Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

skull striping error question
by Subhabrata Chaudhury 23 Oct '13

23 Oct '13

Hi Everyone, I have some data where the skull striping hasnt worked properly and there are some skull remaining. However, upon looking at the white and pial surfaces, those look perfectly fine. My question is will the erroneous skullstriping affect the supratentorial volume estimation ? I will be highly obliged if someone can address this concern. Regards Subha

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Re: [Freesurfer] Projecting voxel intensities to a surface file
by Arash Nazeri 23 Oct '13

23 Oct '13

Sorry. I meant to do that. ---- Original Message ---- From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> To: Arash Nazeri <arashnazeri(a)aol.com> Sent: Wed, Oct 23, 2013 8:25 am Subject: Re: [Freesurfer] Projecting voxel intensities to a surface file Hi Arash can you cc the list on this type of email so that others can answer? Particularly Matt Glasser! I suspect that they have already run bbregister, but I'm not sure. cheers Bruce On Wed, 23 Oct 2013, Arash Nazeri wrote: > Hi Bruce, > Thanks for your response. I think this will do the trick generally, is it > also possible to apply mri_vol2surf to the Human Connectome Project > preprocessed files, or should I rerun the recon-all? In the HCP dataset, the > surface files are in the gifti format and the diffusion images are already > registered to the structural volumes. Based on the documentations it seems > that mri_vol2surf is hard-wired for outputs generated from recon-all. > > Cheers, > Arash > > > > -----Original Message----- > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > To: Arash Nazeri <arashnazeri(a)aol.com> > Cc: freesurfer <freesurfer(a)nmr.mgh.harvard.edu> > Sent: Tue, Oct 22, 2013 10:17 pm > Subject: Re: [Freesurfer] Projecting voxel intensities to a surface file > > Hi Arash > Yes. Register the surface to the volume with bbregister, then use > mri_vol2surf to do the sampling > Cheers > Bruce > > > > On Oct 22, 2013, at 12:13 PM, Arash Nazeri <arashnazeri(a)aol.com> wrote: > > Dear all, > I'm new to the freesurfer. I want to project surrounding cortical > voxel values (intensities) from a given map (e.g. mean diffusivity map > in a nifti format) to a surface file (e.g. mid-cortical surface in a > gifti fromat) to generate scalar maps like ?h.thickness for group-wise > statistics. Can this be carried out using freesurfer commands? > > Cheers, > Arash > > _______________________________________________ > 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. > >

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Re: [Freesurfer] missing eTIV in asegstats2table
by Daniel Ferreira 23 Oct '13

23 Oct '13

Dear Douglas, Please, find attached aseg.stats files for subj1 and subj2. Thanks Daniel

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Extremely intense grey matter being omitted
by Jonathan Holt 23 Oct '13

23 Oct '13

FS experts, Freesurfer has been omitting extremely bright/intense white and grey matter voxels (avg intensity ~150). Mostly this happens in areas that should be encompassed by the surfaces. Is there a way to tell recon-all to include these areas? I fear it may believe they are dura because of the similar intensity values. jon

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reconall error
by Rashmi Singh 23 Oct '13

23 Oct '13

Hello FreeSurfer experts, I am trying to run recon all on my data set, but I got following error message. Please help me understand the message and suggest solution. Thanks, Rashmi #@# Skull Stripping Tue Oct 22 13:57:00 CDT 2013 /home/rsingh/storage/labs/pbellgowan/MTBI/RASHMIANALYSIS/ANAL2013/CombT1T2Practice/FreeSurfer/AA470-2prac/mri mri_em_register -skull nu.mgz /opt/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 reading 1 input volumes... logging results to talairach_with_skull.log reading '/opt/freesurfer/average/RB_all_withskull_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros) ************************************************ spacing=8, using 3481 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 GCAhistoScaleImageIntensities: could not find wm peak resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=6.0 skull bounding box = (130, 148, 130) --> (130, 148, 130) using (130, 148, 130) as brain centroid... mean wm in atlas = 126, using box (130,148,130) --> (129, 147,129) to find MRI wm WARNING: gca.c::GCAhistoScaleImageIntensities: h_mri->nbins=255, mri_peak=-1 before smoothing, mri peak at 0 WARNING2: gca.c::GCAhistoScaleImageIntensities: h_mri->nbins=255, mri_peak=-1 after smoothing, mri peak at 0, scaling input intensities by inf Linux enders 2.6.32-52-server #114-Ubuntu SMP Wed Sep 11 19:06:34 UTC 2013 x86_64 GNU/Linux recon-all -s AA470-2prac exited with ERRORS at Tue Oct 22 13:57:26 CDT 2013 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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Projecting voxel intensities to a surface file
by Arash Nazeri 22 Oct '13

22 Oct '13

Dear all, I'm new to the freesurfer. I want to project surrounding cortical voxel values (intensities) from a given map (e.g. mean diffusivity map in a nifti format) to a surface file (e.g. mid-cortical surface in a gifti fromat) to generate scalar maps like ?h.thickness for group-wise statistics. Can this be carried out using freesurfer commands? Cheers, Arash

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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

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