version of xfmrot that you have now. If it works, we'll include it in the next version. Thanks!
a.y
*From:* freesurfer-bounces@nmr.mgh.harvard.edu [ freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Katherine Damme [katherine.damme@gmail.com] *Sent:* Tuesday, December 13, 2016 9:38 AM
*To:* Freesurfer support list *Subject:* Re: [Freesurfer] Tracula Set: No Match
On Tue, Dec 13, 2016 at 8:34 AM, Yendiki, Anastasia < AYENDIKI@mgh.harvard.edu> wrote:
> Ok, if you also send me the first file, > /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi.ecclog, > I'll see if I can replicate the error. > > ------------------------------ > *From:* freesurfer-bounces@nmr.mgh.harvard.edu [ > freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Katherine > Damme [katherine.damme@gmail.com] > *Sent:* Tuesday, December 13, 2016 9:21 AM > > *To:* Freesurfer support list > *Subject:* Re: [Freesurfer] Tracula Set: No Match > > Yes. I immediately tried to enter the command in manually, checked > the paths, and looked at the command manual for any format errors. > > [ksd770@katelinux Temple_Tracula]$ xfmrot > /media/Data/Temple/Temple_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. > > 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_Trac >>> ula/31313422_10128/dmri/bvecs.norot /media/Data/Temple/Temple_Trac >>> ula/31313422_10128/dmri/bvecs >>> set: No match." >>> >>> _______________________________________________ >>> 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 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 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. > >
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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.
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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.
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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.
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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.
Hi Katherine - You need to have an appropriate field mapping MRI scan.
Best, 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: Sunday, January 01, 2017 5:16 PM To: Freesurfer support list Subject: Re: [Freesurfer] Tracula Set: No Match
Sorry the phase map. How do I generate an appropriately formatted phase map?
On Sun, Jan 1, 2017 at 4:15 PM, Katherine Damme <katherine.damme@gmail.commailto:katherine.damme@gmail.com> wrote: How do I generate a field map?
On Mon, Dec 19, 2016 at 10:09 PM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote: No - there is no relation between B0 field inhomogeneities (measured by a field map) and b=0 volumes. The capital B refers to the magnetic field in the scanner, the small b is the b-value (diffusion weighting).
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Katherine Damme [katherine.damme@gmail.commailto:katherine.damme@gmail.com] Sent: Monday, December 19, 2016 11:01 PM
To: Freesurfer support list Subject: Re: [Freesurfer] Tracula Set: No Match
Is this meant to be calculated from the B0 dicoms?
On Mon, Dec 19, 2016 at 12:44 PM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote: No, it's a separate scan that you provide.
________________________________ From: Katherine Damme [katherine.damme@gmail.commailto:katherine.damme@gmail.com] Sent: Monday, December 19, 2016 1:43 PM
To: Freesurfer support list; Anastasia Yendiki Subject: Re: [Freesurfer] Tracula Set: No Match
This is being generated by an earlier step in the trac-all -prep right?
On Fri, Dec 16, 2016 at 4:23 PM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote: 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.damme@gmail.commailto:katherine.damme@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.eduhttp://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.commailto: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.MRhttp://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.eduhttp://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.edumailto: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 $FREESURFER_HOME/bin, to overwrite the version of xfmrot that you have now. If it works, we'll include it in the next version. Thanks!
a.y
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Katherine Damme [katherine.damme@gmail.commailto:katherine.damme@gmail.com] Sent: Tuesday, December 13, 2016 9:38 AM
To: Freesurfer support list Subject: Re: [Freesurfer] Tracula Set: No Match
On Tue, Dec 13, 2016 at 8:34 AM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote: Ok, if you also send me the first file, /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi.echttp://dwi.ecclog, I'll see if I can replicate the error.
