Hi Anastasia, I have resolved the previous problem by writing configuration file with sudo nano in command line. Now I'm running trac-all -prep but I have this error:
writing registered surface to /Applications/freesurfer/subjects/subject_prova/Diff03/surf/rh.cvs.tocvs_avg35.sphere.reg...expanding nbhd size to 1mris_resample: Command not found. What's happened? Thanks,
Stefano
----Messaggio originale----
Da: stdp82@virgilio.it
Data: 6-giu-2013 0.51
A: ayendiki@nmr.mgh.harvard.edu
Cc: freesurfer@nmr.mgh.harvard.edu
Ogg: [Freesurfer] R: Re: R: Re: Tracula
I obtain /Applications/freesurfer/subjects/subject_prova my DWI file is in Diff01, Diff02 ... that are in subject_prova folder. Thanks,
Stefano
----Messaggio originale---- Da: ayendiki@nmr.mgh.harvard.edu Data: 6-giu-2013 0.42 A: stdp82@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: Tracula
What do you get when you run "echo $SUBJECTS_DIR"?
On Thu, 6 Jun 2013, stdp82@virgilio.it wrote:
Hi Anastasia,
yes, I have check the SUBJECTS_DIR. I do not understand why all previous configuration file start normally and this no. Do you note some line that might be wrong additionally to setenv SUBJECTS_DIR line.
Stefano
----Messaggio originale---- Da: ayendiki@nmr.mgh.harvard.edu Data: 5-giu-2013 16.09 A: stdp82@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: Tracula
Is the "setenv SUBJECTS_DIR" line really commented out? You must set SUBJECTS_DIR, see the example configuration file on the wiki and under $FREESURFER_HOME/bin/dmrirc.example.
On Wed, 5 Jun 2013, stdp82@virgilio.it wrote:
Hi list and Anastasia, I'm performing a set of data with tracula version 3.0. I have change my dmrirc file respect to previous analyses and now I have one problem
"set: Variable name must begin with a letter. ERROR: must specify as many DWI dicoms as subjects".
I do not find the line that is wrong. I think to have approximately used
the
same lines of previous and correct analysis.
I have attached the configuration file. Note that I'm using nii.gz.
Thanks and best regards.
Stefano
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,
A patch is now available for the "mris_resample : Command not found" error you encountered.
Simply download the file from the following link and place it in your $FREESURFER_HOME/bin directory:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/mris_resample
--Lilla
On Thu, 6 Jun 2013, stdp82@virgilio.it wrote:
Hi Anastasia,
I have resolved the previous problem by writing configuration file with sudo nano in command line.
Now I'm running trac-all -prep but I have this error:
writing registered surface to /Applications/freesurfer/subjects/subject_prova/Diff03/surf/rh.cvs.tocvs_avg35.sphere.reg... expanding nbhd size to 1 mris_resample: Command not found.
What's happened?
Thanks,
Stefano
----Messaggio originale---- Da: stdp82@virgilio.it Data: 6-giu-2013 0.51 A: ayendiki@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Ogg: [Freesurfer] R: Re: R: Re: Tracula
I obtain /Applications/freesurfer/subjects/subject_prova my DWI file is in Diff01, Diff02 ... that are in subject_prova folder.
Thanks,
Stefano
----Messaggio originale---- Da: ayendiki@nmr.mgh.harvard.edu Data: 6-giu-2013 0.42 A: stdp82@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: Tracula
What do you get when you run "echo $SUBJECTS_DIR"?
On Thu, 6 Jun 2013, stdp82@virgilio.it wrote:
Hi Anastasia,
yes, I have check the SUBJECTS_DIR. I do not understand why all previous configuration file start normally and this no. Do you note some line that might be wrong additionally to setenv SUBJECTS_DIR line.
Stefano
----Messaggio originale---- Da: ayendiki@nmr.mgh.harvard.edu Data: 5-giu-2013 16.09 A: stdp82@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: Tracula
Is the "setenv SUBJECTS_DIR" line really commented out? You must set SUBJECTS_DIR, see the example configuration file on the wiki and under $FREESURFER_HOME/bin/dmrirc.example.
On Wed, 5 Jun 2013, stdp82@virgilio.it wrote:
Hi list and Anastasia, I'm performing a set of data with tracula version 3.0. I have change my dmrirc file respect to previous analyses and now I have one problem
"set: Variable name must begin with a letter. ERROR: must specify as many DWI dicoms as subjects".
I do not find the line that is wrong. I think to have approximately used
the
same lines of previous and correct analysis.
I have attached the configuration file. Note that I'm using nii.gz.
Thanks and best regards.
Stefano
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.
This issue has come up on the list a few times recently. Please search for your error in the email archives before posting to the list. Thanks.
On Thu, 6 Jun 2013, stdp82@virgilio.it wrote:
Hi Anastasia,
I have resolved the previous problem by writing configuration file with sudo nano in command line.
Now I'm running trac-all -prep but I have this error:
writing registered surface to/Applications/freesurfer/subjects/subject_prova/Diff03/surf/rh.cvs.tocvs_av g35.sphere.reg... expanding nbhd size to 1 mris_resample: Command not found.
What's happened?
Thanks,
Stefano
----Messaggio originale---- Da: stdp82@virgilio.it Data: 6-giu-2013 0.51 A: ayendiki@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Ogg: [Freesurfer] R: Re: R: Re: Tracula
I obtain /Applications/freesurfer/subjects/subject_prova my DWI file is in Diff01, Diff02 ... that are in subject_prova folder.
Thanks,
Stefano
----Messaggio originale---- Da: ayendiki@nmr.mgh.harvard.edu Data: 6-giu-2013 0.42 A: stdp82@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: Tracula
What do you get when you run "echo $SUBJECTS_DIR"?
On Thu, 6 Jun 2013, stdp82@virgilio.it wrote:
Hi Anastasia,
yes, I have check the SUBJECTS_DIR. I do not understand why all previous configuration file start normally and this no. Do you note some line that might be wrong additionally to setenv SUBJECTS_DIR line.
Stefano
----Messaggio originale---- Da: ayendiki@nmr.mgh.harvard.edu Data: 5-giu-2013 16.09 A: stdp82@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: Tracula
Is the "setenv SUBJECTS_DIR" line really commented out? You must set SUBJECTS_DIR, see the example configuration file on the wiki and under $FREESURFER_HOME/bin/dmrirc.example.
On Wed, 5 Jun 2013, stdp82@virgilio.it wrote:
Hi list and Anastasia, I'm performing a set of data with tracula version 3.0. I have change my dmrirc file respect to previous analyses and now I have one problem
"set: Variable name must begin with a letter. ERROR: must specify as many DWI dicoms as subjects".
I do not find the line that is wrong. I think to have approximately used
the
same lines of previous and correct analysis.
I have attached the configuration file. Note that I'm using nii.gz.
Thanks and best regards.
Stefano
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@nmr.mgh.harvard.edu
-
Anastasia Yendiki -
Lilla Zollei -
stdp82＠virgilio.it