Re: [Freesurfer] trac-all using nifti
External Email - Use Caution Hi Anastasia, Sure, I will try that. Thanks for the advice! Regards, Heidi On Fri, Sep 21, 2018 at 4:49 PM Yendiki, Anastasia wrote: > You need to specify one more option, like -prep, etc. Please follow the > instructions on the tutorial and, if the problem persists, send the exact > command line that you ran and the full text of the output that you got. > > On Sep 21, 2018 2:42 AM, Heidi Emmanuel Foo wrote: > > External Email - Use Caution > > Hi Anastasia, > > I think I ran trac-all -c config.txt. > > Regards, > Heidi > > On Thu, Sep 20, 2018 at 10:18 PM Yendiki, Anastasia < > ayend...@mgh.harvard.edu> wrote: > >> What is the trac-all command line that you run? >> -- >> *From:* freesurfer-boun...@nmr.mgh.harvard.edu < >> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Heidi Emmanuel Foo < >> heidifo...@gmail.com> >> *Sent:* Wednesday, September 19, 2018 11:06:09 PM >> *To:* Freesurfer support list >> *Subject:* Re: [Freesurfer] trac-all using nifti >> >> >> External Email - Use Caution >> >> Hi Anastasia, >> >> Nope, I don't actually get any output and/or log file. >> >> Regards, >> Heidi Foo >> >> >> >> On Tue, Sep 18, 2018 at 6:12 PM Yendiki, Anastasia < >> ayend...@mgh.harvard.edu> wrote: >> >> Hi Heidi - The config file that you sent looked fine to me. What is the >> trac-all command line that you run, and do you get any other output (like a >> trac-all.log file)? >> >> >> Best, >> >> a.y >> ---------- >> *From:* freesurfer-boun...@nmr.mgh.harvard.edu < >> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Heidi Emmanuel Foo < >> heidifo...@gmail.com> >> *Sent:* Monday, September 17, 2018 11:03:47 PM >> *To:* Freesurfer support list >> *Subject:* Re: [Freesurfer] trac-all using nifti >> >> >> External Email - Use Caution >> >> Hi Anastasia, >> >> It seems like I do. Could the problem be the config.txt? >> >> Thanks! >> >> Best Regards, >> Heidi Foo >> >> On Tue, Sep 18, 2018 at 12:47 AM Yendiki, Anastasia < >> ayend...@mgh.harvard.edu> wrote: >> >> Hi Heidi – Do you have write permission to create the output directory >> /data_int/heidi/forHeidi/Preprocessed? >> >> a.y >> >> From: on behalf of Heidi >> Emmanuel Foo >> Reply-To: Freesurfer support list >> Date: Monday, September 17, 2018 at 12:55 AM >> To: Freesurfer support list >> Subject: [Freesurfer] trac-all using nifti >> >> External Email - Use Caution >> >> Hi Anastasia, >> >> I am currently trying to run trac-all with my DWI data. I do not have the >> DICOM but only the Nifti files and I would like to use the same bval and >> bvec template for every subject. I created a configiration file as >> attached. However, I have the following error message: >> >> : Command not found. >> : Command not found. >> set: Variable name must begin with a letter. >> does not exist.DIR /data_int/heidi/forHeidi/Preprocessed >> >> It would be great if you could advise me on what to do. >> >> Thank you! >> >> Best Regards, >> Heidi Foo >> >> >> ___ >> 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.partn
Re: [Freesurfer] trac-all using nifti
You need to specify one more option, like -prep, etc. Please follow the instructions on the tutorial and, if the problem persists, send the exact command line that you ran and the full text of the output that you got. On Sep 21, 2018 2:42 AM, Heidi Emmanuel Foo wrote: External Email - Use Caution Hi Anastasia, I think I ran trac-all -c config.txt. Regards, Heidi On Thu, Sep 20, 2018 at 10:18 PM Yendiki, Anastasia mailto:ayend...@mgh.harvard.edu>> wrote: What is the trac-all command line that you run? From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Heidi Emmanuel Foo mailto:heidifo...@gmail.com>> Sent: Wednesday, September 19, 2018 11:06:09 PM To: Freesurfer support list Subject: Re: [Freesurfer] trac-all using nifti External Email - Use Caution Hi Anastasia, Nope, I don't actually get any output and/or log file. Regards, Heidi Foo On Tue, Sep 18, 2018 at 6:12 PM Yendiki, Anastasia mailto:ayend...