Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30097 discussions

[Tracula] Run trac-all with 2 time points for DTI scan but 1 time point for T1 scan. How to?
by r.navarra＠itab.unich.it 23 Jul '13

23 Jul '13

Hi, I need to run trac-all on subjects scanned first time in T1 and DTI, second time DTI only. How to configure dmrirc? I've seen long.example but it seems that it require T1 second run too. Tnx, Riccardo

2 2

infant atlas segmentation
by Mark Plantz 22 Jul '13

22 Jul '13

Hello FreeSurfers, I recently obtained a set of infant templates. Out of curiousity, I decided to view one of the input brains with the provided segmented volume file. It appears that there is some misalignment. I wouldn't expect the alignment to be perfect, since I am basically overlaying an average of multiple brains onto one. However, it looks like this misalignment may be caused by either: 1.) the segmentation volume file being shifted down or 2.) the slices not lining up properly (i.e. one file starts before the other). Any ideas what could cause a problem like this? Could it be that the segmented files are simply not compatible with FreeSurfer? Thanks for the help, Mark

2 1

Skull stripped MNI305
by Fotiadis, Panagiotis 22 Jul '13

22 Jul '13

Hi, I was wondering if there is a skull stripped version of the file /usr/local/freesurfer/stable5_0_0/average/mni305.cor.mgz stored anywhere. I tried applying bet and mri_watershed on the mni305.cor.mgz file (with different frequencies as well) but there were still parts of the skull showing. Thank you for your time! Panos

2 4

recon-all error
by Smian 22 Jul '13

22 Jul '13

Hi everyone, I'm quite new to FreeSurfer, my apologies for asking the obvious. I tried to run recon-all on multi echo T2* weighted data and got the following error: 'input(s) cannot have multiple frames' I was wondering how I should go about running recon-all on multi echo data. Any help would be appreciated! Thank you!

