btw, you are strongly encouraged NOT to use FS 5.2. For TRACULA it is probably fine, but we found some small but systematic problems with the anatomical analysis in 5.2 doug
On 05/16/2014 11:51 AM, McGinnity, Colm wrote: > 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: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 > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