@mgh.harvard.edu>> wrote: Hi Heidi - The config file that you sent looked fine to me. What is the trac-all command line that you run, and do you get any other output (like a trac-all.log file)? Best, a.y From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Heidi Emmanuel Foo mailto:heidifo...@gmail.com>> Sent: Monday, September 17, 2018 11:03:47 PM To: Freesurfer support list Subject: Re: [Freesurfer] trac-all using nifti External Email - Use Caution Hi Anastasia, It seems like I do. Could the problem be the config.txt? Thanks! Best Regards, Heidi Foo On Tue, Sep 18, 2018 at 12:47 AM Yendiki, Anastasia mailto:ayend...@mgh.harvard.edu>> wrote: Hi Heidi – Do you have write permission to create the output directory /data_int/heidi/forHeidi/Preprocessed? a.y From: mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Heidi Emmanuel Foo mailto:heidifo...@gmail.com>> Reply-To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Monday, September 17, 2018 at 12:55 AM To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] trac-all using nifti External Email - Use Caution Hi Anastasia, I am currently trying to run trac-all with my DWI data. I do not have the DICOM but only the Nifti files and I would like to use the same bval and bvec template for every subject. I created a configiration file as attached. However, I have the following error message: : Command not found. : Command not found. set: Variable name must begin with a letter. does not exist.DIR /data_int/heidi/forHeidi/Preprocessed It would be great if you could advise me on what to do. Thank you! Best Regards, Heidi Foo ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nm
Re: [Freesurfer] trac-all using nifti
External Email - Use Caution Hi Anastasia, I think I ran trac-all -c config.txt. Regards, Heidi On Thu, Sep 20, 2018 at 10:18 PM Yendiki, Anastasia < ayend...@mgh.harvard.edu> wrote: > What is the trac-all command line that you run? > -- > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Heidi Emmanuel Foo < > heidifo...@gmail.com> > *Sent:* Wednesday, September 19, 2018 11:06:09 PM > *To:* Freesurfer support list > *Subject:* Re: [Freesurfer] trac-all using nifti > > > External Email - Use Caution > > Hi Anastasia, > > Nope, I don't actually get any output and/or log file. > > Regards, > Heidi Foo > > > > On Tue, Sep 18, 2018 at 6:12 PM Yendiki, Anastasia < > ayend...@mgh.harvard.edu> wrote: > > Hi Heidi - The config file that you sent looked fine to me. What is the > trac-all command line that you run, and do you get any other output (like a > trac-all.log file)? > > > Best, > > a.y > -- > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Heidi Emmanuel Foo < > heidifo...@gmail.com> > *Sent:* Monday, September 17, 2018 11:03:47 PM > *To:* Freesurfer support list > *Subject:* Re: [Freesurfer] trac-all using nifti > > > External Email - Use Caution > > Hi Anastasia, > > It seems like I do. Could the problem be the config.txt? > > Thanks! > > Best Regards, > Heidi Foo > > On Tue, Sep 18, 2018 at 12:47 AM Yendiki, Anastasia < > ayend...@mgh.harvard.edu> wrote: > > Hi Heidi – Do you have write permission to create the output directory > /data_int/heidi/forHeidi/Preprocessed? > > a.y > > From: on behalf of Heidi > Emmanuel Foo > Reply-To: Freesurfer support list > Date: Monday, September 17, 2018 at 12:55 AM > To: Freesurfer support list > Subject: [Freesurfer] trac-all using nifti > > External Email - Use Caution > > Hi Anastasia, > > I am currently trying to run trac-all with my DWI data. I do not have the > DICOM but only the Nifti files and I would like to use the same bval and > bvec template for every subject. I created a configiration file as > attached. However, I have the following error message: > > : Command not found. > : Command not found. > set: Variable name must begin with a letter. > does not exist.DIR /data_int/heidi/forHeidi/Preprocessed > > It would be great if you could advise me on what to do. > > Thank you! > > Best Regards, > Heidi Foo > > > ___ > 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.
