Freesurfer February 2012

freesurfer@nmr.mgh.harvard.edu

124 participants
199 discussions

Interactions between categorical and continuous variables
by Katherine Reiter 15 Feb '12

15 Feb '12

Hey freesurfers, I'm interested in running an interaction between a continuous and categorical variable, covarying for another categorical variable. I understand that this analysis is not possible through the QDEC GUI so I am working through the command line group analysis and setting up the contrast matrix. Discrete Factors: Group with 2 levels: Patient and Control Gender with 2 levels: Male and Female Continuous variables: Age Meaning, I have 8 Regressors: 1: PatientMale intercept 2: PatientFemale intercept 3. ControlMale intercept 4. ControlFemale intercept 5: PatientMale age 6: PatientFemale age 7. ControlMale age 8. ControlFemale age In order to look at the interaction of group and age, covarying for gender, would the matrix be: 0 0 0 0 -.5 .5 -.5 .5 However, this matrix seems looks more like a difference in slopes comparison and less like an interaction. Any help would be much appreciated! Thanks, Katie

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monte carlo simulation question
by Govindarajan, Koushik Athreya 15 Feb '12

15 Feb '12

Hello group, I am running the multiple comparisons simulation after my mri_glmfit finished. I see that it went through all the iterations and then quit with the following error message it could not find the talairach.xfm file in my average brain. I did not use the fsaverage and instead created my own template based on average normal brains. I went back and checked my average subject folder and indeed, there is no talairach.xfm file in there. I also see that the 'tmp' directory in there has a lot of the intermediate files. I do not recollect seeing an error message when I created my average brain. So, was not sure what was going on. My 2 questions are: 1. How can I finish the rest of the make_average_subject processing to create my talairach.xfm file? Do I have to start from scratch or can I continue from where it left off? 2. The same question with the mri_glmfit-sim analysis also. Is there a way for me to continue from where it left off using the new talairach.xfm file or do I have to start from scratch and go through so many hours of simulation again? Thanks a lot for all the help Koushik Govindarajan

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make average subject error
by Adam David Felton 15 Feb '12

15 Feb '12

Hello, I have run into an error while trying to make an average subject using 200 scans. When I ran this command I got an error: *make_average_subject --xform talairach.xfm --out 200avgsub --subjects* The error: Allocing output mri_concat(40491) malloc: *** mmap(size=262144) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIalloc(256, 256, 256): could not allocate 262144 bytes for 13726th slice Cannot allocate memory WARNING: could not create average segmentation for aseg ... ... but continuing make_average_volume done The average sub folder does not contain aseg.mgz and p.aseg.mgz files. *The version of Freesurfer I am using:* v 1.313.2.6 2010/08/04 15:50:56 nicks *My memory:* 8 GB 1333 MHz DDR3 *Hard-drive:* 276.49 GB free MAC OS X v 10.6.8 I have scoured the archives for the answer to my question to no avail. All of the answers before seemed to revolve around versions of Freesurfer which I expect were updated. Nick Schmanksy wrote "sorry, i meant to say include the --no-aseg flag with make_average_volume (make_average_subject is just a wrapper script that calls make_average_volume and make_average_surface)." But wouldn't this prevent segmentation? Is there a way to then add segmentation after? Sorry if these are novice questions (as I am a novice). Thank you, Adam

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Fixing Bad Output From the Talairach Registration
by Miguel Ferreira 15 Feb '12

15 Feb '12

Hello freesurfer group, I'm having trouble in the fixing bad output from the talairach registration step. When I click on the "Save Reg" button to save a transformation that I make the console just hangs on this message "UnZeroing CRAS for fstal output xfm". Anyone have any ideia what the problem might be? Thanks.

