Hi FS developers,
I received errors in one of steps in recon-all. I analyzed 111 individual subjects' T1 data using same method, but there are errors in only 14 subjects.
Below is screenshot image in the end of recon-all.log file. I attached log files from two exemplar subjects below, also.
I’d appreciate if you might help me. Juhyoung.
Hi Juhyoung
can you upload one subject that this happens in to our ftp site?
cheers Bruce On Mon, 6 Feb 2017, Juhyoung Ryu wrote:
Hi FS developers,
I received errors in one of steps in recon-all. I analyzed 111 individual subjects' T1 data using same method, but there are errors in only 14 subjects.
Below is screenshot image in the end of recon-all.log file. I attached log files from two exemplar subjects below, also.
I’d appreciate if you might help me. Juhyoung.
I uploaded 3 set of T1.nii and T2.nii files for 3 example subjects. You can get subject information here : T1_CUBEE{#subject}.nii
#0001 data success FS processing and #0002 / #0010 data is failed. - Success: 0001 - Failed: 0010, 0002
I did FREESURFER processing using both T1 and T2 data after preprocessing and downsampling from 0.85mm to 1mm resolution.
Thank you in advance for any help, Juhyoung
On Feb 6, 2017, at 11:39 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Juhyoung
can you upload one subject that this happens in to our ftp site?
cheers Bruce On Mon, 6 Feb 2017, Juhyoung Ryu wrote:
Hi FS developers,
I received errors in one of steps in recon-all. I analyzed 111 individual subjects' T1 data using same method, but there are errors in only 14 subjects.
Below is screenshot image in the end of recon-all.log file. I attached log files from two exemplar subjects below, also.
I’d appreciate if you might help me. Juhyoung.
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 Juhyoung
can you tar and gzip the entire subject directory tree and upload that?
thanks Bruce
On Tue, 7 Feb 2017, Juhyoung Ryu wrote:
I uploaded 3 set of T1.nii and T2.nii files for 3 example subjects. You can get subject information here : T1_CUBEE{#subject}.nii
#0001 data success FS processing and #0002 / #0010 data is failed.
- Success: 0001
- Failed: 0010, 0002
I did FREESURFER processing using both T1 and T2 data after preprocessing and downsampling from 0.85mm to 1mm resolution.
Thank you in advance for any help, Juhyoung
On Feb 6, 2017, at 11:39 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Juhyoung
can you upload one subject that this happens in to our ftp site?
cheers Bruce On Mon, 6 Feb 2017, Juhyoung Ryu wrote:
Hi FS developers,
I received errors in one of steps in recon-all. I analyzed 111 individual subjects' T1 data using same method, but there are errors in only 14 subjects.
Below is screenshot image in the end of recon-all.log file. I attached log files from two exemplar subjects below, also.
I’d appreciate if you might help me. Juhyoung.
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
Hi Bruce,
Does 'entire subject directory tree' means that the subject’s data containing all preprocessed results before i run FREESURFER? not only raw T1 and T2 file?
Thank you, Juhyoung.
On Feb 7, 2017, at 10:36 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Juhyoung
can you tar and gzip the entire subject directory tree and upload that?
thanks Bruce
On Tue, 7 Feb 2017, Juhyoung Ryu wrote:
I uploaded 3 set of T1.nii and T2.nii files for 3 example subjects. You can get subject information here : T1_CUBEE{#subject}.nii
#0001 data success FS processing and #0002 / #0010 data is failed.
- Success: 0001
- Failed: 0010, 0002
I did FREESURFER processing using both T1 and T2 data after preprocessing and downsampling from 0.85mm to 1mm resolution.
Thank you in advance for any help, Juhyoung
On Feb 6, 2017, at 11:39 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Juhyoung
can you upload one subject that this happens in to our ftp site?
cheers Bruce On Mon, 6 Feb 2017, Juhyoung Ryu wrote:
Hi FS developers,
I received errors in one of steps in recon-all. I analyzed 111 individual subjects' T1 data using same method, but there are errors in only 14 subjects.
Below is screenshot image in the end of recon-all.log file. I attached log files from two exemplar subjects below, also.
I’d appreciate if you might help me. Juhyoung.
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
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 means:
cd $SUBJECTS_DIR tar czvf for_bruce.tgz ${subject_id}
cheers Bruce On Tue, 7 Feb 2017, Juhyoung Ryu wrote:
Hi Bruce,
Does 'entire subject directory tree' means that the subject’s data containing all preprocessed results before i run FREESURFER? not only raw T1 and T2 file?
Thank you, Juhyoung.
On Feb 7, 2017, at 10:36 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Juhyoung
can you tar and gzip the entire subject directory tree and upload that?
thanks Bruce
On Tue, 7 Feb 2017, Juhyoung Ryu wrote:
I uploaded 3 set of T1.nii and T2.nii files for 3 example subjects. You can get subject information here : T1_CUBEE{#subject}.nii
#0001 data success FS processing and #0002 / #0010 data is failed.
- Success: 0001
- Failed: 0010, 0002
I did FREESURFER processing using both T1 and T2 data after preprocessing and downsampling from 0.85mm to 1mm resolution.
Thank you in advance for any help, Juhyoung
On Feb 6, 2017, at 11:39 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Juhyoung
can you upload one subject that this happens in to our ftp site?
cheers Bruce On Mon, 6 Feb 2017, Juhyoung Ryu wrote:
Hi FS developers,
I received errors in one of steps in recon-all. I analyzed 111 individual subjects' T1 data using same method, but there are errors in only 14 subjects.
Below is screenshot image in the end of recon-all.log file. I attached log files from two exemplar subjects below, also.
I’d appreciate if you might help me. Juhyoung.
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
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
Hi Juhyoung
this is a pretty odd bug, but I do have a patch for it. What hardware/software environment are you using?
cheers Bruce On Mon, 6 Feb 2017, Juhyoung Ryu wrote:
Hi FS developers,
I received errors in one of steps in recon-all. I analyzed 111 individual subjects' T1 data using same method, but there are errors in only 14 subjects.
Below is screenshot image in the end of recon-all.log file. I attached log files from two exemplar subjects below, also.
I’d appreciate if you might help me. Juhyoung.
Hello Juhyoung,
I noticed from the recon-all.log files that you are using freesurfer v5.2. It was revealed that this version had issues regarding systematic white surface contraction and placement of the pial surface extending too far:
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-May/029581.html
I would recommend processing these subjects with version 6.0
https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall
-Zeke
On 02/06/2017 01:43 AM, Juhyoung Ryu wrote:
Hi FS developers,
I received errors in one of steps in recon-all. I analyzed 111 individual subjects' T1 data using same method, but there are errors in _only 14 subjects._
Below is screenshot image in the end of recon-all.log file. I attached log files from two exemplar subjects below, also.
I’d appreciate if you might help me. Juhyoung.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Juhyoung Ryu -
Z K