Hi Anastasia,
Many thanks for your help. I did reply but don't see the email on the forum.
I have began using FreeSurfer 5.3.0 instead, thanks. However, I'm a bit confused - I've created a 3-column bvecs format file (I had been using for version 5.2.0).
After running several I've noticed the 'bvecs' file in the dmri folder is slightly different from the input file, whereas the 'bvecs.norot' file matches the input file extactly.
For example: File 2: 0.9200842 0.3251221 0.2185593 File 2: 0.919 0.3311 0.2141
Can you please clarify which is used, and if these differences can be ignored?
Thanks and best wishes, Colm.
-----Original Message----- From: Anastasia Yendiki [mailto:ayendiki@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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