2 1

Re: [Freesurfer] Recon-all difficulties off-site
by Michelle W. Voss 22 Jul '13

22 Jul '13

The MNI directory directly under freesurfer is there, but the MNI_PERL5 directory is not. e.g, bash-3.2$ echo $MNI_PERL5LIB /Applications/freesurfer/mni/lib/../System/Library/Perl/5.8.6 bash-3.2$ cd $MNI_PERL5LIB bash: cd: /Applications/freesurfer/mni/lib/../System/Library/Perl/5.8.6: No such file or directory Is there a patch to fix? thanks Michelle On Mon, Jul 22, 2013 at 9:25 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > Hi Michelle > > is the MNI stuff installed? If seems like ti can't find > "MNI/Startup.pm". Mine is under: $MNI_PERL5LIB/MNI/Startup.pm > > cheers > Bruce > > > On Sun, 21 Jul > 2013, Michelle W. Voss wrote: > > > Hi, I seem to be having the same error, recon all is crashing out with > the > > mri_nu_correct.mni command, e.g., if I run in the mri directory of a > > subject, I get what is pasted below. Any ideas for the fix? > > > > bash-3.2$ mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 > > --no-rescale --i orig.mgz --o orig_nu.mgz > > /Users/mwvoss/Analysis/ChordLearning/Freesurfer/sub100/mri > > /Applications/freesurfer/bin/mri_nu_correct.mni > > --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o > > orig_nu.mgz > > nIters 1 > > $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ > > Darwin dhcp80ff9e7c.dynamic.uiowa.edu 11.4.2 Darwin Kernel Version > 11.4.2: > > Thu Aug 23 16:25:48 PDT 2012; root:xnu-1699.32.7~1/RELEASE_X86_64 x86_64 > > Sun Jul 21 09:25:15 CDT 2013 > > Can't locate MNI/Startup.pm in @INC (@INC contains: > > /Applications/freesurfer/mni/lib/../System/Library/Perl/5.8.6 > > /Library/Perl/5.12/darwin-thread-multi-2level /Library/Perl/5.12 > > /Network/Library/Perl/5.12/darwin-thread-multi-2level > > /Network/Library/Perl/5.12 /Library/Perl/Updates/5.12.3 > > /System/Library/Perl/5.12/darwin-thread-multi-2level > > /System/Library/Perl/5.12 > > /System/Library/Perl/Extras/5.12/darwin-thread-multi-2level > > /System/Library/Perl/Extras/5.12 .) at > > /Applications/freesurfer/mni/bin/nu_correct line 37. > > BEGIN failed--compilation aborted at > > /Applications/freesurfer/mni/bin/nu_correct line 37. > > tmpdir is ./tmp.mri_nu_correct.mni.30026 > > /Users/mwvoss/Analysis/ChordLearning/Freesurfer/sub100/mri > > mri_convert orig.mgz ./tmp.mri_nu_correct.mni.30026/nu0.mnc -odt float > > mri_convert orig.mgz ./tmp.mri_nu_correct.mni.30026/nu0.mnc -odt float > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > > reading from orig.mgz... > > TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00 > > i_ras = (-1, 0, 0) > > j_ras = (0, 0, -1) > > k_ras = (0, 1, 0) > > changing data type from uchar to float (noscale = 0)... > > writing to ./tmp.mri_nu_correct.mni.30026/nu0.mnc... > > > > -------------------------------------------------------- > > Iteration 1 Sun Jul 21 09:25:18 CDT 2013 > > nu_correct -clobber ./tmp.mri_nu_correct.mni.30026/nu0.mnc > > ./tmp.mri_nu_correct.mni.30026/nu1.mnc -tmpdir > > ./tmp.mri_nu_correct.mni.30026/0/ -iterations 1000 -distance 50 > > Can't locate MNI/Startup.pm in @INC (@INC contains: > > /Applications/freesurfer/mni/lib/../System/Library/Perl/5.8.6 > > /Library/Perl/5.12/darwin-thread-multi-2level /Library/Perl/5.12 > > /Network/Library/Perl/5.12/darwin-thread-multi-2level > > /Network/Library/Perl/5.12 /Library/Perl/Updates/5.12.3 > > /System/Library/Perl/5.12/darwin-thread-multi-2level > > /System/Library/Perl/5.12 > > /System/Library/Perl/Extras/5.12/darwin-thread-multi-2level > > /System/Library/Perl/Extras/5.12 .) at > > /Applications/freesurfer/mni/bin/nu_correct line 37. > > BEGIN failed--compilation aborted at > > /Applications/freesurfer/mni/bin/nu_correct line 37. > > ERROR: nu_correct > > > > > > > > On Tue, Jun 4, 2013 at 12:51 PM, Douglas N Greve < > greve(a)nmr.mgh.harvard.edu> > > wrote: > > It looks like it is not finding the MNI tools. Maybe Zeke can > > chime in. > > doug > > On 06/04/2013 01:48 PM, Nitenson, Adam wrote: > > > > > > Hi Doug, > > > > > > The command runs a bit further now but then exits with