Hello, I am new to using Freesurfer and am trying to run the recon-all stages in order to get thickness values for brain regions. I have correctly converted all my dicom images into the correct mgz format as instructed by your manual and have carried out motion correction (even though I only have one acquisition) to create the orig.mgz file. however, when I try and run the following command:
"recon-all -i <in volume 1> -i <in volume 2> -i <in volume 3> -autorecon1 -s bert" using my subject name, I get the following error message:
[fsl@localhost DicomImages]$ recon-all -i CON_ADAMS_MONIQUE/orig.mgz -autorecon1 -s CON_ADAMS_MONIQUE ERROR: cannot find CON_ADAMS_MONIQUE/orig.mgz Linux localhost.localdomain 2.6.18-8.1.8.el5 #1 SMP Tue Jul 10 06:50:22 EDT 2007 i686 i686 i386 GNU/Linux
recon-all exited with ERRORS at Wed Jun 17 08:59:47 BST 2009
Please can you advise me on what the problem is and how to correct it?
Thank you.
Fatima
Fatima, Try this simple procedure to get started.
1) Convert your dicom files to 001.mgz recon-all -i DICOM_FILE_DIR -o 001.mgz
2) Inside your subjects_dir create a subdirectory like this: mkdir -p $SUBJECTS_DIR/test01/mri/orig
3) copy your 001.mgz into that dir cp 001.mgz $SUBJECTS_DIR/test01/mri/orig
4) run recon-all recon-all -s test01 -all
Hope it helps
PPJ
----------------------------------------------------------- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.0 www.Netfilter.com.br
2009/6/17 Ahmed, F, Me fahmed@sun.ac.za fahmed@sun.ac.za
Hello, I am new to using Freesurfer and am trying to run the recon-all stages in order to get thickness values for brain regions. I have correctly converted all my dicom images into the correct mgz format as instructed by your manual and have carried out motion correction (even though I only have one acquisition) to create the orig.mgz file. however, when I try and run the following command:
"recon-all -i <in volume 1> -i <in volume 2> -i <in volume 3> -autorecon1 -s bert" using my subject name, I get the following error message:
[fsl@localhost DicomImages]$ recon-all -i CON_ADAMS_MONIQUE/orig.mgz -autorecon1 -s CON_ADAMS_MONIQUE ERROR: cannot find CON_ADAMS_MONIQUE/orig.mgz Linux localhost.localdomain 2.6.18-8.1.8.el5 #1 SMP Tue Jul 10 06:50:22 EDT 2007 i686 i686 i386 GNU/Linux
recon-all exited with ERRORS at Wed Jun 17 08:59:47 BST 2009
Please can you advise me on what the problem is and how to correct it?
Thank you.
Fatima
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
PPJ,
Thank you for your response, I tried your procedure and got the following message:
[fsl@localhost CON_ADAMS_MONIQUE]$ cp 001.mgz $SUBJECTS_DIR/CON_ADAMS_MONIQUE/mri/orig cp: cannot stat `001.mgz': No such file or directory
I don't know why that happens.
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Pedro Paulo de Magalhães Oliveira Junior Sent: 17 June 2009 15:14 To: Ahmed, F, Me Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] error message
Fatima,
Try this simple procedure to get started.
1) Convert your dicom files to 001.mgz recon-all -i DICOM_FILE_DIR -o 001.mgz
2) Inside your subjects_dir create a subdirectory like this: mkdir -p $SUBJECTS_DIR/test01/mri/orig
3) copy your 001.mgz into that dir cp 001.mgz $SUBJECTS_DIR/test01/mri/orig
4) run recon-all recon-all -s test01 -all
Hope it helps
PPJ
----------------------------------------------------------- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.0 www.Netfilter.com.brhttp://www.Netfilter.com.br
2009/6/17 Ahmed, F, Me <fahmed@sun.ac.zamailto:fahmed@sun.ac.za> <fahmed@sun.ac.zamailto:fahmed@sun.ac.za> Hello, I am new to using Freesurfer and am trying to run the recon-all stages in order to get thickness values for brain regions. I have correctly converted all my dicom images into the correct mgz format as instructed by your manual and have carried out motion correction (even though I only have one acquisition) to create the orig.mgz file. however, when I try and run the following command:
"recon-all -i <in volume 1> -i <in volume 2> -i <in volume 3> -autorecon1 -s bert" using my subject name, I get the following error message:
[fsl@localhost DicomImages]$ recon-all -i CON_ADAMS_MONIQUE/orig.mgz -autorecon1 -s CON_ADAMS_MONIQUE ERROR: cannot find CON_ADAMS_MONIQUE/orig.mgz Linux localhost.localdomain 2.6.18-8.1.8.el5 #1 SMP Tue Jul 10 06:50:22 EDT 2007 i686 i686 i386 GNU/Linux
recon-all exited with ERRORS at Wed Jun 17 08:59:47 BST 2009
Please can you advise me on what the problem is and how to correct it?
