Hello Freesurfer experts,
I am having great difficulty in trying to run the recon-all process on some scans of mine. I have tried running it a number of times, to no avail and the error I have gotten most recently is the nu_correct error. I have attached the log for this recon-all and hope someone may be able to help.
Also, I was told that there is a way one can upload a particular scan via FTP, is this correct and if so, how does one go about doing this?
Thank you! Fatima
Hi Fatima, What is the recon-all command line you are using to start the recon? -Louis
On Mon, 15 Aug 2011, Ahmed, F, Me fahmed@sun.ac.za wrote:
Hello Freesurfer experts,
I am having great difficulty in trying to run the recon-all process on some scans of mine. I have tried running it a number of times, to no avail and the error I have gotten most recently is the nu_correct error. I have attached the log for this recon-all and hope someone may be able to help.
Also, I was told that there is a way one can upload a particular scan via FTP, is this correct and if so, how does one go about doing this?
Thank you! Fatima
Hi Louis,
The command line I am using at the beginning was the following:
recon-all-i NN_117_10/NN117_10.MR.RESEARCH_STELLENBOSCH.2.1.2010.02.09.13.10.21.390625.46080549.IMA -s NN_117_10 -force -autorecon-all
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Louis Nicholas Vinke Sent: 15 August 2011 17:59 To: Ahmed, F, Me fahmed@sun.ac.za Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all error with nu_correct
Hi Fatima, What is the recon-all command line you are using to start the recon? -Louis
On Mon, 15 Aug 2011, Ahmed, F, Me fahmed@sun.ac.za wrote:
Hello Freesurfer experts,
I am having great difficulty in trying to run the recon-all process on some scans of mine. I have tried running it a number of times, to no avail and the error I have gotten most recently is the nu_correct error. I have attached the log for this recon-all and hope someone may be able to help.
Also, I was told that there is a way one can upload a particular scan via FTP, is this correct and if so, how does one go about doing this?
Thank you! Fatima
_______________________________________________ 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.
check this!!!
/bin/mv: cannot move `./tmp.mri_nu_correct.mni.26621/1/nu2_residue.mnc' to `./ tmp.mri_nu_correct.mni.26621/1/nu2_est.mnc': Permission denied
On Mon, Aug 15, 2011 at 6:03 PM, Ahmed, F, Me fahmed@sun.ac.za < fahmed@sun.ac.za> wrote:
Hi Louis,
The command line I am using at the beginning was the following:
recon-all-i NN_117_10/NN117_10.MR.RESEARCH_STELLENBOSCH.2.1.2010.02.09.13.10.21.390625.46080549.IMA -s NN_117_10 -force -autorecon-all
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto: freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Louis Nicholas Vinke Sent: 15 August 2011 17:59 To: Ahmed, F, Me fahmed@sun.ac.za Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all error with nu_correct
Hi Fatima, What is the recon-all command line you are using to start the recon? -Louis
On Mon, 15 Aug 2011, Ahmed, F, Me fahmed@sun.ac.za wrote:
Hello Freesurfer experts,
I am having great difficulty in trying to run the recon-all process on
some scans of mine. I have tried running it a number of times, to no avail and the error I have gotten most recently is the nu_correct error. I have attached the log for this recon-all and hope someone may be able to help.
Also, I was told that there is a way one can upload a particular scan via
FTP, is this correct and if so, how does one go about doing this?
Thank you! Fatima
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
I don't understand why I would all of a sudden be getting permission denied errors, when I ran a complete study prior to this with absolutely no problems at all.
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Rouhollah Abdollahi Sent: 15 August 2011 18:15 To: Ahmed, F, Me Cc: freesurfer@nmr.mgh.harvard.edu; Louis Nicholas Vinke Subject: Re: [Freesurfer] recon-all error with nu_correct
check this!!!
/bin/mv: cannot move `./tmp.mri_nu_correct.mni.26621/1/nu2_residue.mnc' to `./ tmp.mri_nu_correct.mni.26621/1/nu2_est.mnc': Permission denied
On Mon, Aug 15, 2011 at 6:03 PM, Ahmed, F, Me <fahmed@sun.ac.zamailto:fahmed@sun.ac.za> <fahmed@sun.ac.zamailto:fahmed@sun.ac.za> wrote: Hi Louis,
The command line I am using at the beginning was the following:
recon-all-i NN_117_10/NN117_10.MR.RESEARCH_STELLENBOSCH.2.1.2010.02.09.13.10.21.390625.46080549.IMA -s NN_117_10 -force -autorecon-all
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Louis Nicholas Vinke Sent: 15 August 2011 17:59 To: Ahmed, F, Me <fahmed@sun.ac.zamailto:fahmed@sun.ac.za> Cc: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all error with nu_correct
Hi Fatima, What is the recon-all command line you are using to start the recon? -Louis
On Mon, 15 Aug 2011, Ahmed, F, Me <fahmed@sun.ac.zamailto:fahmed@sun.ac.za> wrote:
Hello Freesurfer experts,
I am having great difficulty in trying to run the recon-all process on some scans of mine. I have tried running it a number of times, to no avail and the error I have gotten most recently is the nu_correct error. I have attached the log for this recon-all and hope someone may be able to help.
Also, I was told that there is a way one can upload a particular scan via FTP, is this correct and if so, how does one go about doing this?
Thank you! Fatima
_______________________________________________ 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
-- With Best Regards Rouhollah Abdollahi
did you run recon-all from a directory that you don't have permission to write to? On Mon, 15 Aug 2011, Ahmed, F, Me fahmed@sun.ac.za wrote:
I don?t understand why I would all of a sudden be getting permission denied errors, when I ran a complete study prior to this with absolutely no problems at all.
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Rouhollah Abdollahi Sent: 15 August 2011 18:15 To: Ahmed, F, Me Cc: freesurfer@nmr.mgh.harvard.edu; Louis Nicholas Vinke Subject: Re: [Freesurfer] recon-all error with nu_correct
check this!!!
/bin/mv: cannot move `./tmp.mri_nu_correct.mni.26621/1/nu2_residue.mnc' to `./
tmp.mri_nu_correct.mni.26621/1/nu2_est.mnc': Permission denied
On Mon, Aug 15, 2011 at 6:03 PM, Ahmed, F, Me fahmed@sun.ac.za fahmed@sun.ac.za wrote:
Hi Louis,
The command line I am using at the beginning was the following:
recon-all-iNN_117_10/NN117_10.MR.RESEARCH_STELLENBOSCH.2.1.2010.02.09.13.10.21.390625. 46080549.IMA -s NN_117_10 -force -autorecon-all
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Louis Nicholas Vinke Sent: 15 August 2011 17:59 To: Ahmed, F, Me fahmed@sun.ac.za Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all error with nu_correct
Hi Fatima, What is the recon-all command line you are using to start the recon? -Louis
On Mon, 15 Aug 2011, Ahmed, F, Me fahmed@sun.ac.za wrote:
Hello Freesurfer experts,
I am having great difficulty in trying to run the recon-all process on
some scans of mine. I have tried running it a number of times, to no avail and the error I have gotten most recently is the nu_correct error. I have attached the log for this recon-all and hope someone may be able to help.
Also, I was told that there is a way one can upload a particular scan via
FTP, is this correct and if so, how does one go about doing this?
Thank you! Fatima
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
-- With Best Regards Rouhollah Abdollahi
freesurfer@nmr.mgh.harvard.edu
-
Ahmed, F, Me <fahmed＠sun.ac.za> -
Bruce Fischl -
Louis Nicholas Vinke -
Rouhollah Abdollahi