Freesurfer

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30132 discussions

Re: [Freesurfer] Tracula Error
by Anastasia Yendiki 22 Oct '13

22 Oct '13

If it's important to you to be able to use wildcards instead of the actual file name, you can do it from any directory like this: set dcmlist = (`cd $dcmroot; echo subj238/DTI/i*.MRDC.1`) On Tue, 22 Oct 2013, Jon Wieser wrote: > it works pnly if the directory that you run the trac-all command from, is the same as the directory that is specified by dcmroot. > otherwise it fails. > > we are running the trac-all command from /media/LGI/LGI > > we fixed it by changing the dcmroot amd dcmlist > > > set dcmroot = media/LGI/LGI/ > set dcmlist = (subj238/DTI/i*.MRDC.1) > > it's able to read in the dicom's okay now > > Jon > > > ----- Original Message ----- > From: "Anastasia Yendiki" <ayendiki(a)nmr.mgh.harvard.edu> > To: "Jon Wieser" <wieser(a)uwm.edu> > Cc: freesurfer(a)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(a)nmr.mgh.harvard.edu> >> To: "Jon Wieser" <wieser(a)uwm.edu> >> Cc: freesurfer(a)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(a)nmr.mgh.harvard.edu> >>> To: "Jon Wieser" <wieser(a)uwm.edu> >>> Cc: "ebelleau" <ebelleau(a)uwm.edu>, "freesurfer" <freesurfer(a)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(a)nmr.mgh.harvard.edu> >>>> To: "Jon Wieser" <wieser(a)uwm.edu> >>>> Cc: "freesurfer" <freesurfer(a)nmr.mgh.harvard.edu>, "ebelleau" <ebelleau(a)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(a)nmr.mgh.harvard.edu> >>>>> To: ebelleau(a)uwm.edu >>>>> Cc: freesurfer(a)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(a)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(a)nmr.mgh.harvard.edu> >>>>>> To: ebelleau(a)uwm.edu >>>>>> Cc: freesurfer(a)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(a)uwm.edu wrote: >>>>>> >>>>>>> >>>>>>> >>>>>>> ----- Original Message ----- >>>>>>> From: ebelleau(a)uwm.edu >>>>>>> To: freesurfer(a)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(a)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(a)nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> >>>>> >>>> >>>> >>>> >>> >>> >>> >> >> >> > > >

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Re: [Freesurfer] Tracula Error
by Anastasia Yendiki 22 Oct '13

22 Oct '13

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(a)nmr.mgh.harvard.edu> > To: "Jon Wieser" <wieser(a)uwm.edu> > Cc: freesurfer(a)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(a)nmr.mgh.harvard.edu> >> To: "Jon Wieser" <wieser(a)uwm.edu> >> Cc: "ebelleau" <ebelleau(a)uwm.edu>, "freesurfer" <freesurfer(a)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(a)nmr.mgh.harvard.edu> >>> To: "Jon Wieser" <wieser(a)uwm.edu> >>> Cc: "freesurfer" <freesurfer(a)nmr.mgh.harvard.edu>, "ebelleau" <ebelleau(a)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(a)nmr.mgh.harvard.edu> >>>> To: ebelleau(a)uwm.edu >>>> Cc: freesurfer(a)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(a)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(a)nmr.mgh.harvard.edu> >>>>> To: ebelleau(a)uwm.edu >>>>> Cc: freesurfer(a)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(a)uwm.edu wrote: >>>>> >>>>>> >>>>>> >>>>>> ----- Original Message ----- >>>>>> From: ebelleau(a)uwm.edu >>>>>> To: freesurfer(a)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(a)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(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> >>> >>> >>> >> >> >> > > >

2 1

Re: [Freesurfer] Tracula Error
by Anastasia Yendiki 22 Oct '13

22 Oct '13

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(a)nmr.mgh.harvard.edu> > To: "Jon Wieser" <wieser(a)uwm.edu> > Cc: "ebelleau" <ebelleau(a)uwm.edu>, "freesurfer" <freesurfer(a)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(a)nmr.mgh.harvard.edu> >> To: "Jon Wieser" <wieser(a)uwm.edu> >> Cc: "freesurfer" <freesurfer(a)nmr.mgh.harvard.edu>, "ebelleau" <ebelleau(a)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(a)nmr.mgh.harvard.edu> >>> To: ebelleau(a)uwm.edu >>> Cc: freesurfer(a)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(a)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(a)nmr.mgh.harvard.edu> >>>> To: ebelleau(a)uwm.edu >>>> Cc: freesurfer(a)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(a)uwm.edu wrote: >>>> >>>>> >>>>> >>>>> ----- Original Message ----- >>>>> From: ebelleau(a)uwm.edu >>>>> To: freesurfer(a)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(a)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(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >> >> >> > > >