errors. > > > Unfortunately this time there is no specific stated error. The > > > last few lines of the log are: > > > > > > INFO: extension is mgz > > > #-------------------------------------------- > > > #@# Talairach Tue Jun 4 13:22:08 EDT 2013 > > > /gpfs/data/twhite/anitenso/FreesurferPractice/unpack4/mri > > > > > > mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 > > > --no-rescale --i orig.mgz --o orig_nu.mgz > > > > > > Linux node271 2.6.32-279.2.1.el6.x86_64 #1 SMP Fri Jul 20 > > 01:55:29 > > > UTC 2012 x86_64 x86_64 x86_64 GNU/Linux > > > > > > recon-all -s unpack4 exited with ERRORS at Tue Jun 4 13:22:10 > > EDT > > > 2013 > > > > > > > > > > > > The only other section of the log that seems like it could be > > > related to an error is: > > > > > > Can't locate MNI/Startup.pm in @INC (@INC contains: > > > /gpfs/runtime/opt/perl/5.16.0/lib > > > /gpfs/runtime/opt/perl/5.16.0/lib/site_perl > > /usr/local/lib64/perl5 > > > /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl > > > /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 > > .) > > > at /gpfs/runtime/opt/freesurfer/5.2.0/mni/bin/nu_correct line > > 37. > > > BEGIN failed--compilation aborted at > > > /gpfs/runtime/opt/freesurfer/5.2.0/mni/bin/nu_correct line 37. > > > > > > So, I'm not sure what it's not liking here. > > > > > > Thanks again, > > > Adam > > > > > > > > > On Tue, Jun 4, 2013 at 11:44 AM, Douglas N Greve > > > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > wrote: > > > > > > That dcmunpack command will put the data into a file called > > > unpack3/MPRAGE/002/struct.nii > > > It needs to be put into upack3/mri/orig/002.mgz > > > doug > > > > > > > > > > > > > > > On 06/04/2013 11:22 AM, Nitenson, Adam wrote: > > > > > > Hi Doug, > > > > > > When I try the command as you suggested: > > > recon-all -all -s unpack3 > > > I get the following error: > > > > > > ERROR: no run data found in > > > > > /gpfs/data/twhite/anitenso/FreesurferPractice/unpack3/mri. > > > Make sure to > > > have a volume called 001.mgz in > > > > > /gpfs/data/twhite/anitenso/FreesurferPractice/unpack3/mri/orig > > > > > > Do you know why I might be lacking that volume? This was > > > not usually an issue after running the two unpacksdcmdir > > > commands (for MPRAGE and bold runs). > > > > > > Thanks, > > > Adam > > > > > > > > > On Mon, Jun 3, 2013 at 3:44 PM, Douglas N Greve > > > <greve(a)nmr.mgh.harvard.edu > > > <mailto:greve@nmr.mgh.harvard.edu> > > > <mailto:greve@nmr.mgh.harvard.edu > > > <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > > > > > Hi Adam, if the subject folder exists and you pass > > > recon-all a -i > > > flag, > > > then it will exit with error saying that the data > > > exist (otherwise it > > > would overwrite what is there). However, just > > because > > > the subject > > > folder > > > exists does not mean that there is any data sitting > > in > > > subject/mri/orig. > > > Then it will tell you that it cannot find any data. > > > > > > Note that when you run recon-all, you need to tell > > it > > > to do something > > > (eg, add the "-all" flag to do everything) > > > > > > doug > > > > > > > > > On 06/03/2013 03:21 PM, Nitenson, Adam wrote: > > > > Hello users, > > > > > > > > I am trying to get Freesurfer (5.2) working > > properly > > > off-site and am > > > > encountering errors I did not have while working > > at > > > the Martinos > > > > center. We use the same Siemens 3T Tim Trio > > scanner > > > at Brown, so I > > > > would hope the data is similar to work with. > > > > > > > > I have been using dcmunpack since unpacksdcmdir is > > not > > > identifying the > > > > DICOM files properly. I have successfully unpacked > > the > > > structural and > > > > bold scans using the command (entered from the raw > > > scan data folder: > > > > > > > > dcmunpack -src DICOM -targ > > > (path)/FreesurferPractice/unpack3 -run 2 > > > > MPRAGE nii struct (I also tried using mgz > > > instead of nii, > > > and also > > > > changed struct to other things as it appears to be > > a > > > naming > > > argument) > > > > > > > > dcmunpack -src DICOM -targ > > > (path)/FreesurferPractice/unpack3 -fsfast > > > > -run 3 bold nii f.nii -run 4 bold nii f.nii -run 5 > > > bold nii > > > f.nii -run > > > > 6 bold nii f.nii -run 7 bold nii f.nii -run 8 bold > > > nii f.nii -run 9 > > > > bold nii f.nii > > > > > > > > (path) just being an abbreviate piece of the > > > relevant pathway > > > > > > > > These generate the MPRAGE and bold folders in the > > > subject folder as > > > > expected. I have difficulties with the next > > commands > > > (environment has > > > > been set). > > > > > > > > I try: > > > > recon-all -i <path to structural data> -s <subject > > > name> -force > > > > recon-all -i > > > (path)/FreesurferPractice/unpack/MPRAGE/002 -s unpack3 > > > > (I got an error about using -force so I omitted > > that > > > from my > > > command) > > > > > > > > and get the following Error > > > > ERROR: You are trying to re-run an existing > > subject > > > with (possibly) > > > > new input data (-i). If this is truly new input > > > data, you > > > should delete > > > > the subject folder and re-run, or specify a > > > different subject name. > > > > If you are just continuing an analysis of an > > > existing subject, then > > > > omit all -i flags. > > > > > > > > Yet when I omit -i and just use "recon-all -s > > > unpack3", I get > > > "ERROR: > > > > nothing to do" > > > > > > > > I tried a different tactic and used > > > > > > > > "recon-all -s unpack3 -autorecon1" as well as > > "recon-all > > > > -autorecon-all -s unpack3" > > > > > > > > which both created the various folders (bem, > > label, > > > mri, surf, etc) > > > > but failed with > > > > "ERROR: no run data found in > > > (path)/FreesurferPractice/unpack3/mri. > > > > Make sure to have a volume called 001.mgz in > > > > (path)/FreesurferPractice/unpack3/mri/orig. If you > > > have a second run > > > > of data call it 002.mgz, etc." > > > > > > > > I have tried these commands in both bash and tcsh > > > shells with > > > the same > > > > effect. So the problem, it seems, is that my "mri" > > > file is > > > blank, and > > > > this was not a problem I had running these > > commands > > > at Martinos. Any > > > > idea what the issue might be? > > > > > > > > Best, > > > > > > > > Adam Nitenson > > > > Neuroscience Graduate Program > > > > Laboratory of Affective Neuroscience > > > > Brown University > > > > > > > > > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > > > > > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > -- > > > Douglas N. Greve, Ph.D. > > > MGH-NMR Center > > > greve(a)nmr.mgh.harvard.edu > > > <mailto:greve@nmr.mgh.harvard.edu> > > > <mailto:greve@nmr.mgh.harvard.edu > > > <mailto:greve@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> > > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > > 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/ > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu > > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > The information in this e-mail is intended only for > > > the person to > > > whom it is > > > addressed. If you believe this e-mail was sent to > > you > > > in error and > > > the e-mail > > > contains patient information, please contact the > > Partners > > > Compliance HelpLine at > > > http://www.partners.org/complianceline . If the e-mail > > was > > > sent to > > > you in error > > > but does not contain patient information, please > > > contact the > > > sender and properly > > > dispose of the e-mail. > > > > > > > > > > > > -- > > > Douglas N. Greve, Ph.D. > > > MGH-NMR Center > > > greve(a)nmr.mgh.harvard.edu <mailto:greve@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> > > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > > 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/ > > > > > > > > > > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > greve(a)nmr.mgh.harvard.edu > > Phone Number: 617-724-2358 > > Fax: 617-726-7422 > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > Outgoing: > > 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 > > > > > > > > >

