Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Merging labels for multiple data sets
by Anupa AV 23 May '13

23 May '13

Dear All, I am having a total of 100 subjects for my analysis. My aim is to seperate DLPFC by making coronal cuts. I know the procedure to do for single subjects. Can anyone help me with the command line for mutiple data sets..? Any help will be greatly appreciated..

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temporal lobe left out in pial surface - edits on brainmask.mgz or brain.finalsurfs.mgz?
by Yizhou Ma 22 May '13

22 May '13

Dear FS experts, I have a subject where large portions of temporal lobe is not included in the pial surface. A member in my lab has suggested edits on brain.finalsurfs.mgz. However, in the following page it is indicated that edits on brain.finalsurfs.mgz is only intended for cases regarding inclusion of cerebellum. Can anyone please let me know which volume I should be working on in this case? http://ftp.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits Thanks, Cherry

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Re: [Freesurfer] ERROR in long_mris_slope
by Martin Reuter 22 May '13

22 May '13

Hi Cathy, I think the problem is when there are tabs AND spaces. Only spaces should also work. I can write some code (when I have time) that checks these things, maybe for the next release. Best, Martin On 05/22/2013 02:21 PM, Catherine Bois wrote: > Hi, > > Thank you for your reply. I finally got it working today.thanks for > your help=)! You say the qdec table should have only spaces; however > they only seem to work when they are completely tab separated and not > a single space? If there is accidently a space it will suddenly not > work. Is there a way that can solve this problem that you can think > of? It is very time consuming because suddenly it will jsut stop > working and I need to start from scratch! > > > Quoting Martin Reuter <mreuter(a)nmr.mgh.harvard.edu> on Wed, 22 May > 2013 14:08:44 -0400: > >> Hi Cathy, >> >> it must be something else (I think). The mris_calc command looks >> weird ("--label " looks like the label is not passed, but a space >> instead, it then thinks 'mul' is a file). >> >> qdecfinal is your qdec table? Make sure it contains only spaces to >> separate the fields. It should have at least these columns >> fsid fsid-base time >> >> also in your command below, why are there "?" before do-label and time? >> >> Unless you want to use the stack (within subject stack of thickness >> values), I would drop the --do-stack (maybe also drop do-avg or >> whatever else you don't need). >> >> For debugging, I would create a directory, place a single subject >> there, create a new qdec table with only that subject and try again >> there. If it still happens , let me know. >> >> Best, Martin >> >> >> On 05/20/2013 10:25 AM, Catherine Bois wrote: >>> Dear Freesurfer experts, >>> >>> I am trying to conduct the long_mris_slopes --qdec qdecfinal --meas >>> thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack >>> ?do-label ?time time --qcache fsaverage command for my longitudinal >>> processing. However I keep getting the error message: >>> >>> mris_calc -o /directory/baseX/surf/lh.long.thickness-spc.fwhm0.mgh >>> --label /directory/baseX/surf/lh.long.thickness-spc.fwhm0.mgh mul 100 >>> >>> >>> mris_calc: >>> Sorry, but I seem to have encountered an error. >>> While accessing file 'mul', >>> >>> I read online that this was due to a bug encountered in version 5.1, >>> however I recently upgraded to version 5.3 and the error message >>> persists. As my Long and base runs have been done in version 5.1 >>> still, I was wondering whether in order to fix this problem the long >>> and base runs need to be rerun with version 5.3, or whether the error >>> I am encountering has another solution/ is caused by another problem >>> entirely? >>> >>> Thank you for your help, >>> >>> Best Wishes, >>> >>> Cathy >>> >> >> -- >> Martin Reuter, Ph.D. >> Assistant in Neuroscience - Massachusetts General Hospital >> Instructor in Neurology - Harvard Medical School >> MGH / HMS / MIT >> >> A.A.Martinos Center for Biomedical Imaging >> 149 Thirteenth Street, Suite 2301 >> Charlestown, MA 02129 >> >> Phone: +1-617-724-5652 >> Email: >> mreuter(a)nmr.mgh.harvard.edu >> reuter(a)mit.edu >> Web : http://reuter.mit.edu >> >> >> >> 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. >> >> >> > > > -- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreuter(a)nmr.mgh.harvard.edu reuter(a)mit.edu Web : http://reuter.mit.edu

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ERROR in long_mris_slope
by Catherine Bois 22 May '13