1 0

Re: [Freesurfer] Tracula
by ebelleau＠uwm.edu 22 Oct '13

22 Oct '13

----- Original Message ----- From: ebelleau(a)uwm.edu To: freesurfer(a)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

3 9

ill conditioned matrix with covariates that are unequal between groups
by Laura M. Tully 22 Oct '13

22 Oct '13

Hello freesurfers, I'm trying to run mri_glmfit between groups analysis (patients vs. controls) with gender, age, medication (continuous), and duration of illness as covariates. The problem is, only the patients have medication and duration of illness values - by virtue of being control participants, the control group have values of zero for medication and duration of illness. This causes issues with the matrix and I'm trying to figure out how to get around it. Suggestions would be most appreciated. See output and details below, plus attached files. Thanks! Laura. *Command line: * mri_glmfit --y lh_grpDiffs_thickness10.mgh --fsgd grpdiffs_thickness_lh_Med_Dur.fsgd --fsgd-rescale --C Contrast1A_grp_Diffs_HCvsSZ_Med_Dur.mtx --surf fsaverage lh --cortex --glmdir lh_grpdiffs_lh_thickness_Med_Dur.glmdir * * *Output:* gdfReadHeader: reading grpdiffs_thickness_lh_Med_Dur.fsgd INFO: demeaning continuous variables Continuous Variable Means (all subjects) 0 Age 36.0909 11.4927 1 LH_Mean_Thick 2.34931 0.118499 2 medication 204.545 330.217 3 duration_illness 7.74545 11.4005 Class Means of each Continuous Variable 1 HCmale 34.3000 2.3799 0.0000 0.0000 2 HCfemale 32.5556 2.3723 0.0000 0.0000 3 SZmale 36.5000 2.3124 391.2500 14.6875 4 SZfemale 42.2000 2.3265 499.0000 19.1000 INFO: gd2mtx_method is dods Reading source surface /ncf/snp/04/SCORE/freesurfer_analysis/fsaverage/surf/lh.white Number of vertices 163842 Number of faces 327680 Total area 65416.648438 AvgVtxArea 0.399267 AvgVtxDist 0.721953 StdVtxDist 0.195470 $Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $ cwd /ncf/snp/04/SCORE/freesurfer_analysis/glm_analysis cmdline mri_glmfit --y lh_grpDiffs_thickness10.mgh --fsgd grpdiffs_thickness_lh_Med_Dur.fsgd --fsgd-rescale --C Contrast1A_grp_Diffs_HCvsSZ_Med_Dur.mtx --surf fsaverage lh --cortex --glmdir lh_grpdiffs_lh_thickness_Med_Dur.glmdir sysname Linux hostname ncfws14.rc.fas.harvard.edu machine x86_64 user ltully FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /ncf/snp/04/SCORE/freesurfer_analysis/glm_analysis/lh_grpDiffs_thickness10.mgh logyflag 0 usedti 0 FSGD grpdiffs_thickness_lh_Med_Dur.fsgd labelmask /ncf/snp/04/SCORE/freesurfer_analysis/fsaverage/label/lh.cortex.label maskinv 0 glmdir lh_grpdiffs_lh_thickness_Med_Dur.glmdir IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory lh_grpdiffs_lh_thickness_Med_Dur.glmdir Loading y from /ncf/snp/04/SCORE/freesurfer_analysis/glm_analysis/lh_grpDiffs_thickness10.mgh INFO: gd2mtx_method is dods Saving design matrix to lh_grpdiffs_lh_thickness_Med_Dur.glmdir/Xg.dat Normalized matrix condition is 1e+08 Design matrix ------------------ 0.000 0.000 1.000 0.000 0.000 0.000 0.740 0.000 0.000 0.000 -1.700 0.000 0.000 0.000 0.329 0.000 0.000 0.000 0.817 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 -0.392 0.000 0.000 0.000 0.233 0.000 0.000 0.000 0.632 0.000 0.000 0.000 -0.148 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 -0.191 0.000 0.000 0.000 0.013 0.000 0.000 0.000 -1.511 0.000 0.000 0.000 -0.272; 0.000 0.000 1.000 0.000 0.000 0.000 0.479 0.000 0.000 0.000 0.427 0.000 0.000 0.000 0.212 0.000 0.000 0.000 0.729 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.940 0.000 0.000 0.000 -0.907 0.000 0.000 0.000 0.912 0.000 0.000 0.000 -0.009; 0.000 0.000 1.000 0.000 0.000 0.000 1.436 0.000 0.000 0.000 -0.029 0.000 0.000 0.000 -0.276 0.000 0.000 0.000 1.431 0.000; 1.000 0.000 0.000 0.000 0.757 0.000 0.000 0.000 -0.235 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 1.018 0.000 0.000 0.000 -0.775 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 1.627 0.000 0.000 0.000 -0.032 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000 0.000 1.953 0.000 0.000 0.000 -0.070 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 1.105 0.000 0.000 0.000 0.854 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000 0.000 1.518 0.000 0.000 0.000 -0.864 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 -0.713 0.000 0.000 0.000 0.359 0.000 0.000 0.000 -0.784 0.000 0.000 0.000 -0.886; 0.000 1.000 0.000 0.000 0.000 1.083 0.000 0.000 0.000 0.428 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 -1.088 0.000 0.000 0.000 0.190 0.000 0.000 0.000 0.632 0.000 0.000 0.000 -0.937 0.000; 1.000 0.000 0.000 0.000 -0.548 0.000 0.000 0.000 -0.454 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.375 0.000 0.000 0.000 0.612 0.000 0.000 0.000 1.517 0.000 0.000 0.000 1.395; 1.000 0.000 0.000 0.000 0.496 0.000 0.000 0.000 0.010 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.131 0.000 0.000 0.000 0.435 0.000 0.000 0.000 -1.185 0.000 0.000 0.000 0.378 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 -1.001 0.000 0.000 0.000 -0.864 0.000 0.000 0.000 0.212 0.000 0.000 0.000 -1.201 0.000; 0.000 1.000 0.000 0.000 0.000 -0.222 0.000 0.000 0.000 -2.138 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 0.931 0.000 0.000 0.000 -1.214 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 1.088 0.000 0.000 0.000 -0.856 0.000 0.000 0.000 -0.943 0.000 0.000 0.000 0.992 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.070 0.000 0.000 0.000 0.401 0.000 0.000 0.000 -1.208 0.000 0.000 0.000 0.342; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.114 0.000 0.000 0.000 -1.051 0.000 0.000 0.000 1.214 0.000 0.000 0.000 2.009; 0.000 0.000 1.000 0.000 0.000 0.000 -1.088 0.000 0.000 0.000 -0.147 0.000 0.000 0.000 0.212 0.000 0.000 0.000 -1.113 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 -0.017 0.000 0.000 0.000 -1.219 0.000 0.000 0.000 0.306 0.000 0.000 0.000 0.868; 0.000 0.000 1.000 0.000 0.000 0.000 0.218 0.000 0.000 0.000 -0.721 0.000 0.000 0.000 -0.983 0.000 0.000 0.000 -0.323 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 -1.149 0.000 0.000 0.000 2.139 0.000 0.000 0.000 0.154 0.000 0.000 0.000 -1.325; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 -0.452 0.000 0.000 0.000 -0.325 0.000 0.000 0.000 -0.300 0.000 0.000 0.000 -1.061; 0.000 0.000 1.000 0.000 0.000 0.000 -0.044 0.000 0.000 0.000 0.486 0.000 0.000 0.000 -1.064 0.000 0.000 0.000 -0.060 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.653 0.000 0.000 0.000 -0.392 0.000 0.000 0.000 -0.912 0.000 0.000 0.000 1.080 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 -0.975 0.000 0.000 0.000 -0.021 0.000 0.000 0.000 -0.300 0.000 0.000 0.000 -1.061; 0.000 0.000 1.000 0.000 0.000 0.000 -1.349 0.000 0.000 0.000 0.579 0.000 0.000 0.000 0.026 0.000 0.000 0.000 -1.113 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 -0.566 0.000 0.000 0.000 1.895 0.000 0.000 0.000 0.632 0.000 0.000 0.000 -0.850 0.000; 1.000 0.000 0.000 0.000 0.670 0.000 0.000 0.000 -0.809 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 -0.722 0.000 0.000 0.000 -0.716 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000 0.000 -0.831 0.000 0.000 0.000 1.398 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 1.453 0.000 0.000 0.000 -0.978 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 0.670 0.000 0.000 0.000 -2.429 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000 0.000 -0.744 0.000 0.000 0.000 -0.121 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000 0.000 -0.657 0.000 0.000 0.000 0.082 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 1.018 0.000 0.000 0.000 1.318 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 -1.244 0.000 0.000 0.000 1.208 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000 0.000 -1.179 0.000 0.000 0.000 0.444 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 -1.244 0.000 0.000 0.000 0.364 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 -0.809 0.000 0.000 0.000 1.790 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 -0.983 0.000 0.000 0.000 0.558 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 -1.157 0.000 0.000 0.000 0.254 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 -1.157 0.000 0.000 0.000 0.752 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000 0.000 -0.918 0.000 0.000 0.000 0.841 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 1.088 0.000 0.000 0.000 -1.354 0.000 0.000 0.000 3.660 0.000 0.000 0.000 1.343 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 -0.305 0.000 0.000 0.000 1.819 0.000 0.000 0.000 -1.185 0.000 0.000 0.000 -1.025 0.000; 1.000 0.000 0.000 0.000 -0.461 0.000 0.000 0.000 0.870 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 -1.418 0.000 0.000 0.000 -0.336 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000; -------------------------------- ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 -- -- Laura M. Tully, PhD Post-Doctoral Fellow in Psychiatry UC Davis Imaging Research Center 4701 X Street, Sacramento, CA 95817 Phone: (916) 734-7927 Fax: (916) 734-8750 Alumnus of Social Neuroscience & Psychopathology Lab, Harvard University ltully(a)fas.harvard.edu Follow me on twitter: @tully_laura --

