The problem is that the command "set dcmlist = (i*.MRDC.1)" is executed as soon as it is read. So this will end up with an empty dcmlist, because there are no files named i*.MRDC.1 in the current directory.
On Tue, 22 Oct 2013, Jon Wieser wrote: > > Hi anastasia, > I work with Emily. the wild card she used i*.MRDC.1 specifies only the > first dicom image. the dicoms are in the format: > > i727056.MRDC.1 i727065.MRDC.10 i727074.MRDC.19 i727083.MRDC.28 > i727092.MRDC.37 i727101.MRDC.46 i727110.MRDC.55 i727119.MRDC.64 > i727128.MRDC.73 i727137.MRDC.82 i727146.MRDC.91 > i727057.MRDC.2 i727066.MRDC.11 i727075.MRDC.20 i727084.MRDC.29 > i727093.MRDC.38 i727102.MRDC.47 i727111.MRDC.56 i727120.MRDC.65 > i727129.MRDC.74 i727138.MRDC.83 i727147.MRDC.92 > i727058.MRDC.3 i727067.MRDC.12 i727076.MRDC.21 i727085.MRDC.30 > i727094.MRDC.39 i727103.MRDC.48 i727112.MRDC.57 i727121.MRDC.66 > i727130.MRDC.75 i727139.MRDC.84 i727148.MRDC.93 > i727059.MRDC.4 i727068.MRDC.13 i727077.MRDC.22 i727086.MRDC.31 > i727095.MRDC.40 i727104.MRDC.49 i727113.MRDC.58 i727122.MRDC.67 > i727131.MRDC.76 i727140.MRDC.85 i727149.MRDC.94 > i727060.MRDC.5 i727069.MRDC.14 i727078.MRDC.23 i727087.MRDC.32 > i727096.MRDC.41 i727105.MRDC.50 i727114.MRDC.59 i727123.MRDC.68 > i727132.MRDC.77 i727141.MRDC.86 i727150.MRDC.95 > i727061.MRDC.6 i727070.MRDC.15 i727079.MRDC.24 i727088.MRDC.33 > i727097.MRDC.42 i727106.MRDC.51 i727115.MRDC.60 i727124.MRDC.69 > i727133.MRDC.78 i727142.MRDC.87 i727151.MRDC.96 > i727062.MRDC.7 i727071.MRDC.16 i727080.MRDC.25 i727089.MRDC.34 > i727098.MRDC.43 i727107.MRDC.52 i727116.MRDC.61 i727125.MRDC.70 > i727134.MRDC.79 i727143.MRDC.88 i727152.MRDC.97 > i727063.MRDC.8 i727072.MRDC.17 i727081.MRDC.26 i727090.MRDC.35 > i727099.MRDC.44 i727108.MRDC.53 i727117.MRDC.62 i727126.MRDC.71 > i727135.MRDC.80 i727144.MRDC.89 i727153.MRDC.98 > i727064.MRDC.9 i727073.MRDC.18 i727082.MRDC.27 i727091.MRDC.36 > i727100.MRDC.45 i727109.MRDC.54 i727118.MRDC.63 i727127.MRDC.72 > i727136.MRDC.81 i727145.MRDC.90 i727154.MRDC.99 etc > > > > so i*.MRDC.1 would specify only the file i727056.MRDC.1, the first dicom > image > > Jon > > ----- Original Message ----- > From: "Anastasia Yendiki" <ayend...@nmr.mgh.harvard.edu> > To: ebell...@uwm.edu > Cc: freesurfer@nmr.mgh.harvard.edu > Sent: Tuesday, October 22, 2013 10:09:13 AM > Subject: Re: [Freesurfer] Tracula Error > > > Hi Emily - You're using "*" to specify all the dicom files in the series. > You should specify just one file. > > BTW, do you have the latest version of freesurfer and the tutorials? This > dmrirc looks like it might have been adapted from an older version of the > tutorials. If so, I highly recommend downloading the latest version of > everything. > > Hope this helps, > a.y > > On Mon, 21 Oct 2013, ebell...@uwm.edu wrote: > >> Hello, >> >> I am running into the following error when I try to run trac-all: >> >> set: No match. >> ERROR: must specify as many DWI dicoms as subjects >> >> I have taken my script and examined it line by line and have made several >> attempts at debugging it. >> >> I was wondering if you had any suggestions? Attached is my >> dmrirc_single_subject configuration. >> >> I am brand new to freesurfer and tracula and would appreciate any guidance >> you can give me! >> >> Thanks! >> >> Emily >> >> ----- Original Message ----- >> From: "Anastasia Yendiki" <ayend...@nmr.mgh.harvard.edu> >> To: ebell...@uwm.edu >> Cc: freesurfer@nmr.mgh.harvard.edu >> Sent: Thursday, October 10, 2013 3:53:29 PM >> Subject: Re: [Freesurfer] Tracula >> >> >> Hi Emily - The first version of tracula was in freesurfer 5.1. However, I >> would *highly* recommend using the newer version of tracula, now in 5.3, >> as it has improvements in both performance and speed. >> >> The processing in trac-all is supposed to happen in parallel for each of >> the subjects included in the configuration file, if you run trac-all on a >> cluster. However, not all clusters have the same set-up, and you may have >> to make modifications for it to work on your cluster, with the help of >> your cluster admins. There should be previous questions on this in this >> list's email archives. Let me know if you have any other questions. >> >> a.y >> >> On Thu, 10 Oct 2013, ebell...@uwm.edu wrote: >> >>> >>> >>> ----- Original Message ----- >>> From: ebell...@uwm.edu >>> To: freesurfer@nmr.mgh.harvard.edu >>> Sent: Thursday, October 10, 2013 3:14:06 PM >>> Subject: Tracula >>> >>> Hello, >>> >>> I had a question regarding batch processing in trac all. >>> >>> When you batch process and put in multiple subjects in your subject list in >>> your configuration file, are the subjects run parallel or serial? >>> >>> Also, I am having a hard time finding the linux version of tracula that is >>> compatible with Freesurfer version 5.0 (assuming it exists)? >>> >>> Thank you so much and I appreciate your guidance as I am brand new to >>> freesurfer and tracula. >>> >>> Emily >>> _______________________________________________ >>> 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. >> >> > _______________________________________________ > 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