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
Sorry. I mistyped the first command (Wrong) recon-all -i DICOM_FILE_DIR -o 001.mgz
(Correct) mri_convert -i DICOM_FILE_DIR -o 001.mgz ----------------------------------------------------------- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.0 www.Netfilter.com.br
2009/6/17 Ahmed, F, Me fahmed@sun.ac.za fahmed@sun.ac.za
PPJ,
Thank you for your response, I tried your procedure and got the following message:
[fsl@localhost CON_ADAMS_MONIQUE]$ cp 001.mgz $SUBJECTS_DIR/CON_ADAMS_MONIQUE/mri/orig
cp: cannot stat `001.mgz': No such file or directory
I don’t know why that happens.
*From:* freesurfer-bounces@nmr.mgh.harvard.edu [mailto: freesurfer-bounces@nmr.mgh.harvard.edu] *On Behalf Of *Pedro Paulo de Magalhães Oliveira Junior *Sent:* 17 June 2009 15:14 *To:* Ahmed, F, Me *Cc:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] error message
Fatima,
Try this simple procedure to get started.
- Convert your dicom files to 001.mgz
recon-all -i DICOM_FILE_DIR -o 001.mgz
- Inside your subjects_dir create a subdirectory like this:
mkdir -p $SUBJECTS_DIR/test01/mri/orig
- copy your 001.mgz into that dir
cp 001.mgz $SUBJECTS_DIR/test01/mri/orig
- run recon-all
recon-all -s test01 -all
Hope it helps
PPJ
Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.0 www.Netfilter.com.br
2009/6/17 Ahmed, F, Me fahmed@sun.ac.za fahmed@sun.ac.za
Hello, I am new to using Freesurfer and am trying to run the recon-all stages in order to get thickness values for brain regions. I have correctly
converted all my dicom images into the correct mgz format as instructed by your manual and have carried out motion correction (even though I only have
one acquisition) to create the orig.mgz file. however, when I try and run the following command:
"recon-all -i <in volume 1> -i <in volume 2> -i <in volume 3> -autorecon1 -s bert" using my subject name, I get the following error message:
[fsl@localhost DicomImages]$ recon-all -i CON_ADAMS_MONIQUE/orig.mgz -autorecon1 -s CON_ADAMS_MONIQUE
ERROR: cannot find CON_ADAMS_MONIQUE/orig.mgz
Linux localhost.localdomain 2.6.18-8.1.8.el5 #1 SMP Tue Jul 10 06:50:22 EDT 2007 i686 i686 i386 GNU/Linux
recon-all exited with ERRORS at Wed Jun 17 08:59:47 BST 2009
Please can you advise me on what the problem is and how to correct it?
Thank you.
Fatima
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Fatima,
You probably would find it easier easier to just point recon-all directly at the dicoms with -i. It saves the conversion step. If you do the conversion and put the runs in the orig dir then you don't need -i anymore, it will find them.