2 3

Subject processing difference between computers
by West, John D. 22 Oct '13

22 Oct '13

Hello. We are moving our processing from an older super computer to a new one here at Indiana University. Preliminary testing is showing a significant difference between final summary stats results between subjects processed on the old system versus the new. The version of freesurfer on both systems is identical. Comparing the logs of the same subject run on both systems, I've found that the differences seem to start with the mri_watershed function specifically the main basin size. For the same subject we find: Old computer: main basin size=22667431830 voxels, voxel volume =1.000 = 22667431830 mmm3 = 22667431.936 cm3 New computer: main basin size=22208239350 voxels, voxel volume =1.000 = 22208239350 mmm3 = 22208239.616 cm3 As you can see they are very different. My theory is this is propagating through the rest of the process and giving us different summary stats at the end. I should note that both aseg and aparc stats are affected. I am also enclosing the logs for both runs as well as the differences found through the diff command (this is a lot parse through as even time stamp differences are picked up). Essentially what I am trying to find out is if these differences we are noticing are typical when changing computers and if not what could be causing these differences that I may not be picking up on. Thanks for the help. -John

1 0

result is L-R fliped in native space
by wen.zhang55 22 Oct '13

22 Oct '13

Dear Freesurfer： I am now working in converting cortical labels from freesurfer to volumetric masks. First i gained the registration matrix by bbregister, then applied those matrix to tranform ROI labels into native space using label2vol. However, when i got the final .NII results, both of them turn out to be L-R fliped. (left ROI on the right hemisphere). From my understanding, freesurfer will automaticly recognize the head direction of the original T1 images and my original T1 data contains the flip information due to the way we scaned. So why this happen? By the way, the recon-all results did good. Thank you very much! best, Cowen 2013-10-22 wen.zhang55

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QDEC
by Franklin, Crystal G 22 Oct '13

22 Oct '13

Freesurfer, I want to make sure I am setting up my group analysis correctly. I have 2 groups, one a control population and the other a patient population , that I am wanting to see where there are differences controlling for age. I set the group as the fixed factor and I demeaned the ages and used them as the nuisance factor. Is it necessary to demean the ages before running QDEC? Thanks, Crystal