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Pial boundary overshoot
by Victor Kovac 22 Jul '13

22 Jul '13

Dear Freesurfer experts, I have run recon-all on brains atrophied by a neurodegenerative disease. as you can see in the attached images, the pial boundary seems to have overshot and contains mostly arachnoid space, and the white matter boundary (yellow) includes substantial amounts of cortical gray matter. This is the case in all slices in three of the most atrophied brains. Do you have any suggestion as to what I can do to get these brains analyzed properly? Would perhaps changing the threshold for white matter intensity with control points help? I have manually adjusted the talairach, but it has not improved this issue. Thank you for your help! Victor

1 0

possible to use multiple B value DTI in Tracula?
by Salil Soman 22 Jul '13

22 Jul '13

Hi, I was wondering - is it possible to use DTI data of multiple B values in Tracula (acquired during the same session and same TE)? Best wishes, Sal Salil Soman, MD, MS

3 3

error with fast_selxavg3
by Leila Reddy 22 Jul '13

22 Jul '13

Hi, I am running into an error with fast_selxavg3 (NaN values in XtX). Other have people reported similar problems on the mailing list and I've tried implementing some of the suggestions (namely, using -nowhiten and checking that all events exist in my paradigm file), but I can't get rid of the error. I have an event-related design with very short events (duration of 1 screen refresh = 16.6ms) presented at random intervals. The error only occurs for the -gammafit and -spmhrf analyses and not for -fir. When I check the Xtmp.mat there are indeed NaNs in the first 2 columns of the X matrix. The commands I issue and the output of bugr are below.I attach the paradigm file from one run of the experiment (there are 5 runs in all but I started focusing on just one in order to troubleshoot). TR=2 and numTRs=172. Any help would be much appreciated. Thanks in advance, Leila mkanalysis-sess -fsd bold -surface fsaverage lh -fwhm 3 -event-related -paradigm VRpara.para -nconditions 1 -gammafit 2.25 1.25 -TR 2 -refeventdur 0.016 -polyfit 2 -mcextreg -analysis TargDist-gammafit-sm3.lh -per-run -rlf runlist -force -nowhiten mkcontrast-sess -analysis TargDist-gammafit-sm3.lh -contrast VR -a 1 selxavg3-sess -s $subj -analysis TargDist-gammafit-sm3.lh Error message: ------------------------- $Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $ /APPLICATIONS/freesurfer/fsfast/toolbox/fast_selxavg3.m /APPLICATIONS/freesurfer/fsfast/toolbox/fast_ldanaflac.m /APPLICATIONS/freesurfer/matlab/MRIread.m ------------------------- outtop = /Volumes/LEILA_DATA/fMRI/Rodika/EEG_IRMF Extension format = nii.gz 1 VR.mat nruns = 1 autostimdur = outanadir = /Volumes/LEILA_DATA/fMRI/Rodika/EEG_IRMF/BT/bold/TargDist-gammafit-sm3.lh Found 149786/163842 (91.4) voxels in mask Creating Design Matrix ... creation time = 0.005 sec DoMCFit = 1 ntptot = 172, nX = 7, DOF = 165 Saving X matrix to /Volumes/LEILA_DATA/fMRI/Rodika/EEG_IRMF/BT/bold/TargDist-gammafit-sm3.lh/Xtmp.mat Error using svd Input to SVD must not contain NaN or Inf. Error in cond (line 36) s = svd(A); Error in fast_selxavg3 (line 279) XCond = cond(XtX); >> ------------------------------------------ ERROR: fast_selxavg3() failed\n Output of bugr: --------------------------------------------------------------------- FREESURFER_HOME: /APPLICATIONS/freesurfer Build stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 Kernel info: Darwin 12.0.0 x86_64 ---------------------------------------------------------------------

2 1

rtview
by Nicholas Paul Denisuk 22 Jul '13

22 Jul '13

Dear Freesurfer Users, I am running a retinotopic analysis in the 5.1.0 version of freesurfer. As tksurfer is not ideal for viewing the retinotopic data, I have been trying to find a download for rtview. I tried to go to the following link: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/rtview. However, this like will not work for me. Is there anywhere else that I can download rtview? Thanks, Nick

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autorecon2-wm without mri_fill in v4.5?
by Caspar M. Schwiedrzik 22 Jul '13

22 Jul '13

Hi Freesurfer Experts, I am working on a primate anatomy and I am having problems with the white matter filling in the temporal lobe in version 4.5. I manually edited wm.mgz and recreated filled.mgz using mri_fill. I then manually edited filled.mgz. However, when I then run autorecon-all -autorecon2-wm, all my manual edits in filled.mgz are overwritten. Is there a way to autorecon2-wm without mri_fill in v4.5? Thank you very much, Caspar

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