cheers, Bruce
On Wed, 17 Jun 2009, Ahmed, F, Me fahmed@sun.ac.za wrote:
Hello, I am new to using Freesurfer and am trying to run the recon-all stages in order to get thickness values for brain regions. I have correctly converted all my dicom images into the correct mgz format as instructed by your manual and have carried out motion correction (even though I only have one acquisition) to create the orig.mgz file. however, when I try and run the following command:
"recon-all -i <in volume 1> -i <in volume 2> -i <in volume 3> -autorecon1 -s bert" using my subject name, I get the following error message:
[fsl@localhost DicomImages]$ recon-all -i CON_ADAMS_MONIQUE/orig.mgz -autorecon1 -s CON_ADAMS_MONIQUE ERROR: cannot find CON_ADAMS_MONIQUE/orig.mgz Linux localhost.localdomain 2.6.18-8.1.8.el5 #1 SMP Tue Jul 10 06:50:22 EDT 2007 i686 i686 i386 GNU/Linux
recon-all exited with ERRORS at Wed Jun 17 08:59:47 BST 2009
Please can you advise me on what the problem is and how to correct it?
Thank you.
Fatima
Hello,
What does it mean when it says to re-run with "force" - when I do this for autorecon 1, it says that there is the following error:
nu_correct: Command not found. ERROR: nu_correct Linux localhost.localdomain 2.6.18-8.1.8.el5 #1 SMP Tue Jul 10 06:50:22 EDT 2007 i686 i686 i386 GNU/Linux
recon-all exited with ERRORS at Thu Jun 18 07:59:02 BST 2009
When I start this process using "force" it seems to be running, but then comes into problems with the "nu_correct" error.
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: 17 June 2009 17:12 To: Ahmed, F, Me fahmed@sun.ac.za Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] error message
Hi Fatima,
You probably would find it easier easier to just point recon-all directly at the dicoms with -i. It saves the conversion step. If you do the conversion and put the runs in the orig dir then you don't need -i anymore, it will find them.
cheers, Bruce
On Wed, 17 Jun 2009, Ahmed, F, Me fahmed@sun.ac.za wrote:
Hello, I am new to using Freesurfer and am trying to run the recon-all stages in order to get thickness values for brain regions. I have correctly converted all my dicom images into the correct mgz format as instructed by your manual and have carried out motion correction (even though I only have one acquisition) to create the orig.mgz file. however, when I try and run the following command:
"recon-all -i <in volume 1> -i <in volume 2> -i <in volume 3> -autorecon1 -s bert" using my subject name, I get the following error message:
[fsl@localhost DicomImages]$ recon-all -i CON_ADAMS_MONIQUE/orig.mgz -autorecon1 -s CON_ADAMS_MONIQUE ERROR: cannot find CON_ADAMS_MONIQUE/orig.mgz Linux localhost.localdomain 2.6.18-8.1.8.el5 #1 SMP Tue Jul 10 06:50:22 EDT 2007 i686 i686 i386 GNU/Linux
recon-all exited with ERRORS at Wed Jun 17 08:59:47 BST 2009
Please can you advise me on what the problem is and how to correct it?
Thank you.
Fatima
're-run with force' means that the subject name exists and using the 'force' flag will overwrite it. As for the error, the info in this post might be helpful.
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06793.html
On Thu, 18 Jun 2009, Ahmed, F, Me fahmed@sun.ac.za wrote:
Hello,
What does it mean when it says to re-run with "force" - when I do this for autorecon 1, it says that there is the following error:
nu_correct: Command not found. ERROR: nu_correct Linux localhost.localdomain 2.6.18-8.1.8.el5 #1 SMP Tue Jul 10 06:50:22 EDT 2007 i686 i686 i386 GNU/Linux
recon-all exited with ERRORS at Thu Jun 18 07:59:02 BST 2009
When I start this process using "force" it seems to be running, but then comes into problems with the "nu_correct" error.
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: 17 June 2009 17:12 To: Ahmed, F, Me fahmed@sun.ac.za Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] error message
Hi Fatima,
You probably would find it easier easier to just point recon-all directly at the dicoms with -i. It saves the conversion step. If you do the conversion and put the runs in the orig dir then you don't need -i anymore, it will find them.
