Hi Colm - Yes, it's fine to run bedpostx directly, with the path to the
dmri directory as its argument.
Since you're using 5.2, note that although there were no issues with
tracula in that version, it is not advisable to use freesurfer recons
produced with 5.2. There was a bug in that version, which is why 5.3 was
released shortly after 5.2:
http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes
Hope this helps,
a.y
On Tue, 18 Mar 2014, McGinnity, Colm wrote:
Dear Anastasia,
Hello, many thanks for your quick reply, sorry for the delay.
I have switched to 3-column format and that does indeed get the process a
little further, so many thanks for that. Unfortunately however I get this new
error during the trac-all -bedp stage:
An exception has been thrown
ERROR: Could not open image
/home/k1193186/FreeSurfer/TRACULA/ROLAND03A/dmri/data_slice_0000
Trace:read_volume4DROI.
I saw that similar errors had been identified in the past, but I wasn't really
clear from the dialogue what the cause was or how to correct. Could you
explain, please?
I have tried to run bedpostx directly as previously advised, it seems to be
running at present.
IF it is successful, can I just always do this instead and then continue with
trac-all -path? Or do I need to use trac-all -bedp specifically?
Many thanks in advance,
Best wishes,
Colm.
Colm McGinnity
King's College London
-----Original Message-----
From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu]
Sent: 11 March 2014 00:39
To: McGinnity, Colm
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] TRACULA preprocessing error, FreeSurfer 5.2.0
Hi Colm - Note that the information in the tutorial (particularly the part
where gradient tables can be formatted in 3 rows or 3 columns) pertains to the
latest tracula update:
http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates
You're using an older version that only supports the 3-column format. I have no
idea if this is what's causing the error without looking at your trac-all.log,
but this would be a first guess.
a.y
On Mon, 10 Mar 2014, McGinnity, Colm wrote:
Dear Experts,
I am very new to TRACULA, I apologise for what is probably a silly question.
I’ve got the following error on running trac-all –prep (FreeSurfer 5.2.0):
awk: cmd. line:1: fatal: cannot open file `0' for reading (No such
file or
directory)
mri_concat --i
/home/k1193186/FreeSurfer/TRACULA/ROLAND03A/dmri/dwi_frame.nii.gz
--mean --o /home/k1193186/
FreeSurfer/TRACULA/ROLAND03A/dmri/lowb.nii.gz
niiRead(): error opening file /home/k1193186/
FreeSurfer/TRACULA/ROLAND03A/dmri/dwi_frame.nii.gz
ninputs = 1
Checking inputs
ERROR: reading
/home/k1193186/FreeSurfer/TRACULA/ROLAND03A/dmri/dwi_frame.nii.gz
Can anyone tell me what this means and how to fix this, please?
I’m guessing I’ve set up my configuration wrong or have the files in
the wrong place?
Many thanks!
Best wishes,
Colm.
King's College London
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