22 May '13

Dear Freesurfer experts, I am trying to conduct the long_mris_slopes --qdec qdecfinal --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack ?do-label ?time time --qcache fsaverage command for my longitudinal processing. However I keep getting the error message: mris_calc -o /directory/baseX/surf/lh.long.thickness-spc.fwhm0.mgh --label /directory/baseX/surf/lh.long.thickness-spc.fwhm0.mgh mul 100 mris_calc: Sorry, but I seem to have encountered an error. While accessing file 'mul', I read online that this was due to a bug encountered in version 5.1, however I recently upgraded to version 5.3 and the error message persists. As my Long and base runs have been done in version 5.1 still, I was wondering whether in order to fix this problem the long and base runs need to be rerun with version 5.3, or whether the error I am encountering has another solution/ is caused by another problem entirely? Thank you for your help, Best Wishes, Cathy -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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recon-all error
by Yizhou Ma 22 May '13

22 May '13

Dear FS experts, I have a recon-all error regarding one of my subjects. The scan suffers from weakened signals at the lower part of the brain. Skullstrip stripped most of the cerebellum at first, and we fixed it manually. After running recon-all for the first time, large portions of the temporal lobes were left out of the brain. Knowing that this may not be the correct way, we still tried to fixed that by adding lots of control points. The second run of recon-all, then, came back with the following error message:" Loading source data Reading curvature file /space/mdeh3/3/halgdev/projects/nyuproj/subjects/sub4422b/surf/rh.thickness ERROR: number of vertices in /space/mdeh3/3/halgdev/projects/nyuproj/subjects/sub4422b/surf/rh.thickness does not match surface (192226,134773) ERROR: reading curvature file Linux mmil-compute-1-11.local 2.6.18-308.16.1.el5 #1 SMP Tue Oct 2 22:01:43 EDT 2012 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub4422b exited with ERRORS at Mon May 20 " Any ideas for why it is, or how we can fix the problem at the temporal lobes, will be really appreciated. Thanks, Cherry

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FreeSurfer v5.3.0
by Kristina Nalbandian 21 May '13

21 May '13

Hello I am interested in downloading the FreeSurfer v5.3.0. I will be running it on a virtual machine platform in Windows (xubuntu). Are there any specific instructions for this on the FreeSurfer website because I noticed it runs on CentOS 6 x86_64 (64b). Or does the download come with the virtual machine? Thank you for your help, Kristina

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Re: [Freesurfer] tracula error
by Anastasia Yendiki 21 May '13

21 May '13

Hi Skyler - When you say it's been working fine, have you checked that the orientations are correct by viewing dtifit_V1.nii.gz and dtifit_FA.nii.gz, like in the snapshot that I sent you? If those orientations aren't correct, the gradient table isn't correct either. a.y On Tue, 21 May 2013, Skyler Gabriel Shollenbarger wrote: > Hi Anastasia, > > Thank you for all of your help! 'trac-all' has been working fine with > the other subjects, so it doesn't appear to be the gradient vector file. > Yes, unfortunately the resolution is not the best. > > Would you consider this subject a loss or are there other fixes you suggest? > > Thanks again! > Skyler > > > ----- Original Message ----- > From: "Anastasia Yendiki" <ayendiki(a)nmr.mgh.harvard.edu> > To: shollen2(a)uwm.edu > Cc: freesurfer(a)nmr.mgh.harvard.edu > Sent: Tuesday, May 21, 2013 10:40:59 AM > Subject: Re: [Freesurfer] tracula error > > > Hi Skyler - A couple of things. I'm attaching a screenshot of the FA map > and primary tensor eigenvectors of your subject. First, it looks like your > gradient directions are incorrect, given how the eigenvectors are oriented > in the corpus callosum (yellow arrows in the coronal and axial slice). The > eigenvectors follow the shape of the corpus callosum in the axial view but > not in the coronal view. My guess is your gradient vectors need to be > flipped in the z-direction. > > Second, your resolution is 4mm. There's going to be a lot of partial > voluming. You'll have to give up on the thinner tracts, like ccg/cab (see > purple arrow in sagittal view pointing to cingulum, you can barely resolve > it from the corpus callosum). > > Third, you have 14 gradient directions, so fitting the ball-and-stick > model to this data, which is done by bedpostx and which you need for the > tract reconstruction step, is going to be challening. > > I don't want to discourage you, but tractography may be a bit more than > this data can support. > > Please let me know if you have more questions, > a.y > > On Mon, 20 May 2013, shollen2(a)uwm.edu wrote: > >> Hi Anastasia, >> >> They were uploaded. Thanks for your help! >> >> Skyler >> >> Sent from my iPhone >> >> On May 20, 2013, at 10:20 AM, Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> wrote: >> >>> >>> Hi Skyler - If you upload the dmri/dmri.bedpostX/dlabel/scripts directories of your subject for me, I'll take a look. >>> >>> http://gate.nmr.mgh.harvard.edu/filedrop2/ >>> >>> a.y >>> >>> On Fri, 17 May 2013, shollen2(a)uwm.edu wrote: >>> >>>> Hi Anastasia, >>>> >>>> The brain mask looks fine. Any other suggestions? >>>> >>>> Thanks for your help, >>>> Skyler >>>> Sent from my iPhone >>>> >>>> On May 17, 2013, at 12:24 PM, Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> wrote: >>>> >>>>> >>>>> Hi Skyler - How does the brain mask look like? Any major chunks of brain missing in the area of the left uncinate? That's the tract where the error occurs, and based on this info in the log file, I'm guessing it's a masking issue: >>>>> >>>>> [...] >>>>> INFO: Rejected 4221 streamlines for straying off mask >>>>> INFO: Rejected 2 streamlines for reversing direction >>>>> INFO: Rejected 9 streamlines as length outliers >>>>> INFO: Have 56 total streamlines (min/mean/max length: 1/13/33) >>>>> [...] >>>>> >>>>> Hope this helps, >>>>> a.y >>>>> >>>>> On Wed, 15 May 2013, Skyler Gabriel Shollenbarger wrote: >>>>> >>>>>> Hi all, >>>>>> >>>>>> We ran tracula prep stage and it exited with errors: 'Selected streamline has fewer than 5 points'. We have attached the log and error files if needed. >>>>>> >>>>>> Thank you in advance! >>>>>> Skyler >>>>> >>>>> >>>>> 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] v5.2.0 preproc-sess failing on 3dvolreg.afni
by Joseph Dien 21 May '13