cheers, Bruce
On Wed, 17 Jun 2009, Ahmed, F, Me fahmed@sun.ac.za wrote:
Hello, I am new to using Freesurfer and am trying to run the recon-all stages in order to get thickness values for brain regions. I have correctly converted all my dicom images into the correct mgz format as instructed by your manual and have carried out motion correction (even though I only have one acquisition) to create the orig.mgz file. however, when I try and run the following command:
"recon-all -i <in volume 1> -i <in volume 2> -i <in volume 3> -autorecon1 -s bert" using my subject name, I get the following error message:
[fsl@localhost DicomImages]$ recon-all -i CON_ADAMS_MONIQUE/orig.mgz -autorecon1 -s CON_ADAMS_MONIQUE ERROR: cannot find CON_ADAMS_MONIQUE/orig.mgz Linux localhost.localdomain 2.6.18-8.1.8.el5 #1 SMP Tue Jul 10 06:50:22 EDT 2007 i686 i686 i386 GNU/Linux
recon-all exited with ERRORS at Wed Jun 17 08:59:47 BST 2009
Please can you advise me on what the problem is and how to correct it?
Thank you.
Fatima
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi,
Thank you for your help and in providing that link. I found "perl" and set it to the correct place, tried to do "fixup_mni_paths", and got the following message when trying to find "nu_correct"
[fsl@localhost bin]$ nu_correct Can't locate MNI/Startup.pm in @INC (@INC contains: /usr/lib/perl5/site_perl/5.8.8/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.7/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.6/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl/5.8.7 /usr/lib/perl5/site_perl/5.8.6 /usr/lib/perl5/site_perl/5.8.5 /usr/lib/perl5/site_perl /usr/lib/perl5/vendor_perl/5.8.8/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.7/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.6/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.5/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl/5.8.7 /usr/lib/perl5/vendor_perl/5.8.6 /usr/lib/perl5/vendor_perl/5.8.5 /usr/lib/perl5/vendor_perl /usr/lib/perl5/5.8.8/i386-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /home/fsl/Desktop/freesurfer/mni/bin/nu_correct line 37. BEGIN failed--compilation aborted at /home/fsl/Desktop/freesurfer/mni/bin/nu_correct line 37.
This all seems very confusing and I'm not sure what is going on. Everything seems to be in place in order for freesurfer to find "nu_correct" but it's just not working. Please help!
Thank you. Fatima
-----Original Message----- From: Sita Kakunoori [mailto:sita@nmr.mgh.harvard.edu] Sent: 18 June 2009 18:29 To: Ahmed, F, Me fahmed@sun.ac.za Cc: Bruce Fischl; freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] error message
're-run with force' means that the subject name exists and using the 'force' flag will overwrite it. As for the error, the info in this post might be helpful.
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06793.html
On Thu, 18 Jun 2009, Ahmed, F, Me fahmed@sun.ac.za wrote:
Hello,
What does it mean when it says to re-run with "force" - when I do this for autorecon 1, it says that there is the following error:
nu_correct: Command not found. ERROR: nu_correct Linux localhost.localdomain 2.6.18-8.1.8.el5 #1 SMP Tue Jul 10 06:50:22 EDT 2007 i686 i686 i386 GNU/Linux
recon-all exited with ERRORS at Thu Jun 18 07:59:02 BST 2009
When I start this process using "force" it seems to be running, but then comes into problems with the "nu_correct" error.
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: 17 June 2009 17:12 To: Ahmed, F, Me fahmed@sun.ac.za Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] error message
Hi Fatima,
You probably would find it easier easier to just point recon-all directly at the dicoms with -i. It saves the conversion step. If you do the conversion and put the runs in the orig dir then you don't need -i anymore, it will find them.
cheers, Bruce
On Wed, 17 Jun 2009, Ahmed, F, Me fahmed@sun.ac.za wrote:
Hello, I am new to using Freesurfer and am trying to run the recon-all stages in order to get thickness values for brain regions. I have correctly converted all my dicom images into the correct mgz format as instructed by your manual and have carried out motion correction (even though I only have one acquisition) to create the orig.mgz file. however, when I try and run the following command:
"recon-all -i <in volume 1> -i <in volume 2> -i <in volume 3> -autorecon1 -s bert" using my subject name, I get the following error message:
[fsl@localhost DicomImages]$ recon-all -i CON_ADAMS_MONIQUE/orig.mgz -autorecon1 -s CON_ADAMS_MONIQUE ERROR: cannot find CON_ADAMS_MONIQUE/orig.mgz Linux localhost.localdomain 2.6.18-8.1.8.el5 #1 SMP Tue Jul 10 06:50:22 EDT 2007 i686 i686 i386 GNU/Linux
recon-all exited with ERRORS at Wed Jun 17 08:59:47 BST 2009
Please can you advise me on what the problem is and how to correct it?
