Doug, can you do me a favor and check to see if this modified version of
recon-all works on your data?
https://gate.nmr.mgh.harvard.edu/safelinks/greve/recon-all
On 11/30/2016 11:41 AM, Douglas Merkitch wrote:
> Hmmm it is a dicom file. Could it be that the lack of file extension
> gives it
Actually, it is the lack of a dot (".") in the file name. This is a
short-coming of recon-all. I'm really surprised that it took this long
to manifest itself. The short-term fix is to convert the files to mgz,
then pass the mgz files to recon-all.
On 11/30/2016 11:41 AM, Douglas Merkitch
It is not recognizing that the input is a dicom file. Is 4355-0005-1
a dicom file? Or is it a folder?
On 11/29/2016 05:51 PM, Douglas Merkitch wrote:
> Here is the command/output with the -debug flag:
>
> recon-all -debug -i
>
Can you run it with -debug and send the terminal output?
On 11/29/2016 05:39 PM, Douglas Merkitch wrote:
> Hello Bruce & Doug,
>
> There are no spaces in the filenames (just a lot of underscores and
> dashes!).
>
> I don't think it's a permissions issue because it is able to write the
> first
Hello Bruce & Doug,
There are no spaces in the filenames (just a lot of underscores and dashes!).
I don't think it's a permissions issue because it is able to write the first of
the two files that I input (regardless of which one I feed it first), but fails
to write the second file (what would
Do you have write permission into that folder, ie,
/Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039/mri/orig ? Can
you run it with -debug as the first argument and send the terminal output?
On 11/29/2016 05:00 PM, Douglas Merkitch wrote:
> Hello again,
>
> I did, in fact, encounter
Hi Doug
do you have any spaces in your filenames? That can cause this kind of
thing. It's hard to tell from your email
cheers
Bruce
On Tue, 29 Nov 2016, Douglas Merkitch wrote:
Hello again,
I did, in fact, encounter another error that resulted in only the first
mri/orig/001.mgz
and not
Hello again,
I did, in fact, encounter another error that resulted in only the first
mri/orig/001.mgz and not the mr/orig/002.mgz file to be written. Below is the
command line and terminal output:
===
recon-all -i