21 May '13

Perhaps the problem has already been solved but I just ran into the same issue (on OS X 10.8.2). After poking around, what I found was that while the current AFNI distribution does not have a file named 3dvolreg.afni, it does have one named 3dvolreg. I'm guessing the problem is that it has been renamed. I fixed the problem by creating a link: ln 3dvolreg 3dvolreg.afni I suppose FSFAST needs to be updated to take this new name into account. Cheers! Joe > Hi Doug, > > Here's the output from cat /proc/version: > Linux version 2.6.32-45-generic (buildd@batsu) (gcc version 4.4.3 (Ubuntu > 4.4.3-4ubuntu5.1) ) #101-Ubuntu SMP Mon Dec 3 15:39:38 UTC 2012 > > This is the result of cat $FREESURFER_HOME/build-stamp.txt > > freesurfer-Linux-centos4_x86_64-stable-pub-v5.2.0 > > Thanks. > > -Yuhong > > On Thu, Mar 21, 2013 at 1:12 PM, Douglas N Greve > <gr...(a)nmr.mgh.harvard.edu>wrote: > > > which version of CentOS? Also, can you send me the result of > > cat $FREESURFER_HOME/build-stamp.**txt > > > > > > > > On 03/21/2013 02:09 PM, Y.V. Jiang wrote: > > > >> Hi Doug, > >> > >> I am using Linux: x86_64 GNU/Linux. Thanks. > >> > >> -Yuhong > >> > >> On Thu, Mar 21, 2013 at 12:57 PM, Douglas N Greve < > >> gr...(a)nmr.mgh.harvard.edu > >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...(a)nmr.mgh.harvard.edu>>> > >> wrote: > >> > >> what platform are you using? > >> > >> > >> On 03/21/2013 01:24 PM, Y.V. Jiang wrote: > >> > >> Hi Doug, > >> > >> Thanks for the reply. From the command line the command > >> 3dvolreg.afni returned the following error: > >> > >> 3dvolreg.afni: symbol lookup error: 3dvolreg.afni: undefined > >> symbol: afni_ncerr > >> > >> -Yuhong > >> > >> On Thu, Mar 21, 2013 at 12:08 PM, Douglas N Greve > >> <gr...(a)nmr.mgh.harvard.edu > >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...(a)nmr.mgh.harvard.edu> > >> > > >> <mailto:gr...@nmr.mgh.harvard.**edu <gr...(a)nmr.mgh.harvard.edu> > >> > >> <mailto:gr...@nmr.mgh.harvard.**edu <gr...(a)nmr.mgh.harvard.edu>>>> > >> wrote: > >> > >> > >> Hi Yuhong, > >> What happens when you run 3dvolreg.afni from the command > >> line without > >> any args? > >> doug > >> > >> On 03/21/2013 12:38 PM, Y.V. Jiang wrote: > >> > Hi Doug, > >> > > >> > I was running preproc-sess in the newly released > >> freesurfer-5.2.0. The > >> > command I used was: > >> > > >> > preproc-sess -sf sessid -df sessdir -fsd bold -surface > >> fsaverage lhr > >> > -mni305 -fwhm 6 -per-run > >> > > >> > The program failed with the following errors: > >> > > >> > 3dvolreg.afni -verbose -dfile 004/fmcpr.mcdat -1Dmatrix_save > >> > 004/fmcpr.mat -base > >> 004/tmp.mc-afni2.29239/**tempvol.nii.gz -prefix > >> > 004/tmp.mc-afni2.29239/outvol.**nii.gz > >> 004/tmp.mc-afni2.29239/invol.**nii.gz > >> > 3dvolreg.afni: symbol lookup error: 3dvolreg.afni: > >> undefined symbol: > >> > afni_ncerr > >> > ERROR: 3dvolreg.afni > >> > Invalid null command. > >> > > >> > I have the file 3dvolreg.afni in $FREESURFER_HOME/bin. > >> There is > >> > another file of the same name under afni/bin. > >> Preproc-sess is > >> relying > >> > on the version in $FREESURFER_HOME/bin. > >> > > >> > Do you know what the problem is? Should I replace > >> freesurfer's > >> copy of > >> > 3dvolreg.afni with AFNI's copy of 3dvolreg.afni? > >> > > >> > Thanks. > >> > > >> > -Yuhong > >> > > >> > > >> > ______________________________**_________________ > >> > Freesurfer mailing list > >> > Freesurfer(a)nmr.mgh.harvard.edu > >> > >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> > >> > > >> > >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> > >> > >> > >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> > >> >> > >> > >> > https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/** > >> freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > >> > >> -- > >> Douglas N. Greve, Ph.D. > >> MGH-NMR Center > >> gr...