Hi Doug,
I do not believe the files have changed in any way since I started using them;
I uploaded some dicoms for you to look at and the recon-all log to the file
drop a few minutes ago (with more details). Thank you for all your help!
Joseph Aloi
Graduate Student, MD/PhD Scholars Program
Depa
Have the dicom files changed in any way? In the failure, the problem
maybe that it thinks that the series is truncated (the header thing is
not a problem). Do you still have perms to all the files in that folder?
I noticed in the analysis that succeeded had a bunch of these statements
(never se
The log files you can just attach to the email to the list (or to me
directly if there is something in there that you don't want to post)
On 05/20/2016 04:02 PM, Aloi, Joseph wrote:
> Excellent, thank you! To do that, do I send an e-mail to the listserv
> with the log files attached or do I us
Excellent, thank you! To do that, do I send an e-mail to the listserv with the
log files attached or do I use the filedrop?
yea, can you post the log file of both the successful and failing runs?
On 05/19/2016 11:28 AM, Aloi, Joseph wrote:
>
> Hi Doug,
>
> No that’s not how I usually store my
yea, can you post the log file of both the successful and failing runs?
On 05/19/2016 11:28 AM, Aloi, Joseph wrote:
>
> Hi Doug,
>
> No that’s not how I usually store my files- I have a folder for the
> particular study that I am working on then the dicoms for each subject
> in that study are st
Hi Doug,
No that’s not how I usually store my files- I have a folder for the particular
study that I am working on then the dicoms for each subject in that study are
stored in individual subject folders within the study folder.
I got a chance to look around the recon-all logs this morning for a
I don't have any idea what is going wrong. I noticed that the file that it is
having problems with is here
/Users/alojos/Applications/freesurfer/subjects/sub_.dcm
Do you really keep all your dicom files in that location?
On 05/17/2016 11:47 PM, Aloi, Joseph wrote:
> Hi Doug,
> Sorry- I've a
Hi Doug,
Sorry- I've added entire correspondence onto the end of this e-mail. I don't
think the disk filled up as I am on a 3 TB hard drive and I still have ~2 TB of
free space on my disk. Anything else you think it could be?
Thanks!
Joseph Aloi
Please remember to include previous c
Please remember to include previous correspondence otherwise we can't
keep track of the problem!
Eg, I don't have the previous email to see what the error was. Is it
possible that the disk filled up?
On 05/17/2016 09:49 AM, Aloi, Joseph wrote:
> Hi Doug,
>
> Yes, you are correct- data I have pre
Hi Doug,
Yes, you are correct- data I have previously processed without any problems is
no longer being processed.
My version of freesurfer is 5.3.0; I only downloaded it a few weeks ago so I
have not changed my freesurfer version recently.
Thanks!
Joseph Aloi
Graduate Student, MD/PhD Schola
So the exact same data set is now generating an error whereas it ran
smoothly before? What version of FS are you using? Did you change versions?
doug
On 05/16/2016 09:49 AM, Aloi, Joseph wrote:
>
> Hi freesurfer experts,
>
> I have recently begun to use freesurfer to do structural MRI
> analyses
Hi freesurfer experts,
I have recently begun to use freesurfer to do structural MRI analyses. I have
been able to successfully process about 40 structural scans with recon-all thus
far, but starting a few days ago, I started getting this error whenever I run
recon-all:
WARNING: file /Users/al
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