Re: [Freesurfer] trac-all using nifti
What is the trac-all command line that you run? From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Heidi Emmanuel Foo Sent: Wednesday, September 19, 2018 11:06:09 PM To: Freesurfer support list Subject: Re: [Freesurfer] trac-all using nifti External Email - Use Caution Hi Anastasia, Nope, I don't actually get any output and/or log file. Regards, Heidi Foo On Tue, Sep 18, 2018 at 6:12 PM Yendiki, Anastasia mailto:ayend...@mgh.harvard.edu>> wrote: Hi Heidi - The config file that you sent looked fine to me. What is the trac-all command line that you run, and do you get any other output (like a trac-all.log file)? Best, a.y From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Heidi Emmanuel Foo mailto:heidifo...@gmail.com>> Sent: Monday, September 17, 2018 11:03:47 PM To: Freesurfer support list Subject: Re: [Freesurfer] trac-all using nifti External Email - Use Caution Hi Anastasia, It seems like I do. Could the problem be the config.txt? Thanks! Best Regards, Heidi Foo On Tue, Sep 18, 2018 at 12:47 AM Yendiki, Anastasia mailto:ayend...@mgh.harvard.edu>> wrote: Hi Heidi – Do you have write permission to create the output directory /data_int/heidi/forHeidi/Preprocessed? a.y From: mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Heidi Emmanuel Foo mailto:heidifo...@gmail.com>> Reply-To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Monday, September 17, 2018 at 12:55 AM To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] trac-all using nifti External Email - Use Caution Hi Anastasia, I am currently trying to run trac-all with my DWI data. I do not have the DICOM but only the Nifti files and I would like to use the same bval and bvec template for every subject. I created a configiration file as attached. However, I have the following error message: : Command not found. : Command not found. set: Variable name must begin with a letter. does not exist.DIR /data_int/heidi/forHeidi/Preprocessed It would be great if you could advise me on what to do. Thank you! Best Regards, Heidi Foo ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] trac-all using nifti
External Email - Use Caution Hi Anastasia, Nope, I don't actually get any output and/or log file. Regards, Heidi Foo On Tue, Sep 18, 2018 at 6:12 PM Yendiki, Anastasia wrote: > Hi Heidi - The config file that you sent looked fine to me. What is the > trac-all command line that you run, and do you get any other output (like a > trac-all.log file)? > > > Best, > > a.y > -- > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Heidi Emmanuel Foo < > heidifo...@gmail.com> > *Sent:* Monday, September 17, 2018 11:03:47 PM > *To:* Freesurfer support list > *Subject:* Re: [Freesurfer] trac-all using nifti > > > External Email - Use Caution > > Hi Anastasia, > > It seems like I do. Could the problem be the config.txt? > > Thanks! > > Best Regards, > Heidi Foo > > On Tue, Sep 18, 2018 at 12:47 AM Yendiki, Anastasia < > ayend...@mgh.harvard.edu> wrote: > > Hi Heidi – Do you have write permission to create the output directory > /data_int/heidi/forHeidi/Preprocessed? > > a.y > > From: on behalf of Heidi > Emmanuel Foo > Reply-To: Freesurfer support list > Date: Monday, September 17, 2018 at 12:55 AM > To: Freesurfer support list > Subject: [Freesurfer] trac-all using nifti > > External Email - Use Caution > > Hi Anastasia, > > I am currently trying to run trac-all with my DWI data. I do not have the > DICOM but only the Nifti files and I would like to use the same bval and > bvec template for every subject. I created a configiration file as > attached. However, I have the following error message: > > : Command not found. > : Command not found. > set: Variable name must begin with a letter. > does not exist.DIR /data_int/heidi/forHeidi/Preprocessed > > It would be great if you could advise me on what to do. > > Thank you! > > Best Regards, > Heidi Foo > > > ___ > 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.