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Fwd: 2nd Whistler Scientific Workshop on Brain Function, March 9-12, 2014
by Thomas Yeo 22 Oct '13

22 Oct '13

---------- Forwarded message ---------- From: Todd Constable <todd.constable(a)yale.edu> Date: Thu, Oct 17, 2013 at 9:25 AM Subject: 2nd Whistler Scientific Workshop on Brain Function, March 9-12, 2014 To: Todd Constable <todd.constable(a)yale.edu> Cc: Todd Constable <todd.constable(a)yale.edu> The 2nd Whistler Scientific Workshop on Brain Functional Organization, Connectivity and Behavior Whistler, BC, Canada March 9-12, 2014 There has been an explosion of activity recently in the area of functional MRI and connectivity mapping and this small workshop in the beautiful town of Whistler BC is aimed at exploring the latest breakthroughs in analysis approaches, models, and applications. Emphasis will be on methods, the relationship of network measures to behavior, and the implications of network mapping in terms of broadening our understanding of functional neuroanatomy and basic neuroscience. The workshop will be kept small (less than 100 attendees) in order to facilitate discussion amongst all participants so please register early to ensure a spot. Abstracts: One page Abstracts for proffered talks or posters can be submitted to:lesley.nadeau@yale.edu. Topics: 1. Functional connectivity methods - network measures 2. Connectivity and Behavior 3. Integrated structural and functional connectivity – methods & stationarity and spectral components 4. Clinical applications of functional connectivity or multimodal measures of connectivity 5. Neuroanatomy and brain mapping For more information and to register please visit: fmriworkshop.yale.edu Target Audience: Experts in functional brain imaging and connectivity mapping, neuroscientists, psychologists, clinicians, and trainees (pre- and postdoctoral fellows, residents and clinical fellows), with an interest in brain function, functional organization, and neuroimaging. Organizing Committee: R. Todd Constable, Committee Chair, Yale University, New Haven, CT, USA Karla Miller, Oxford Centre for Functional MRI of the Brain, Oxford University, UK Marvin Chun, Yale University, Department of Psychology, New Haven, CT USA Bruce Pike, Division of Image Science, University of Calgary, Alberta, Canada Xiaoping Hu, Coulter Dept. of BME at Georgia Tech and Emory, Atlanta, GA USA Invited Speakers: Michael Breakspear, Systems Neuroscience, Queensland Inst. of Med. Research, AU Mark Chiew, Oxford University Centre for Functional MRI of the Brain, Oxford, UK Jessica Damoiseaux, Institute of Gerontology, Wayne State University, Detroit, MI Manus Donahue, Vanderbilt University Institute of Imaging Science, Nashville, TN Lila Davachi, Center for Neural Science & Center for Brain Imaging, NYU, NY, NY Maxime Guye, Centre de Resonance Magnetique Biologique et Medicale, France Xiaoping Hu, Coulter Dept. of BME at Georgia Tech and Emory, Atlanta, GA Angela Laird, Department of Physics, Florida International University, Miami, Fl Tom Liu, USD Center for Functional MRI, La Jolla, CA Zhongming Liu, Biomedical Engineering, Purdue University, West Lafayette, Indiana Joseph Mandeville, Martinos Center for Biomedical Imaging, Harvard, Boston, MA Galit Pelled, Kennedy Krieger Institute, Baltimore, MD Amir Shmuel, Montreal Neurological Institute, McGill University, Montreal, Canada Nick Turk-Browne, Department of Psychology, Princeton University, Princeton, NJ Martijn van den Heuvel, Dept. of Psychiatry, Rudolf Magnus Inst, Utrecht, Netherlands Gael Varoquaux, NeuroSpin, CEA Saclay, Gif-sur-Yvette, France Thomas Yeo, Dept. of Electrical and Computer Engineering, Natl. Univ. of Singapore Program: Sunday, March 9 Check-in: noon – 6pm 6:00 – 8:00pm Opening cocktail party Monday, March 10 7:30-8:30am Breakfast Session 1 Session Chair: 8:30 – 9:00am Gael Varoquaux: “What can we learn of brain connectivity by mining resting-state?” 