(a)nmr.mgh.harvard.edu > >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...(a)nmr.mgh.harvard.edu> > >> > > >> <mailto:gr...@nmr.mgh.harvard.**edu <gr...(a)nmr.mgh.harvard.edu> > >> > >> <mailto:gr...@nmr.mgh.harvard.**edu <gr...(a)nmr.mgh.harvard.edu>>> > >> Phone Number: 617-724-2358 <tel:617-724-2358> > >> <tel:617-724-2358 <tel:617-724-2358>> > >> Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > >> > >> <tel:617-726-7422>> > >> > >> Bugs: > >> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > >> > >> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > >> > > >> > >> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > >> > > >> FileDrop: > >> > >> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > >> > >> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > >> > > >> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.** > >> html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> > >> > >> Outgoing: > >> ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** > >> greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > >> > >> ______________________________**_________________ > >> Freesurfer mailing list > >> Freesurfer(a)nmr.mgh.harvard.edu > >> > >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> > >> > > >> > >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> > >> > >> > >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> > >> >> > >> > >> > >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<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. > >> > >> > >> > >> -- Douglas N. Greve, Ph.D. > >> MGH-NMR Center > >> gr...(a)nmr.mgh.harvard.edu > >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...(a)nmr.mgh.harvard.edu> > >> > > >> Phone Number: 617-724-2358 <tel:617-724-2358> > >> Fax: 617-726-7422 <tel:617-726-7422> > >> > >> Bugs: > >> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > >> > >> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > >> > > >> FileDrop: > >> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > >> > >> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > >> > > >> Outgoing: > >> > >> ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > >> > >> > >> > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > gr...(a)nmr.mgh.harvard.edu > > Phone Number: 617-724-2358 > > Fax: 617-726-7422 > > > > Bugs: > > surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > FileDrop: > > www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** > > greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > > > > > _______________________________________________ > 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. -------------------------------------------------------------------------------- Joseph Dien, Senior Research Scientist University of Maryland E-mail: jdien07(a)mac.com Phone: 301-226-8848 Fax: 301-226-8811 http://joedien.com//

2 1

question abt dt-recon
by Ritobrato Datta 21 May '13

21 May '13

Hello All, I havent used dt-recon yet but I have a question abt it. When the dt-recon computes the FA maps, whats the dimensions of these FA maps ? Are they resampled to the freesurfer anatomical voxel size (1x1x1) or are they in their native voxel size (in which they were collected) ? If I want to extract say the meanFA from one of the ROIs that freesurfer dumps in aseg/wmparc, can I do that ? Thanks Ri

2 1

Overlay thickness for BA areas
by _andreia_＠sapo.pt 21 May '13

21 May '13

Hello list! Is there a way to display the thickness of individual Bordmann areas in the inflated surface using tksurfer? I'm able to show surface area with File-> Label -> Load label and choosing the thresholded label. Now, I qould like to do the same but with cortical thickness, is this possible? I'm using FS 5.0. Thank you in advance, Andreia

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