Re: [Freesurfer] trac-all using nifti
Hi Heidi - The config file that you sent looked fine to me. What is the trac-all command line that you run, and do you get any other output (like a trac-all.log file)? Best, a.y From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Heidi Emmanuel Foo Sent: Monday, September 17, 2018 11:03:47 PM To: Freesurfer support list Subject: Re: [Freesurfer] trac-all using nifti External Email - Use Caution Hi Anastasia, It seems like I do. Could the problem be the config.txt? Thanks! Best Regards, Heidi Foo On Tue, Sep 18, 2018 at 12:47 AM Yendiki, Anastasia mailto:ayend...@mgh.harvard.edu>> wrote: Hi Heidi – Do you have write permission to create the output directory /data_int/heidi/forHeidi/Preprocessed? a.y From: mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Heidi Emmanuel Foo mailto:heidifo...@gmail.com>> Reply-To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Monday, September 17, 2018 at 12:55 AM To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] trac-all using nifti External Email - Use Caution Hi Anastasia, I am currently trying to run trac-all with my DWI data. I do not have the DICOM but only the Nifti files and I would like to use the same bval and bvec template for every subject. I created a configiration file as attached. However, I have the following error message: : Command not found. : Command not found. set: Variable name must begin with a letter. does not exist.DIR /data_int/heidi/forHeidi/Preprocessed It would be great if you could advise me on what to do. Thank you! Best Regards, Heidi Foo ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] trac-all using nifti
External Email - Use Caution Hi Anastasia, It seems like I do. Could the problem be the config.txt? Thanks! Best Regards, Heidi Foo On Tue, Sep 18, 2018 at 12:47 AM Yendiki, Anastasia < ayend...@mgh.harvard.edu> wrote: > Hi Heidi – Do you have write permission to create the output directory > /data_int/heidi/forHeidi/Preprocessed? > > a.y > > From: on behalf of Heidi > Emmanuel Foo > Reply-To: Freesurfer support list > Date: Monday, September 17, 2018 at 12:55 AM > To: Freesurfer support list > Subject: [Freesurfer] trac-all using nifti > > External Email - Use Caution > > Hi Anastasia, > > I am currently trying to run trac-all with my DWI data. I do not have the > DICOM but only the Nifti files and I would like to use the same bval and > bvec template for every subject. I created a configiration file as > attached. However, I have the following error message: > > : Command not found. > : Command not found. > set: Variable name must begin with a letter. > does not exist.DIR /data_int/heidi/forHeidi/Preprocessed > > It would be great if you could advise me on what to do. > > Thank you! > > Best Regards, > Heidi Foo > > > ___ > 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.
Re: [Freesurfer] trac-all using nifti
Hi Heidi – Do you have write permission to create the output directory /data_int/heidi/forHeidi/Preprocessed? a.y From: mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Heidi Emmanuel Foo mailto:heidifo...@gmail.com>> Reply-To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Monday, September 17, 2018 at 12:55 AM To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] trac-all using nifti External Email - Use Caution Hi Anastasia, I am currently trying to run trac-all with my DWI data. I do not have the DICOM but only the Nifti files and I would like to use the same bval and bvec template for every subject. I created a configiration file as attached. However, I have the following error message: : Command not found. : Command not found. set: Variable name must begin with a letter. does not exist.DIR /data_int/heidi/forHeidi/Preprocessed It would be great if you could advise me on what to do. Thank you! Best Regards, Heidi Foo ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] trac-all using nifti
External Email - Use Caution Hi Anastasia, I am currently trying to run trac-all with my DWI data. I do not have the DICOM but only the Nifti files and I would like to use the same bval and bvec template for every subject. I created a configiration file as attached. However, I have the following error message: : Command not found. : Command not found. set: Variable name must begin with a letter. does not exist.DIR /data_int/heidi/forHeidi/Preprocessed It would be great if you could advise me on what to do. Thank you! Best Regards, Heidi Foo # FreeSurfer SUBJECTS_DIR # T1 images and FreeSurfer segmentations are expected to be found here setenv SUBJECTS_DIR /data_int/heidi/forHeidi/Preprocessed # Output directory where trac-all results will be saved set dtroot = /data_int/heidi/forHeidi/Preprocessed # Subject IDs set subjlist = (FS1 FS2 FS3) # Input diffusion DICOMs # If original DICOMs don't exist, these can be in other image format # but then the gradient table and b-value table must be specified (see below) set dcmroot = /data_int/heidi/forHeidi/DWI/dwi set dcmlist = (dwi_1.nii dwi_2.nii dwi_3.nii) # Specify diffusion-encoding table set bvecfile = /data_int/heidi/forHeidi/DWI/bvecs.txt # Specify b-value table set bvalfile = /data_int/heidi/forHeidi/DWI/bvals.txt # Eddy-current set doeddy = 1 # If gradients will be rotated to match eddy-current compensation set dorotbvecs = 1 # If anatomical brain mask will be used set usemaskanat = 1 # Threshold for DWI-based brain mask extraction set thrbet = 0.3 # Intra-subject registration method set doregflt = 0 set doregbbr = 1 # Inter-subject registration method set doregmni = 1 set doregcsv = 0 set mnitemp = $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz set doregcvs = 0 # Specify which white-matter pathways to reconstruct set pathlist = ( lh.cst_AS rh.cst_AS \ lh.ilf_AS rh.ilf_AS \ lh.unc_AS rh.unc_AS \ fmajor_PP fminor_PP \ lh.atr_PP rh.atr_PP \ lh.cab_PP rh.cab_PP \ lh.ccg_PP rh.ccg_PP \ lh.slfp_PP rh.slfp_PP \ lh.slft_PP rh.slft_PP ) # Specify the number of path control points set ncpts = (6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5) ___ 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.
