Thank you for your help! We were able to work out the issue!
Emily
----- Original Message ----- From: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@uwm.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, October 22, 2013 2:21:49 PM Subject: Re: [Freesurfer] Tracula Error
Jon - Thank you for your suggestion. However, the wiki is correct. The file names in dcmlist should be relative to the directory name in dcmroot.
The problem is that essentially you are doing this: set dcmlist = ( ) Because of how you're using the wildcard character *, you end up with an empty dcmlist. Nowhere does the wiki suggest that an empty dcmlist is ok.
a.y
On Tue, 22 Oct 2013, Jon Wieser wrote:
You should change the wiki so that it says that the dcmlist is relative to the current working directory that the trac-all command is executed, not the dcmroot the trac-all program is source'ing the dmrirc config file in the currect working directory of the trac-all process. Jon
----- Original Message ----- From: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@uwm.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, October 22, 2013 2:05:35 PM Subject: Re: [Freesurfer] Tracula Error
There is no * character in the example on the wiki. What do you think should change?
On Tue, 22 Oct 2013, Jon Wieser wrote:
that makes perfect sense, but you should change the instructions in the Tracula wiki to reflect this. the tracula wiki says:
Step 5: Specify the location of diffusion DICOM files
set dcmroot = $TUTORIAL_DATA/diffusion_tutorial Use this variable to specify the directory under which the diffusion DICOM files for all subjects can be found.
Step 6: Specify the list of input DWIs
set dcmlist = ( elmo.2005/orig/656000-11-1.dcm \ elmo.2008/orig/97000-000017-000001.dcm \ elmo.2012/orig/MR.1.3.12.2.1107.5.2.32.35006.2012121819455034689828982 ) Use this variable to specify the input DWI data, one entry per subject. The file names are assumed be relative to the directory specified in dcmroot above.
Jon
----- Original Message ----- From: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@uwm.edu Cc: "ebelleau" ebelleau@uwm.edu, "freesurfer" freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, October 22, 2013 1:47:05 PM Subject: Re: [Freesurfer] Tracula Error
It's the * and its interpretation by the unix shell that does this, so it has nothing to do with tracula.
When you run this command: set dcmlist = (i*.MRDC.1) you're telling unix to find all files that match this pattern and to make the dcmlist variable equal to the list of files. If it doesn't find any files like this (and it'll look in the current directory unless you specify the full path), then dcmlist will be empty.
When you run this command: set dcmlist = (i727056.MRDC.1) you're telling unix to make the dcmlist variable equal to the string i727056.MRDC.1, so it won't search to find any files.
Does this make sense?
On Tue, 22 Oct 2013, Jon Wieser wrote:
according to the tracula wiki:
http://freesurfer.net/fswiki/FsTutorial/Tracula
the program should look in the directory specified by "dcmroot" to look for the dicom list
excerpt from the wiki page:
Step 5: Specify the location of diffusion DICOM files
set dcmroot = $TUTORIAL_DATA/diffusion_tutorial Use this variable to specify the directory under which the diffusion DICOM files for all subjects can be found.
Step 6: Specify the list of input DWIs
set dcmlist = ( elmo.2005/orig/656000-11-1.dcm \ elmo.2008/orig/97000-000017-000001.dcm \ elmo.2012/orig/MR.1.3.12.2.1107.5.2.32.35006.2012121819455034689828982 )
Jon
----- Original Message ----- From: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu To: "Jon Wieser" wieser@uwm.edu Cc: "freesurfer" freesurfer@nmr.mgh.harvard.edu, "ebelleau" ebelleau@uwm.edu Sent: Tuesday, October 22, 2013 12:24:22 PM Subject: Re: [Freesurfer] Tracula Error
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" ayendiki@nmr.mgh.harvard.edu To: ebelleau@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, ebelleau@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" ayendiki@nmr.mgh.harvard.edu To: ebelleau@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, ebelleau@uwm.edu wrote:
----- Original Message ----- From: ebelleau@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.
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