I think so. The attached one is definitely correct. On Mon, Jan 5, 2015 at 4:01 PM, Anastasia Yendiki < ayend...@nmr.mgh.harvard.edu> wrote:
> > Based on the log file, you ran "trac-all -prep -c dmrirc.all". The > configuration that you attached was called dmrirc.all.txt. Are these files > the same? > > On Mon, 5 Jan 2015, Katherine Damme wrote: > > Sorry I just copied that from remotely accessing my desktop and viewing >> the doc in the terminal. Attached is the complete log. >> >> On Sat, Jan 3, 2015 at 9:45 PM, Anastasia Yendiki < >> ayend...@nmr.mgh.harvard.edu> wrote: >> >> There should be a few more lines at the top of the log file, >> showing the exact trac-all command line that was executed, >> etc. Is this the entire log file? >> >> On Sat, 3 Jan 2015, Katherine Damme wrote: >> >> Here is the log. >> >> On Sat, Jan 3, 2015 at 9:19 AM, Anastasia Yendiki >> <ayend...@nmr.mgh.harvard.edu> wrote: >> >> It looks like it's not finding the file that you >> specify - not >> like it's finding it but it's in the wrong format. But >> I can't >> tell just from one line, I need to see the entire >> output of >> trac-all, which is saved in trac-all.log. >> >> On Fri, 2 Jan 2015, Katherine Damme wrote: >> >> I still get the error: >> mv -f >> /home/k/ksd770/Desktop/Subj/ >> 042/dmri/dwi_orig_flip.mghdti.bvecs >> /home/k/ksd770/Desktop/Subj/042/dmri/bvecs >> mv: cannot stat >> `/home/k/ksd770/Desktop/Subj/ >> 042/dmri/dwi_orig_flip.mghdti.bvecs': >> No such >> file or directory >> Linux kate.ad.wcas.northwestern.edu >> 2.6.32-431.3.1.el6.x86_64 #1 SMP Fri Dec >> 13 06:58:20 EST 2013 x86_64 x86_64 x86_64 >> GNU/Linux >> >> trac-preproc exited with ERRORS at Fri Jan 2 >> 18:55:26 CST 2015 >> >> Is there a way to avoid specifying a bvec/bval >> file >> and allowing it to pull >> this information from the dicom? >> >> The bvec/bval files that I was specifying came >> from >> previous processing of >> the data with FSL-bedpost, could this be causing >> the >> error? >> >> On Wed, Dec 31, 2014 at 8:05 PM, Anastasia Yendiki >> <ayend...@nmr.mgh.harvard.edu> wrote: >> >> You need to follow the format of >> $FREESURFER_HOME/bin/dmrirc.example. Enter >> single files for >> bvalfile and bvecfile, not lists of files. >> >> On Wed, 31 Dec 2014, Katherine Damme wrote: >> >> Now it is crashing giving me an if: >> Expression >> Syntax Error. See below >> >> On Wed, Dec 31, 2014 at 7:27 PM, >> Anastasia Yendiki >> <ayend...@nmr.mgh.harvard.edu> wrote: >> >> Hi Kate - It's not finding the >> gradient table. >> You'll have to >> specify the gradient table and >> b-value table >> as you did for the >> first subject. >> >> You can use the same config file >> for all your >> subjects, see the >> example in >> $FREESURFER_HOME/bin/dmrirc.example. >> >> Happy new year, >> a.y >> >> On Wed, 31 Dec 2014, Katherine >> Damme wrote: >> >> Hello Everyone! >> >> I was able to get tracula >> to >> run on one >> subject but >> I am now getting the >> following error with my >> new >> subjects. >> >> mv: cannot stat >> >> >> `/home/k/ksd770/Desktop/Subj/ >> 043/dmri/dwi_orig_flip.mghdti.bvecs': >> No such >> file or directory >> >> Let me know if you have >> any >> ideas why it >> is not >> makeing the >> dwi_orig_flip.mghdti.bvecs >> in the prep >> >> Thank you and have a Happy >> New Year!!! >> >> On Thu, Dec 18, 2014 at >> 5:38 >> PM, >> Anastasia Yendiki >> >> <ayend...