Thank you.
Fatima
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Sorry, according to the thread that you provided me, nu_correct uses perl, so make sure that perl is found at:
/usr/bin/perl
"perl" is found at /usr/bin/perl, so it is in the correct place and theoretically, it should be working. But it isn't. Is there any reason why that could be happening?
Sorry for the constant questions.
-----Original Message----- From: Sita Kakunoori [mailto:sita@nmr.mgh.harvard.edu] Sent: 18 June 2009 18:29 To: Ahmed, F, Me fahmed@sun.ac.za Cc: Bruce Fischl; freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] error message
're-run with force' means that the subject name exists and using the 'force' flag will overwrite it. As for the error, the info in this post might be helpful.
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06793.html
On Thu, 18 Jun 2009, Ahmed, F, Me fahmed@sun.ac.za wrote:
Hello,
What does it mean when it says to re-run with "force" - when I do this for autorecon 1, it says that there is the following error:
nu_correct: Command not found. ERROR: nu_correct Linux localhost.localdomain 2.6.18-8.1.8.el5 #1 SMP Tue Jul 10 06:50:22 EDT 2007 i686 i686 i386 GNU/Linux
recon-all exited with ERRORS at Thu Jun 18 07:59:02 BST 2009
When I start this process using "force" it seems to be running, but then comes into problems with the "nu_correct" error.
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: 17 June 2009 17:12 To: Ahmed, F, Me fahmed@sun.ac.za Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] error message
Hi Fatima,
You probably would find it easier easier to just point recon-all directly at the dicoms with -i. It saves the conversion step. If you do the conversion and put the runs in the orig dir then you don't need -i anymore, it will find them.
cheers, Bruce
On Wed, 17 Jun 2009, Ahmed, F, Me fahmed@sun.ac.za wrote:
Hello, I am new to using Freesurfer and am trying to run the recon-all stages in order to get thickness values for brain regions. I have correctly converted all my dicom images into the correct mgz format as instructed by your manual and have carried out motion correction (even though I only have one acquisition) to create the orig.mgz file. however, when I try and run the following command:
"recon-all -i <in volume 1> -i <in volume 2> -i <in volume 3> -autorecon1 -s bert" using my subject name, I get the following error message:
[fsl@localhost DicomImages]$ recon-all -i CON_ADAMS_MONIQUE/orig.mgz -autorecon1 -s CON_ADAMS_MONIQUE ERROR: cannot find CON_ADAMS_MONIQUE/orig.mgz Linux localhost.localdomain 2.6.18-8.1.8.el5 #1 SMP Tue Jul 10 06:50:22 EDT 2007 i686 i686 i386 GNU/Linux
recon-all exited with ERRORS at Wed Jun 17 08:59:47 BST 2009
Please can you advise me on what the problem is and how to correct it?
Thank you.
Fatima
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
try running:
fixup_mni_paths
On Fri, 2009-06-19 at 09:38 +0200, Ahmed, F, Me wrote:
Sorry, according to the thread that you provided me, nu_correct uses perl, so make sure that perl is found at:
/usr/bin/perl
"perl" is found at /usr/bin/perl, so it is in the correct place and theoretically, it should be working. But it isn't. Is there any reason why that could be happening?
Sorry for the constant questions.
-----Original Message----- From: Sita Kakunoori [mailto:sita@nmr.mgh.harvard.edu] Sent: 18 June 2009 18:29 To: Ahmed, F, Me fahmed@sun.ac.za Cc: Bruce Fischl; freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] error message
're-run with force' means that the subject name exists and using the 'force' flag will overwrite it. As for the error, the info in this post might be helpful.