9:00 – 9:30am Thomas Yeo: “Organization of the Human Brain Estimated by Intrinsic Functional Connectivity” 9:30 – 10:00am Tom Liu: “What can we learn from multimodal Imaging (fMRI, EEG, MEG) of resting state brain activity?” 10:00 – 10:30am Coffee 10:30-12 noon Proffered talks 10 – 15min each depending upon how many 12 noon Box Lunch 12:00 – 4:30pm Break 4:30 – 5:00pm Coffee Session 2 Session Chair: 5:00 – 5:30pm Galit Pelled: “Mapping and manipulating neuroplasticity” 5:30 – 6:00pm Lila Davachi: “Dynamic alterations in low-frequency BOLD connectivity related to memory encoding, retrieval and consolidation” 6:00 – 6:30pm Nick Turk-Browne: “Attention and modulation of connectivity between high and low level visual areas (or) category-specific connectivity in the visual cortex” 6:30 – 7:15pm Proffered talks Tuesday, March 11, 2014 7:30-8:30am Breakfast Session 3 Session Chair: Noam Harel 8:30 – 9:00am Martijn van den Heuvel: “The Rich Club: an anatomical infrastructure for communication and integration among functional brain networks” 9:00 – 9:30am Michael Breakspear: “Dwelling quietly in the rich club: Network determinants of mood and interoception” 9:30 – 10:00am 2-3 proffered talks 10:00 – 10:30am Coffee Break 10:30 – 11:00am Amir Shmuel: “Neurophysiological mechanisms underlying spontaneous fluctuations in hemodynamic signals” 11:00 – 11:30am Manus Donahue: “Hemodynamic and neurochemical constructs of functional connectivity” 11:30 – 12:00 Joe Mandeville: “Interpreting fMRI through PET correlations with occupancy within and beyond the classical model” 12 noon Box Lunch 12:00 – 4:30pm Break 4:30 – 5:00pm Coffee Session 4 Session Chair: 5:00 – 5:30pm 2-3 Proffered talks 5:30 – 6:00pm Zhongming Liu: “Multimodal Hyperspectral Imaging of Brain Activity and Connectivity” 6:00 – 6:30pm Mark Chiew: “Accelerating resting state FMRI acquisition with rank-constrained image reconstruction” 6:30 – 7:15pm 3-4 Proffered talks 7:30 – 9:30 Dinner/Reception Wednesday, March 12, 2014 7:30-8:30am Breakfast Session 5 Session Chair: 8:30 – 9:00am Jessica Damoiseaux: “Early detection of abnormal functional connectivity changes in older adults” 9:00 – 9:30am Maxime Guye: “Functional connectivity in epilepsy” 9:30 – 10:00am 2-3 Proffered talks 10:00 – 10:30am Coffee Break 10:30 – 11:00am Angela Laird: “Understanding Intrinsic Connectivity Networks: A Meta-Analytic Approach” 11:00 – 11:30am Xiaoping Hu: “Dealing with Individual Variability in Resting state Functional Connectivity” 11:30 – 12:00 2-3 Proffered talks 12:00 – 12:15pm Wrap up 12:15pm Box Lunch – meeting adjourned For additional information please go to: http://mrrc.yale.edu/home/seminars/workshop/index.aspx R. Todd Constable, Ph.D. Professor Diagnostic Radiology, Biomedical Engineering, and Neurosurgery Director MRI Research co-Director Yale MRRC Yale University School of Medicine The Anlyan Center 300 Cedar Street PO Box 208043 New Haven, CT 06520-8043 Tel: 203-785-5296 Fax: 203-785-6534 Website: http://mri.med.yale.edu Whistler Workshop on Brain Function, March 9-12, 2014 http://mrrc.yale.edu/home/seminars/workshop/index.aspx

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Segmentation and Surface Errors
by Jonathan Holt 22 Oct '13

22 Oct '13

Hi Guys, I'm having an issue with a brain involving both inaccurate surfaces and incorrectly segmented voxels. Basically, a sulcus is being skipped over by the main surface where and a bunch of basically empty space is being segmented as white matter. I've edited the segmentation myself by removing it and then I ran recon-all -autorecon2-noaseg -subjid <SUBJID> The problem is still persisting and the surface is still inaccurate. I can attach photos if needed. jon

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