Thanks Anastasia - I decided to made an entirely new txt file and the proper dmri/bvec file is now being created. Unfortunately now I'm running into a memory allocation problem. Since I'm running on ubuntu I'm not sure its the same problem that mac users are facing. Any suggestions for how to proceed?
Ammar Moiyadi, BS Professional Research Assistant Department of Psychiatry University of Colorado Anschutz Medical Campus 303-724-5490 ________________________________________ From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu] Sent: Wednesday, August 03, 2011 10:37 AM To: Moiyadi, Ammar Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] trac-all -path errors Yes, that's the lang that I got, too. But the text file shows up with ^M's where the ends of lines should be on darwin and on centos only the first 2 lines show up. On Wed, 3 Aug 2011, Moiyadi, Ammar wrote: > Hi - I created the text file with gedit in Lucid Ubuntu. I checked my locale > and my lang reads en_US.UTF-8, is this the same for you? > > Thank you, > > Ammar Moiyadi, BS > Professional Research Assistant > Department of Psychiatry > University of Colorado Anschutz Medical Campus > 303-724-5490 > ________________________________________ > From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu] > Sent: Wednesday, August 03, 2011 10:25 AM > To: Moiyadi, Ammar > Cc: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] trac-all -path errors > > Hi Ammar - It looks like it's the same text file formatting issue that > someone else had recently. Did you create this file in excel by any > chance? It can't be read properly under unix. > > a.y > > On Wed, 3 Aug 2011, Moiyadi, Ammar wrote: > >> Hi - The txt files are missing for all the tracts as it turns out trac-all >> -prep exited with errors before getting to -prior. It appears there is a >> problem with my bvec file since the dmri/bvec is reading all 0's. As a >> result, i get this error "Error: bvecs and bvals don't have the same number >> of entries". I have attached my bvec.txt file and trac-all log - any ideas >> to where the problem may lie? >> >> Thank You, >> >> Ammar Moiyadi, BS >> Professional Research Assistant >> Department of Psychiatry >> University of Colorado Anschutz Medical Campus >> 303-724-5490 >> ________________________________________ >> From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu] >> Sent: Monday, August 01, 2011 12:32 PM >> To: Moiyadi, Ammar >> Cc: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] trac-all -path errors >> >> Hi Ammar - Yes, -prior is the last step included in -prep. Are the text >> files missing for all tracts, or specifically for lh.cst? >> >> Thanks, >> a.y >> >> On Mon, 1 Aug 2011, Moiyadi, Ammar wrote: >> >>> Hi, >>> I am also getting the error where the txt files cannot be opened because >>> they were not created beforehand. Where does the trac-all -prior step take >>> place? Does it appear within the trac-all -prep script? >>> >>> Thank you, >>> >>> Ammar Moiyadi, BS >>> Professional Research Assistant >>> Department of Psychiatry >>> University of Colorado Anschutz Medical Campus >>> 303-724-5490 >>> ________________________________________ >>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>> [freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of >>> freesurfer-requ...@nmr.mgh.harvard.edu >>> [freesurfer-requ...@nmr.mgh.harvard.edu] >>> Sent: Friday, July 29, 2011 10:00 AM >>> To: freesurfer@nmr.mgh.harvard.edu >>> Subject: Freesurfer Digest, Vol 89, Issue 99 >>> >>> Send Freesurfer mailing list submissions to >>> freesurfer@nmr.mgh.harvard.edu >>> >>> To subscribe or unsubscribe via the World Wide Web, visit >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> or, via email, send a message with subject or body 'help' to >>> freesurfer-requ...@nmr.mgh.harvard.edu >>> >>> You can reach the person managing the list at >>> freesurfer-ow...@nmr.mgh.harvard.edu >>> >>> When replying, please edit your Subject line so it is more specific >>> than "Re: Contents of Freesurfer digest..." >>> >>> >>> Today's Topics: >>> >>> 1. trac-all -path errors (Ping-Hong Yeh) >>> 2. Re: trac-all -path errors (Priti Srinivasan) >>> >>> >>> ---------------------------------------------------------------------- >>> >>> Message: 1 >>> Date: Fri, 29 Jul 2011 11:09:28 -0400 >>> From: Ping-Hong Yeh <pinghong...@gmail.com> >>> Subject: [Freesurfer] trac-all -path errors >>> To: freesurfer@nmr.mgh.harvard.edu >>> Message-ID: >>> <cal1nnmp2+kde5cnmvh4-qhnvsemeqa7ajq+cp-qpftmgv3a...@mail.gmail.com> >>> Content-Type: text/plain; charset=ISO-8859-1 >>> >>> Hi, >>> >>> I got the error running "trac-all -path -c configure.txt" >>> >>> ERROR: Could not open >>> ${SUBJECTS_DIR}/$Subject/dlabel/diff/lh.cst_AS_avg33_mni_flt_cpts_5.txt >>> >>> >>> I can only find only image files in the "dlabel/diff" directory, but >>> not text files. >>> >>> Which step(s) create the lh.cst_AS_avg33_mni_flt_cpts_5.txt file? >>> >>> Thanks, >>> >>> Ping >>> >>> >>> ------------------------------ >>> >>> Message: 2 >>> Date: Fri, 29 Jul 2011 11:26:13 -0400 (EDT) >>> From: "Priti Srinivasan" <rspr...@nmr.mgh.harvard.edu> >>> Subject: Re: [Freesurfer] trac-all -path errors >>> To: "Ping-Hong Yeh" <pinghong...@gmail.com> >>> Cc: freesurfer@nmr.mgh.harvard.edu >>> Message-ID: >>> <42727.132.183.139.239.1311953173.squir...@mail.nmr.mgh.harvard.edu> >>> Content-Type: text/plain;charset=iso-8859-1 >>> >>> Hi Ping, >>> >>> The text files get created in the trac-all -prior stage. Maybe something >>> went wrong in that step. Is this the case for all the tracts or just for >>> this tract? If you can send us the trac-all.log file under the scripts >>> directory it'll be easier to troubleshoot as to what went wrong. >>> >>> -Priti >>> >>> >>>> Hi, >>>> >>>> I got the error running "trac-all -path -c configure.txt" >>>> >>>> ERROR: Could not open >>>> ${SUBJECTS_DIR}/$Subject/dlabel/diff/lh.cst_AS_avg33_mni_flt_cpts_5.txt >>>> >>>> >>>> I can only find only image files in the "dlabel/diff" directory, but >>>> not text files. >>>> >>>> Which step(s) create the lh.cst_AS_avg33_mni_flt_cpts_5.txt file? >>>> >>>> Thanks, >>>> >>>> Ping >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> >>> >>> >>> >>> ------------------------------ >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> End of Freesurfer Digest, Vol 89, Issue 99 >>> ****************************************** >>> >>> >>> 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 >>> >>> >>> >> > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