@nmr.mgh.harvard.edu> wrote: >> >> Hi Kate - The option >> to use >> row-formatted >> (instead of >> column-formatted) >> gradient tables >> was added in >> a tracula update >> that came out after >> freesurfer 5.3 >> was >> released. If you want to >> use this format, you >> can download >> the update >> here: >> >> >> >> http://surfer.nmr.mgh.harvard. >> edu/fswiki/Tracula#Updates >> >> You should make sure >> to download >> the same >> build as your 5.3 >> build, which should >> be >> the CentOS >> 6 64-bit, >> based on this line >> that I got from your >> trac-all.log: >> >> >> build-stamp.txt: >> >> >> >> freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 >> >> a.y >> >> On Wed, 17 Dec 2014, >> Katherine >> Damme wrote: >> >> Thanks! That >> was >> exactly it! >> It was a >> FAT server and >> so that >> resolved >> that issue. >> >> Tracula is >> claiming that the >> bvecs and >> bvals don't >> have the same >> number of >> entries. These >> were the >> bvecs and bval >> files created >> during the >> trac-all prep >> process, but >> when I >> preprocesed the >> data >> previously >> with FSL the >> bvecs and >> bvals that >> were created >> did >> have equal >> numbers. I >> tried to >> specify >> to use >> these fsl made >> bvecs and >> bvals in the >> configuration >> file and it >> continues to >> default to the >> ones that it >> made. >> >> Any ideas? >> >> Thank you! >> >> Kate >> >> On Mon, Dec >> 15, >> 2014 at 7:42 >> PM, Watson, >> Christopher >> >> >> >> <christopher.wat...@childrens.harvard.edu> wrote: >> I think >> certain >> filesystems don't >> support sym >> linking (e.g. >> FAT32). So >> that might be >> it. >> >> >> >> ________________________________________ >> From: >> >> freesurfer-boun...@nmr.mgh.harvard.edu >> >> [freesurfer-boun...@nmr.mgh. >> harvard.edu] >> on behalf >> of Katherine >> Damme >> >> [katherine.da...@gmail.com] >> Sent: >> Monday, December >> 15, 2014 >> 5:29 PM >> To: >> Anastasia Yendiki >> Cc: >> Freesurfer support >> list >> Subject: >> Re: >> [Freesurfer] From >> bedpostX and >> recon-all to >> tracula >> >> After >> removing this I >> have a new >> (possibly >> unrelated >> error): >> mv -f >> >> /media/Sokol/Subj/041/dmri/bvecs >> >> /media/Sokol/Subj/041/dmri/ >> bvecs.norot >> xfmrot >> >> /media/Sokol/Subj/041/dmri/dwi.ecclog >> >> /media/Sokol/Subj/041/dmri/ >> bvecs.norot >> >> /media/Sokol/Subj/041/dmri/bvecs >> ln -sf >> >> /media/Sokol/Subj/041/dmri/dwi.nii.gz >> >> /media/Sokol/Subj/041/dmri/ >> data.nii.gz >> ln: >> creating symbolic >> link >> >> >> >> `/media/Sokol/Subj/041/dmri/data.nii.gz': >> Operation >> not permitted >> >> This >> persists even >> when I run the >> command as >> the root user >> and regardless >> of the >> permissions >> settings of >> the >> folder and >> the >> >> fdwi.nii.gz file. >> >> Any >> ideas? >> >> On Mon, >> Dec 15, 2014 >> at 3:07 PM, >> Anastasia >> Yendiki >> >> >> >> <ayend...@nmr.mgh.harvard.edu<mailto: >> ayend...@nmr.mgh.harvard.edu>> >> wrote: >> >> It's >> hard >> to tell >> what's causing >> the error >> without seeing >> the entire >> trac-all.log. >> However, by >> glancing at >> your >> config file >> you seem >> to still have >> B0 >> inhomogeneity >> correction >> turned on (dob0 = >> 1) but >> without >> specifying any >> field map >> dicoms. I'd >> turn >> it off >> and >> see if that >> fixes it. >> >> >> On Mon, >> 15 >> Dec 2014, >> Katherine >> Damme wrote: >> >> Where >> would I be >> specifying a >> directory as an >> input/output? >> >> I used >> the >> following >> cmd: >> >> /usr/local/freesurfer/bin/trac-all >> -prep >> -c dmri.fy >> >> On Sun, >> Dec 14, 2014 >> at 7:12 PM, >> Bruce Fischl >> >> >> >> <fis...