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 > > > > > 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