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06793.html
On Thu, 18 Jun 2009, Ahmed, F, Me fahmed@sun.ac.za wrote:
Hello,
What does it mean when it says to re-run with "force" - when I do this for autorecon 1, it says that there is the following error:
nu_correct: Command not found. ERROR: nu_correct Linux localhost.localdomain 2.6.18-8.1.8.el5 #1 SMP Tue Jul 10 06:50:22 EDT 2007 i686 i686 i386 GNU/Linux
recon-all exited with ERRORS at Thu Jun 18 07:59:02 BST 2009
When I start this process using "force" it seems to be running, but then comes into problems with the "nu_correct" error.
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: 17 June 2009 17:12 To: Ahmed, F, Me fahmed@sun.ac.za Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] error message
Hi Fatima,
You probably would find it easier easier to just point recon-all directly at the dicoms with -i. It saves the conversion step. If you do the conversion and put the runs in the orig dir then you don't need -i anymore, it will find them.
cheers, Bruce
On Wed, 17 Jun 2009, Ahmed, F, Me fahmed@sun.ac.za wrote:
Hello, I am new to using Freesurfer and am trying to run the recon-all stages in order to get thickness values for brain regions. I have correctly converted all my dicom images into the correct mgz format as instructed by your manual and have carried out motion correction (even though I only have one acquisition) to create the orig.mgz file. however, when I try and run the following command:
"recon-all -i <in volume 1> -i <in volume 2> -i <in volume 3> -autorecon1 -s bert" using my subject name, I get the following error message:
[fsl@localhost DicomImages]$ recon-all -i CON_ADAMS_MONIQUE/orig.mgz -autorecon1 -s CON_ADAMS_MONIQUE ERROR: cannot find CON_ADAMS_MONIQUE/orig.mgz Linux localhost.localdomain 2.6.18-8.1.8.el5 #1 SMP Tue Jul 10 06:50:22 EDT 2007 i686 i686 i386 GNU/Linux
recon-all exited with ERRORS at Wed Jun 17 08:59:47 BST 2009
Please can you advise me on what the problem is and how to correct it?
Thank you.
Fatima
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Nick,
I tried running fixup_mni_paths and got the following output (see attached).
Fatima
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Nick Schmansky Sent: 19 June 2009 23:24 To: Ahmed, F, Me fahmed@sun.ac.za Cc: Sita Kakunoori; Freesurfer Mailing List Subject: RE: [Freesurfer] error message
try running:
fixup_mni_paths
On Fri, 2009-06-19 at 09:38 +0200, Ahmed, F, Me wrote:
Sorry, according to the thread that you provided me, nu_correct uses perl, so make sure that perl is found at:
/usr/bin/perl
"perl" is found at /usr/bin/perl, so it is in the correct place and theoretically, it should be working. But it isn't. Is there any reason why that could be happening?
Sorry for the constant questions.
-----Original Message----- From: Sita Kakunoori [mailto:sita@nmr.mgh.harvard.edu] Sent: 18 June 2009 18:29 To: Ahmed, F, Me fahmed@sun.ac.za Cc: Bruce Fischl; freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] error message
're-run with force' means that the subject name exists and using the 'force' flag will overwrite it. As for the error, the info in this post might be helpful.
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06793.html
On Thu, 18 Jun 2009, Ahmed, F, Me fahmed@sun.ac.za wrote:
Hello,
What does it mean when it says to re-run with "force" - when I do this for autorecon 1, it says that there is the following error:
nu_correct: Command not found. ERROR: nu_correct Linux localhost.localdomain 2.6.18-8.1.8.el5 #1 SMP Tue Jul 10 06:50:22 EDT 2007 i686 i686 i386 GNU/Linux
recon-all exited with ERRORS at Thu Jun 18 07:59:02 BST 2009
When I start this process using "force" it seems to be running, but then comes into problems with the "nu_correct" error.