@nmr.mgh.harvard.edu<mailto: >> fis...@nmr.mgh.harvard.edu>> >> wrote: >> Hi >> Katerine >> >> >> the >> COR-* format >> is an old >> one that we >> don't use >> anymore. If you >> specify a >> directory as an >> >> input/output we >> will assume >> that it >> contains COR >> files, which is >> probably >> what you are >> seeing. >> >> >> cheers >> >> Bruce >> >> >> On >> Sun, 14 Dec >> 2014, >> Katherine Damme >> wrote: >> >> >> >> At what >> point is the >> COR-*.info >> file made? >> >> >> I got the >> following >> error: >> >> >> >> corRead(): >> can't open >> file >> >> /media/Sokol/Subj/COR-.info >> >> >> $Id: >> mri_convert.c,v >> 1.179.2.7 >> 2012/09/05 >> 21:55:16 mreuter >> Exp $ >> >> >> reading >> from >> /media/Sokol/Subj/... >> >> >> Linux >> >> >> >> kate.ad.wcas.northwestern.edu< >> http://kate.ad.wcas.northwestern.edu> >> >> 2.6.32-431.3.1.el6.x86_64 #1 >> SMP Fri Dec >> >> >> 13 >> 06:58:20 EST 2013 >> x86_64 x86_64 >> x86_64 >> GNU/Linux >> >> >> >> >> trac-preproc exited >> with ERRORS at >> Fri Dec 12 >> 12:54:40 CST 2014 >> >> >> >> >> [ksd770@kate 041]# ls >> >> /media/Sokol/Subj/COR-* >> >> >> >> On Thu, >> Dec 11, 2014 >> at 2:48 PM, >> Anastasia >> Yendiki >> >> >> >> >> >> >> <ayend...@nmr.mgh.harvard.edu<mailto: >> ayend...@nmr.mgh.harvard.edu>> >> wrote: >> >> >> >> No, >> those are >> field maps >> used to >> correct >> for >> inhomogeneities in >> >> >> the >> main >> magnetic field >> (which in MRI >> lingo is >> referred to as >> >> >> the >> B0 field, >> not to be >> confused with >> the b=0 >> images). You can >> >> >> skip >> that >> correction (you >> have to skip >> it >> if you don't >> have >> >> >> >> field maps). >> >> >> >> On >> Thu, 11 Dec >> 2014, >> Katherine >> Damme >> wrote: >> >> >> >> >> I am >> sorry, I am a bit >> confused. What >> am I supposed >> >> >> >> to be >> specifying under >> >> >> >> the >> b0mlist and >> b0plist? >> >> >> >> >> I thought >> that it was >> the B0 low-b >> image from >> >> >> >> diffusion. >> >> >> >> >> Thank you! >> >> >> >> >> On Thu, >> Dec 11, 2014 >> at 2:25 PM, >> Anastasia >> Yendiki >> >> >> >> >> >> >> >> <ayend...@nmr.mgh.harvard.edu<mailto: >> ayend...@nmr.mgh.harvard.edu>> >> wrote: >> >> >> >> >> Hi >> Kate - The >> screenshot >> looks >> more like a >> >> >> >> low-b >> image from a >> >> >> >> >> diffusion scan >> than a field >> map. In case >> this >> >> >> >> helps, the >> phase >> >> >> >> map >> data will >> have either 2 >> volumes (2 >> phase >> >> >> >> maps >> acquired at >> >> >> >> >> different echo >> times) or 1 >> volume (the >> >> >> >> difference >> of 2 such >> >> >> >> >> phase maps). >> >> >> >> >> >> Best, >> >> >> >> a.y >> >> >> >> >> On >> Thu, 11 Dec >> 2014, >> Katherine >> Damme wrote: >> >> >> >> >> >> Hello >> >> >> >> >> >> >> Has anyone >> else had the >> problem of >> >> >> >> tracula >> not >> >> >> >> >> >> recognizing >> the >> format of >> the >> >> >> >> >> phase map? >> >> >> >> >> >> I opened >> the B0 in >> fslview and it >> >> >> >> appeared >> normal >> >> >> >> >> (see >> screenshot). >> Any >> >> >> >> >> help that >> you can offer >> would be >> greatly >> >> >> >> >> > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > 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. > >
dmrirc.all
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