Freesurfer

freesurfer@nmr.mgh.harvard.edu

3 participants
30090 discussions

inflate surface until sphere
by Lo, Yiping 23 Jul '13

23 Jul '13

Hi Freesurfer, I am tring to inflate pial surface until the sphere. I have tried mris_inflate and set the number of iteration to be large. However, it seems to inflate the brain to a limit and no further inflation. I have also tried mris_sphere, but it seems not what I want. It more likely to map the pial surface onto a sphere and inflate it along the sphere. I should say in advance, I only got .pial file. What should I do to get what I want? Best Wishes, Yi-Ping DISCLAIMER: This email is intended solely for the addressee. It may contain private and confidential information. If you are not the intended addressee, please take no action based on it nor show a copy to anyone. In this case, please reply to this email to highlight the error. Opinions and information in this email that do not relate to the official business of Nottingham Trent University shall be understood as neither given nor endorsed by the University. Nottingham Trent University has taken steps to ensure that this email and any attachments are virus-free, but we do advise that the recipient should check that the email and its attachments are actually virus free. This is in keeping with good computing practice.

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help needed with fsgd file and contrast matrix for correlation analysis
by Robert Schulz 23 Jul '13

23 Jul '13

Dear all, I have 2 short questions regarding a correlation analysis I'd like to perform with mri_glmfit (surface-based DTI data are correctly preprocessed and concatenated into mgh file, statistics are performed on fsaverage space). 1) I'd like to look for correlation between the surface-data and a behavioural measure BEH in one group, correcting for gender and age. I set up the following fsgd: GroupDescriptorFile 1 Class Male Class Female Variables BEH Age Input subj1 Male 0.76 72 Input subj2 Male 0.44 67 Input subj3 Female 0.33 80 .... My contrast file is: 0 0 0.5 0.5 0 0 (referring to the FSGD examples Fsgd2G2V, GLM with 2*(2+1) columns). Is this setup correct? If not, how would I have to set up fsgd and C? 2) In a next step, I'd like to answer the question (now including another group2): Where does group1 (OLD) show increased correlation with BEH compared to group2 (YOUNG), correcting for GENDER and AGE within each group. I wonder because AGE is the relevant difference between both groups. GroupDescriptorFile 1 Class OldMale Class OldFemale Class YoungMale Class YoungFemale Variables BEH Age Input subj1 OldMale 0.76 72 Input subj2 OldMale 0.44 67 Input subj3 OldFemale 0.33 80 .... Input subj11 YoungMale 0.80 20 Input subj12 YoungMale 0.55 21 Input subj13 YoungFemale 0.44 31 .... My contrast file would look like: 0 0 0 0 0.5 0.5 -0.5 -0.5 0 0 0 0 (referring to GLM with 4*(2+1) columns). Correct? Thank you very much for your help! I am really not sure whether I did it correctly and whether I can trust my results. -- Besuchen Sie uns auf: www.uke.de _____________________________________________________________________ Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg Vorstandsmitglieder: Prof. Dr. Martin Zeitz (Vorsitzender), Prof. Dr. Dr. Uwe Koch-Gromus, Astrid Lurati (komm.), Joachim Prölß, Matthias Waldmann (komm.) _____________________________________________________________________ SAVE PAPER - THINK BEFORE PRINTING

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Errors when launching SPM8
by xxxxx xxxxx 23 Jul '13

23 Jul '13

Hi all, Someone asked about the following error message when opening SPM8 in Matlab back in December: Initialising SPM...Error using fileparts Too many output arguments. Error in cfg_util>local_initapps (line 1217) [p n e v] = fileparts(appcfgs{k}); Error in cfg_util (line 587) local_initapps; Error in spm_jobman (line 149) cfg_util('initcfg'); % This must be the first call to cfg_util Error in spm (line 344) spm_jobman('initcfg'); Error while evaluating uicontrol Callback I get the exact same errors (on MATLAB2013a newly installed on iMac). Please can someone tell me if this problem was solved? Thanks!

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[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

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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

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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

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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!

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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

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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

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