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ERROR mri_volcluster
by Antonella Kis 15 Feb '12

15 Feb '12

Dear Doug, Can I run the mri_volcluter without --reg ? I am asking this because when I run: mri_glmfit-sim \ --glmdir GroupAnalysis_ADC.glmdir \ --grf 3 neg \ --cwpvalthresh .05 \ --overwrite gives me the following error (I also attached the log file): Also, does neg means now that Class1 (=controls)< Class2 (=Patients) for my MD values? Many thanks. Antonella $Id: mri_glmfit-sim,v 1.36.2.1 2011/03/28 15:46:10 greve Exp $ Tue Feb 14 14:28:11 EST 2012 Linux EW-LNX3 2.6.32.26-175.fc12.x86_64 #1 SMP Wed Dec 1 21:39:34 UTC 2010 x86_64 x86_64 x86_64 GNU/Linux elysa setenv SUBJECTS_DIR /media/2Tra/Antonella_2011/DTI_FS/GLM_CVS FREESURFER_HOME /usr/local/freesurfer Original mri_glmfit command line: cmdline mri_glmfit --y GroupAnalysis-ADC-MASKED.ANAT+CVS-to-avg35.mgz --fsgd GroupAnalysis.fsgd dods --C contrast.mtx --glmdir GroupAnalysis_ADC.glmdir DoSim = 0 UseCache = 0 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = 2.252995 mri_volcluster --in GroupAnalysis_ADC.glmdir/contrast/sig.mgh --mask GroupAnalysis_ADC.glmdir/mask.mgh --reg /usr/local/freesurfer/subjects/fsaverage/mri.2mm/reg.2mm.dat --no-fixmni --cwsig GroupAnalysis_ADC.glmdir/contrast/grf.th3.neg.sig.cluster.mgh --sum GroupAnalysis_ADC.glmdir/contrast/grf.th3.neg.sig.cluster.summary --ocn GroupAnalysis_ADC.glmdir/contrast/grf.th3.neg.sig.ocn.mgh --cwpvalthresh .05 --seg fsaverage aparc+aseg.mgz --fwhmdat GroupAnalysis_ADC.glmdir/fwhm.dat --sign neg --thmin 3 Adjusting threshold for 1-tailed test. If the input is not a -log10(p) volume, re-run with --no-adjust. Using defalt ctab /usr/local/freesurfer/FreeSurferColorLUT.txt INFO: loading mask volume: GroupAnalysis_ADC.glmdir/mask.mgh INFO: MRIbinarize01(): nhits = 961260 Found 961260 voxels in mask ERROR: Input volume voxel dimensions do not match those in the registration file. If the input volume is in bshort/bfloat format, check that there is an accompanying bhdr file.

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Repost Clusters locations
by Antonella Kis 15 Feb '12