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Katherine Damme [katherine.damme@gmail.commailto:katherine.damme@gmail.com] Sent: Tuesday, December 13, 2016 9:21 AM
To: Freesurfer support list Subject: Re: [Freesurfer] Tracula Set: No Match
Yes. I immediately tried to enter the command in manually, checked the paths, and looked at the command manual for any format errors.
[ksd770@katelinux Temple_Tracula]$ xfmrot /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi.echttp://dwi.ecclog /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 <AYENDIKI@mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Katherine Damme [katherine.damme@gmail.commailto: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.edumailto: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.commailto: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.echttp://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.
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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.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.
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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.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.edumailto: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.edumailto: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.
Is it possible to run tracula with out a phase mapping MRI scan? All I have in this data is a MPRAGE and DWI images weighted at either 0 or 1000.
Thank you.
On Tue, Jan 3, 2017 at 1:07 PM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edu
wrote:
Hi Katherine - You need to have an appropriate field mapping MRI scan.
Best, 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:* Sunday, January 01, 2017 5:16 PM
*To:* Freesurfer support list *Subject:* Re: [Freesurfer] Tracula Set: No Match
Sorry the phase map. How do I generate an appropriately formatted phase map?
On Sun, Jan 1, 2017 at 4:15 PM, Katherine Damme <katherine.damme@gmail.com
wrote:
How do I generate a field map?
On Mon, Dec 19, 2016 at 10:09 PM, Yendiki, Anastasia < AYENDIKI@mgh.harvard.edu> wrote:
No - there is no relation between B0 field inhomogeneities (measured by a field map) and b=0 volumes. The capital B refers to the magnetic field in the scanner, the small b is the b-value (diffusion weighting).
*From:* freesurfer-bounces@nmr.mgh.harvard.edu [ freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Katherine Damme [ katherine.damme@gmail.com] *Sent:* Monday, December 19, 2016 11:01 PM
*To:* Freesurfer support list *Subject:* Re: [Freesurfer] Tracula Set: No Match
Is this meant to be calculated from the B0 dicoms?
On Mon, Dec 19, 2016 at 12:44 PM, Yendiki, Anastasia < AYENDIKI@mgh.harvard.edu> wrote:
No, it's a separate scan that you provide.
*From:* Katherine Damme [katherine.damme@gmail.com] *Sent:* Monday, December 19, 2016 1:43 PM
*To:* Freesurfer support list; Anastasia Yendiki *Subject:* Re: [Freesurfer] Tracula Set: No Match
This is being generated by an earlier step in the trac-all -prep right?
On Fri, Dec 16, 2016 at 4:23 PM, Yendiki, Anastasia < AYENDIKI@mgh.harvard.edu> wrote:
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.damme@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_Trac ula/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_Trac ula/31313422_10128/dmri/b0pha.nii.gz
mri_probedicom --i //media/Data/Temple/Temple_Tra cula/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_Trac ula/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 $FREESURFER_HOME/bin, to overwrite > the version of xfmrot that you have now. If it works, we'll include it in > the next version. Thanks! > > a.y > > ------------------------------ > *From:* freesurfer-bounces@nmr.mgh.harvard.edu [ > freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Katherine > Damme [katherine.damme@gmail.com] > *Sent:* Tuesday, December 13, 2016 9:38 AM > > *To:* Freesurfer support list > *Subject:* Re: [Freesurfer] Tracula Set: No Match > > > > On Tue, Dec 13, 2016 at 8:34 AM, Yendiki, Anastasia < > AYENDIKI@mgh.harvard.edu> wrote: > >> Ok, if you also send me the first file, >> /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi.ecclog, >> I'll see if I can replicate the error. >> >> ------------------------------ >> *From:* freesurfer-bounces@nmr.mgh.harvard.edu [ >> freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Katherine >> Damme [katherine.damme@gmail.com] >> *Sent:* Tuesday, December 13, 2016 9:21 AM >> >> *To:* Freesurfer support list >> *Subject:* Re: [Freesurfer] Tracula Set: No Match >> >> Yes. I immediately tried to enter the command in manually, checked >> the paths, and looked at the command manual for any format errors. >> >> [ksd770@katelinux Temple_Tracula]$ xfmrot >> /media/Data/Temple/Temple_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. >> >> 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_Trac >>>> ula/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 >>>> 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. >>> >>> >> >> _______________________________________________ >> 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 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. > >
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It absolutely is. The field map is completely optional, as shown in the tutorial and in the sample configuration file.