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: 17 June 2009 17:12 To: Ahmed, F, Me fahmed@sun.ac.za Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] error message
Hi Fatima,
You probably would find it easier easier to just point recon-all directly at the dicoms with -i. It saves the conversion step. If you do the conversion and put the runs in the orig dir then you don't need -i anymore, it will find them.
cheers, Bruce
On Wed, 17 Jun 2009, Ahmed, F, Me fahmed@sun.ac.za wrote:
Hello, I am new to using Freesurfer and am trying to run the recon-all stages in order to get thickness values for brain regions. I have correctly converted all my dicom images into the correct mgz format as instructed by your manual and have carried out motion correction (even though I only have one acquisition) to create the orig.mgz file. however, when I try and run the following command:
"recon-all -i <in volume 1> -i <in volume 2> -i <in volume 3> -autorecon1 -s bert" using my subject name, I get the following error message:
[fsl@localhost DicomImages]$ recon-all -i CON_ADAMS_MONIQUE/orig.mgz -autorecon1 -s CON_ADAMS_MONIQUE ERROR: cannot find CON_ADAMS_MONIQUE/orig.mgz Linux localhost.localdomain 2.6.18-8.1.8.el5 #1 SMP Tue Jul 10 06:50:22 EDT 2007 i686 i686 i386 GNU/Linux
recon-all exited with ERRORS at Wed Jun 17 08:59:47 BST 2009
Please can you advise me on what the problem is and how to correct it?
Thank you.
Fatima
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Fatima,
Can you send me the output of this command:
env | grep PERL
Nick
On Mon, 2009-06-22 at 09:56 +0200, Ahmed, F, Me wrote:
Nick,
I tried running fixup_mni_paths and got the following output (see attached).
Fatima
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Nick Schmansky Sent: 19 June 2009 23:24 To: Ahmed, F, Me fahmed@sun.ac.za Cc: Sita Kakunoori; Freesurfer Mailing List Subject: RE: [Freesurfer] error message
try running:
fixup_mni_paths
On Fri, 2009-06-19 at 09:38 +0200, Ahmed, F, Me wrote:
Sorry, according to the thread that you provided me, nu_correct uses perl, so make sure that perl is found at:
/usr/bin/perl
"perl" is found at /usr/bin/perl, so it is in the correct place and theoretically, it should be working. But it isn't. Is there any reason why that could be happening?
Sorry for the constant questions.
-----Original Message----- From: Sita Kakunoori [mailto:sita@nmr.mgh.harvard.edu] Sent: 18 June 2009 18:29 To: Ahmed, F, Me fahmed@sun.ac.za Cc: Bruce Fischl; freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] error message
're-run with force' means that the subject name exists and using the 'force' flag will overwrite it. As for the error, the info in this post might be helpful.
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06793.html
On Thu, 18 Jun 2009, Ahmed, F, Me fahmed@sun.ac.za wrote:
Hello,
What does it mean when it says to re-run with "force" - when I do this for autorecon 1, it says that there is the following error:
nu_correct: Command not found. ERROR: nu_correct Linux localhost.localdomain 2.6.18-8.1.8.el5 #1 SMP Tue Jul 10 06:50:22 EDT 2007 i686 i686 i386 GNU/Linux
recon-all exited with ERRORS at Thu Jun 18 07:59:02 BST 2009
When I start this process using "force" it seems to be running, but then comes into problems with the "nu_correct" error.
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: 17 June 2009 17:12 To: Ahmed, F, Me fahmed@sun.ac.za Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] error message
Hi Fatima,
You probably would find it easier easier to just point recon-all directly at the dicoms with -i. It saves the conversion step. If you do the conversion and put the runs in the orig dir then you don't need -i anymore, it will find them.
cheers, Bruce
On Wed, 17 Jun 2009, Ahmed, F, Me fahmed@sun.ac.za wrote:
Hello, I am new to using Freesurfer and am trying to run the recon-all stages in order to get thickness values for brain regions. I have correctly converted all my dicom images into the correct mgz format as instructed by your manual and have carried out motion correction (even though I only have one acquisition) to create the orig.mgz file. however, when I try and run the following command:
"recon-all -i <in volume 1> -i <in volume 2> -i <in volume 3> -autorecon1 -s bert" using my subject name, I get the following error message:
[fsl@localhost DicomImages]$ recon-all -i CON_ADAMS_MONIQUE/orig.mgz -autorecon1 -s CON_ADAMS_MONIQUE ERROR: cannot find CON_ADAMS_MONIQUE/orig.mgz Linux localhost.localdomain 2.6.18-8.1.8.el5 #1 SMP Tue Jul 10 06:50:22 EDT 2007 i686 i686 i386 GNU/Linux
recon-all exited with ERRORS at Wed Jun 17 08:59:47 BST 2009
Please can you advise me on what the problem is and how to correct it?