15 Feb '12

Hi Doug, By "more exactly location" I want to say that I would like to have the MNI coordinates and also the annotation location or the nearst cortical label (for example precentral or lateraloccipital, etc). Also,after I ran the mri_segstatsI don't have the MNI coordinates. Thanks for helping. Antonella From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> To: Antonella Kis <atorok9(a)yahoo.com>; freesurfer <freesurfer(a)nmr.mgh.harvard.edu> Sent: Tuesday, February 14, 2012 1:18 PM Subject: Re: [Freesurfer] Clusters locations Antonella Kis wrote: > Hi Doug, > > 1) I would like to report the MNI coordinates and also a more exactly > region I mean if possible tto find exactly where in the > Left-Cerebral-White-Matter and Right-Cerebral-White-Matter my cluster > is located. What do you me by "exactly where"? The nearest cortical label? The fiber bundle? > > 2)Can you please tell me if for the mean diffusivity I should use the > simulation with the perm (as I use for the FA due to the fact that is > not so Gaussian) option or it is OK to use the grf option. I think you can use GRF for this as it corresponds to a normal contrast in a GLM. Note that the permutation is the stronger (but more conservative) test. > > > 3) Can you please explain what exactly means for my clusters if I hit > the positive sign under DISPLAY in Qdec? I mean if I compare the > cortical thickness between two classes: controls vs. Patients and > I am not interested in the sex or age differences just differences > between the two classes will positive mean clusters where cortical > thickness graeter in Class 1 than Class2 (Class1>Class2)? > > I have C = +1 -1 and my Class 1 = controls while Class2 = PAtients. Positive is Controls > Patients doug > > > THANKS YOU. > Antonella > ------------------------------------------------------------------------ > *From:* Douglas Greve <greve(a)nmr.mgh.harvard.edu> > *To:* Antonella Kis <atorok9(a)yahoo.com>; free surfer > <freesurfer(a)nmr.mgh.harvard.edu> > *Sent:* Tuesday, February 14, 2012 9:59 AM > *Subject:* Re: [Freesurfer] Clusters locations > > Hi Antonella, what level of detail do you want? I think that most > people are reporting MNI coordinates. > doug > > On 2/13/12 2:44 PM, Antonella Kis wrote: >> Hi Doug, >> >> I will be very grateful if you give me some directions regarding how >> I can get my clusters location ( my output is too general telling me >> just Left-Cerebral-White-Matter and Right-Cerebral-White-Matter) and >> the coordinates (MNI) when I run the: >> >> mri_volcluster --in GroupAnalysis_pos.glmdir/contrast/sig.mgh --mask >> GroupAnalysis_pos.glmdir/mask.mgh --no-fixmni --cwsig >> GroupAnalysis_pos.glmdir/contrast/permcsd.sig.cluster.mgh --sum >> GroupAnalysis_pos.glmdir/contrast/permcsd.sig.cluster.summary --ocn >> GroupAnalysis_pos.glmdir/contrast/permcsd.sig.ocn.mgh --cwpvalthresh >> .09 --seg cvs_avg35 aseg.mgz --csdpdf >> GroupAnalysis_pos.glmdir/contrast/permcsd.pdf.dat --csd >> GroupAnalysis_pos.glmdir/csd/permcsd.j001-contrast.csd --vwsig >> GroupAnalysis_pos.glmdir/contrast/permcsd.sig.voxel.mgh >> >> and >> >> >> mri_segstats --seg permcsd.sig.ocn.mgh --exclude 0 --i >> /media/2Tra/Antonella_2011/DTI_FS/GLM_CVS/GroupAnalysis-FA-MASKED.ANAT+CVS-to-avg35.nii.gz >> --avgwf fa.avg.dat --sum permcsd.sig.cluster.summary >> >> >> Thank you. >> Antonella > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)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 Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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recon-all error (nu_correct problem)
by EK Kim 15 Feb '12

15 Feb '12

Hello, Freesurfers, I got an error message when I trying to use recon-all function in freesurfer on the XUbuntu system installed on the VirtualBox on a Windows 7 machine. I searched the e-mailing list but I can't find any answers. My problem is related to the nu_correct and nu_estimate_np_and_em. However, nu_correct and nu_estimate_np_and_em were located to exact path (/home/virtualuser/freesurfer/mni/bin). echo $MNI_DATAPATH, echo $MNI_PERL5LIB showed exact path. In addition, I already tried to use fixup_mni_paths. Could anyone give me an advice for fixing up this problem? Thanks in advance. Cheers, EK error message! -------------------------------------------------------------------------------------------- #@# Nu Intensity Correction Wed Feb 15 01:23:24 EST 2012 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /home/virtualuser/Desktop/DATA/30664304/mri /home/virtualuser/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.18 2011/03/02 20:16:39 nicks Exp $ Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux Wed Feb 15 01:23:25 EST 2012 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@fishie (i686-pc-linux-gnu) on 2010-02-20 at 20:19:13 tmpdir is ./tmp.mri_nu_correct.mni.17682 /home/virtualuser/Desktop/DATA/30664304/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.17682/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.17682/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $ reading from orig.mgz... TR=0.00, 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.17682/nu0.mnc... -------------------------------------------------------- Iteration 1 Wed Feb 15 01:23:37 EST 2012 nu_correct -clobber ./tmp.mri_nu_correct.mni.17682/nu0.mnc ./tmp.mri_nu_correct.mni.17682/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.17682/0/ [virtualuser@FreeSurfer:/home/virtualuser/Desktop/DATA/30664304/mri/] [2012-02-15 01:23:37] running: /home/virtualuser/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.17682/0/ ./tmp.mri_nu_correct.mni.17682/nu0.mnc ./tmp.mri_nu_correct.mni.17682/nu1.imp Assertion failed at line 827 in file templates/CachedArray.cc nu_estimate_np_and_em: crashed while running volume_stats (termination status=256) nu_correct: crashed while running nu_estimate_np_and_em (termination status=256) ERROR: nu_correct Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux

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nu_correct error
by Karla Zúñiga 15 Feb '12

15 Feb '12

Hello, Freesurfers, I got an error message when I trying to use recon-all function in freesurfer on the Mandriva 2008 system installed on a Linux Dell precision T3500 Machine. I was unable to find an answer in the mailing list. my SUBJECTS_DIR is : /neurospin/grip/protocols/MRI/childrenNS5_7y_Monzalvo_2012/Subject/ (from the "neurospin/grip" network in my lab). I am using the 5.1 version of freesurfer. An the command line I ran was the following : recon-all -s ab080228 -all This is error message I received : Iteration 1 jeu fév 9 10:53:09 CET 2012 nu_correct -clobber ./tmp.mri_nu_correct.mni.3269/nu0.mnc ./tmp.mri_nu_correct.mni.3269/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.3269/0/ nu_correct: Command not found. ERROR: nu_correct Linux is145054 2.6.22.19-server-2mdv #1 SMP Mon May 5 21:13:00 EDT 2008 i686 Intel(R) Xeon(R) CPU E5540 @ 2.53GHz GNU/Linux recon-all -s ab080228 exited with ERRORS at jeu fév 9 10:53:09 CET 2012 For more details, see the log file /neurospin/grip/protocols/MRI/childrenNS5_7y_Monzalvo_2012/subtry/ab080228/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Thank you for your help, Karla Monzalvo -- Karla Monzalvo Inserm U.992 - Neuroimagerie Cognitive CEA/SAC/DSV/I2BM/NeuroSpin Bât 145, Point Courrier 156 F-91191 GIF/YVETTE, FRANCE Tél : 33 (0)1 69 08 90 66 Fax : 33 (0)1 69 08 79 73 karla.monzalvo(a)cea.fr http://www.unicog.org/

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Question about hippocampal-subfield probability map
by Joshua Lee 15 Feb '12

15 Feb '12

Dear experts, The hippocampal-subfield are expressed as probability maps. For each subfield, each voxel is assigned a probability of inclusion on a scale of [0-255]=[0-1]. However, If I were to select only voxels from each subfield's probability map corresponding to a >50% chance (i.e. mri_binarize -min 150), then I would expect that no subfield would overlap with another (i.e. a voxel shouldn't have greater than 50% probability of belonging CA1, AND a greater than 50% probability of belonging to CA4-DG. However it appears that this is not the case, and overlap does occur. Thus, unless I messed up, subfields are not mutually exclusive. Have I got this right? And if so, how do I obtain binary maps of subfields with no overlap? Thanks Josh

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Re: [Freesurfer] Extraction of vertex identifiers from a significant cluster
by Douglas N Greve 14 Feb '12

14 Feb '12

You can do it in tksurfer using the Tools->CustomFill, then select fill to threshold (or something like that). I think there's a way to do it in QDEC too. Try looking at the tutorial. doug Florsek wrote: > Hi Doug, > > do I have to manually draw the new label or can I somehow custom fill > the cluster in tksurfer to create a label? > Thank you for your quick answer! > > Florian > > > Am 14.02.12 19:37, schrieb Douglas N Greve: >> Hi Florian, you can save the cluster as a label. This is a text file >> with xyz values for each vertex. The xyz values are in mni305 space. >> doug >> >> Florsek wrote: >>> Dear all, >>> >>> We have performed a cluster analysis in Qdec and found a significant >>> vertex-cluster after correction for multiple testing using the Monte >>> Carlo simulation. Now, we would like to extract the (unique) >>> identifiers of all vertices that form the significant cluster. We >>> then would like to look up the spatial information (x, y, z) of >>> these vertices. Our final aim is to map the vertices to an atlas >>> which is different from that of Desikan. >>> >>> Is this a way suitable to achieve our aim? >>> >>> Many thanks for your help in advance! >>> >>> Best regards, >>> >>> Florian >>> >>> >>> >> > > -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Freesurfer February 2012