________________________________ From: Katherine Damme [katherine.damme@gmail.com] Sent: Tuesday, January 03, 2017 7:47 PM To: Freesurfer support list; Anastasia Yendiki Subject: Re: [Freesurfer] Tracula Set: No Match
Is it possible to run tracula with out a phase mapping MRI scan? All I have in this data is a MPRAGE and DWI images weighted at either 0 or 1000.
Thank you.
On Tue, Jan 3, 2017 at 1:07 PM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote: Hi Katherine - You need to have an appropriate field mapping MRI scan.
Best, a.y
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Katherine Damme [katherine.damme@gmail.commailto:katherine.damme@gmail.com] Sent: Sunday, January 01, 2017 5:16 PM
To: Freesurfer support list Subject: Re: [Freesurfer] Tracula Set: No Match
Sorry the phase map. How do I generate an appropriately formatted phase map?
On Sun, Jan 1, 2017 at 4:15 PM, Katherine Damme <katherine.damme@gmail.commailto:katherine.damme@gmail.com> wrote: How do I generate a field map?
On Mon, Dec 19, 2016 at 10:09 PM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote: No - there is no relation between B0 field inhomogeneities (measured by a field map) and b=0 volumes. The capital B refers to the magnetic field in the scanner, the small b is the b-value (diffusion weighting).
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Katherine Damme [katherine.damme@gmail.commailto:katherine.damme@gmail.com] Sent: Monday, December 19, 2016 11:01 PM
To: Freesurfer support list Subject: Re: [Freesurfer] Tracula Set: No Match
Is this meant to be calculated from the B0 dicoms?
On Mon, Dec 19, 2016 at 12:44 PM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote: No, it's a separate scan that you provide.
________________________________ From: Katherine Damme [katherine.damme@gmail.commailto:katherine.damme@gmail.com] Sent: Monday, December 19, 2016 1:43 PM
To: Freesurfer support list; Anastasia Yendiki Subject: Re: [Freesurfer] Tracula Set: No Match
This is being generated by an earlier step in the trac-all -prep right?
On Fri, Dec 16, 2016 at 4:23 PM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote: 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.damme@gmail.commailto:katherine.damme@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.eduhttp://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.commailto: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.MRhttp://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.eduhttp://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.edumailto: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 $FREESURFER_HOME/bin, to overwrite the version of xfmrot that you have now. If it works, we'll include it in the next version. Thanks!
a.y
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Katherine Damme [katherine.damme@gmail.commailto:katherine.damme@gmail.com] Sent: Tuesday, December 13, 2016 9:38 AM
To: Freesurfer support list Subject: Re: [Freesurfer] Tracula Set: No Match
On Tue, Dec 13, 2016 at 8:34 AM, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote: Ok, if you also send me the first file, /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi.echttp://dwi.ecclog, I'll see if I can replicate the error.
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Katherine Damme [katherine.damme@gmail.commailto:katherine.damme@gmail.com] Sent: Tuesday, December 13, 2016 9:21 AM
To: Freesurfer support list Subject: Re: [Freesurfer] Tracula Set: No Match
Yes. I immediately tried to enter the command in manually, checked the paths, and looked at the command manual for any format errors.
[ksd770@katelinux Temple_Tracula]$ xfmrot /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi.echttp://dwi.ecclog /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 <AYENDIKI@mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Katherine Damme [katherine.damme@gmail.commailto: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.edumailto: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.commailto: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.echttp://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.
freesurfer@nmr.mgh.harvard.edu
-
Katherine Damme -
Yendiki, Anastasia