Thank you.
Fatima
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Nick,
There is no output, I typed that in and got nothing.
[fsl@localhost freesurfer]$ env | grep PERL [fsl@localhost freesurfer]$
Fatima
-----Original Message----- From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: 22 June 2009 14:41 To: Ahmed, F, Me fahmed@sun.ac.za Cc: Sita Kakunoori; Freesurfer Mailing List Subject: RE: [Freesurfer] error message
Fatima,
Can you send me the output of this command:
env | grep PERL
Nick
On Mon, 2009-06-22 at 09:56 +0200, Ahmed, F, Me wrote:
Nick,
I tried running fixup_mni_paths and got the following output (see attached).
Fatima
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Nick Schmansky Sent: 19 June 2009 23:24 To: Ahmed, F, Me fahmed@sun.ac.za Cc: Sita Kakunoori; Freesurfer Mailing List Subject: RE: [Freesurfer] error message
try running:
fixup_mni_paths
On Fri, 2009-06-19 at 09:38 +0200, Ahmed, F, Me wrote:
Sorry, according to the thread that you provided me, nu_correct uses perl, so make sure that perl is found at:
/usr/bin/perl
"perl" is found at /usr/bin/perl, so it is in the correct place and theoretically, it should be working. But it isn't. Is there any reason why that could be happening?
Sorry for the constant questions.
-----Original Message----- From: Sita Kakunoori [mailto:sita@nmr.mgh.harvard.edu] Sent: 18 June 2009 18:29 To: Ahmed, F, Me fahmed@sun.ac.za Cc: Bruce Fischl; freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] error message
're-run with force' means that the subject name exists and using the 'force' flag will overwrite it. As for the error, the info in this post might be helpful.
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06793.html
On Thu, 18 Jun 2009, Ahmed, F, Me fahmed@sun.ac.za wrote:
Hello,
What does it mean when it says to re-run with "force" - when I do this for autorecon 1, it says that there is the following error:
nu_correct: Command not found. ERROR: nu_correct Linux localhost.localdomain 2.6.18-8.1.8.el5 #1 SMP Tue Jul 10 06:50:22 EDT 2007 i686 i686 i386 GNU/Linux
recon-all exited with ERRORS at Thu Jun 18 07:59:02 BST 2009
When I start this process using "force" it seems to be running, but then comes into problems with the "nu_correct" error.
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: 17 June 2009 17:12 To: Ahmed, F, Me fahmed@sun.ac.za Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] error message
Hi Fatima,
You probably would find it easier easier to just point recon-all directly at the dicoms with -i. It saves the conversion step. If you do the conversion and put the runs in the orig dir then you don't need -i anymore, it will find them.
cheers, Bruce
On Wed, 17 Jun 2009, Ahmed, F, Me fahmed@sun.ac.za wrote:
Hello, I am new to using Freesurfer and am trying to run the recon-all stages in order to get thickness values for brain regions. I have correctly converted all my dicom images into the correct mgz format as instructed by your manual and have carried out motion correction (even though I only have one acquisition) to create the orig.mgz file. however, when I try and run the following command:
"recon-all -i <in volume 1> -i <in volume 2> -i <in volume 3> -autorecon1 -s bert" using my subject name, I get the following error message:
[fsl@localhost DicomImages]$ recon-all -i CON_ADAMS_MONIQUE/orig.mgz -autorecon1 -s CON_ADAMS_MONIQUE ERROR: cannot find CON_ADAMS_MONIQUE/orig.mgz Linux localhost.localdomain 2.6.18-8.1.8.el5 #1 SMP Tue Jul 10 06:50:22 EDT 2007 i686 i686 i386 GNU/Linux
recon-all exited with ERRORS at Wed Jun 17 08:59:47 BST 2009
Please can you advise me on what the problem is and how to correct it?
Thank you.
Fatima
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Ahmed, F, Me <fahmed＠sun.ac.za> -
Bruce Fischl -
Nick Schmansky -
Pedro Paulo de Magalhães Oliveira Junior -
Sita Kakunoori