Freesurfer

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30088 discussions

About GroupAnalysis
by bowang21＠mail.ustc.edu.cn 26 Apr '12

26 Apr '12

Dear All, I am learning GroupAnalysis and I have some problem about the vector that embodies the hypothesis we want to test(such as:0 0 0.5 0.5).I just want to know how each number of the vector involve in the calculating process of mri_glmfit.That is, I want to acquire some materials of how mri_glmfit process the data? Bobo

2 1

mri_convert - returns different image size
by Popescu, V. 26 Apr '12

26 Apr '12

Dear all, I want to use N3 on nifti images, and I have different versions installed on two machines. On one machine I have an older version of N3 (1.7.2.2) which uses mri_convert version 4 and everything works fine. On the other machine I have N3 version 1.12 which uses mri_convert version 5; this one returns a 256/256/256 image volume instead of the original-like volume. Is there anything I can do to "fix" it or is there a problem if I just use mri_convert version 4 instead of 5 for the newer N3? Thank you very much in advance! Best regards, Veronica Popescu VU University Medical Center, Department of Radiology De Boelelaan 1118, 1081 HZ Amsterdam, The Netherlands Room PK -1 X 108 Phone: +31 (0) 204 444 596 Fax: +31 (0) 204 440 397

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longitudinal data check problem
by Charlotte Bernard 25 Apr '12

25 Apr '12

Dear Freesurfer users, I try to visualize my longitudinal data for one subject whit the command line given in the freesurfer website: freeview -v 00049_T1/mri/norm.mgz -f 00049_T1/surf/lh.pial:edgecolor=red 00049_T1/surf/rh.pial:edgecolor=red 00049_T1/surf/lh.white:edgecolor=blue 00049_T1/surf/rh.white:edgecolor=blue I can open the norm.mgz but then the sofware crash for pial and white surf! I have that error message: MatrixMultiply: m2 is null! I don't understand where the problem is? Can somebody help me? Thanks for all, Charlotte

2 1

trakula segmentation fault
by Viviana Siless 25 Apr '12

25 Apr '12

Hello, I'm trying to run trac-all prec and I'm getting a segmentation fault error. Loading streamlines from /media/vivi/code/freesurfer/trctrain/trc032/dlabel/mni/lh.cst_AS.flt.trk Loading streamline start ROI from /media/vivi/code/freesurfer/trctrain/trc033/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz Loading streamline end ROI from /media/vivi/code/freesurfer/trctrain/trc033/dlabel/mni/lh.cst_AS_roi2.flt.nii.gz Loading streamlines from /media/vivi/code/freesurfer/trctrain/trc033/dlabel/mni/lh.cst_AS.flt.trk INFO: Rejected 0 streamlines for straying off mask INFO: Rejected 0 streamlines for reversing direction Segmentation fault Linux vivi-ThinkStation-C20X 2.6.38-8-generic #42-Ubuntu SMP Mon Apr 11 03:31:24 UTC 2011 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Wed Apr 4 18:24:21 CEST 2012 - When I look at the trak-all.error I see this error: ------------------------------ SUBJECT 000000112288Proc DATE Wed Apr 4 18:24:21 CEST 2012 USER vivi HOST vivi-ThinkStation-C20X PROCESSOR x86_64 OS Linux Linux vivi-ThinkStation-C20X 2.6.38-8-generic #42-Ubuntu SMP Mon Apr 11 03:31:24 UTC 2011 x86_64 x86_64 x86_64 GNU/Linux $Id: trac-preproc,v 1.17.2.5 2011/05/20 06:51:51 ayendiki Exp $ /media/vivi/code/freesurfer/bin/trac-preproc PWD /media/vivi/code/freesurfer CMD /media/vivi/code/freesurfer/bin/dmri_train --outdir /media/vivi/images/freesurfer/000000112288Proc/dlabel/mni --out lh.cst_AS_avg33_mni_flt rh.cst_AS_avg33_mni_flt lh.unc_AS_avg33_mni_flt rh.unc_AS_avg33_mni_flt lh.ilf_AS_avg33_mni_flt rh.ilf_AS_avg33_mni_flt fmajor_PP_avg33_mni_flt fminor_PP_avg33_mni_flt lh.atr_PP_avg33_mni_flt rh.atr_PP_avg33_mni_flt lh.ccg_PP_avg33_mni_flt rh.ccg_PP_avg33_mni_flt lh.cab_PP_avg33_mni_flt rh.cab_PP_avg33_mni_flt lh.slfp_PP_avg33_mni_flt rh.slfp_PP_avg33_mni_flt lh.slft_PP_avg33_mni_flt rh.slft_PP_avg33_mni_flt --slist /tmp/subj33.000000112288Proc.16360.txt --trk dlabel/mni/lh.cst_AS.flt.trk dlabel/mni/rh.cst_AS.flt.trk dlabel/mni/lh.unc_AS.flt.trk dlabel/mni/rh.unc_AS.flt.trk dlabel/mni/lh.ilf_AS.flt.trk dlabel/mni/rh.ilf_AS.flt.trk dlabel/mni/fmajor_PP.flt.trk dlabel/mni/fminor_PP.flt.trk dlabel/mni/lh.atr_PP.flt.trk dlabel/mni/rh.atr_PP.flt.trk dlabel/mni/lh.ccg_PP.flt.trk dlabel/mni/rh.ccg_PP.flt.trk dlabel/mni/lh.cab_PP.flt.trk dlabel/mni/rh.cab_PP.flt.trk dlabel/mni/lh.slfp_PP.flt.trk dlabel/mni/rh.slfp_PP.flt.trk dlabel/mni/lh.slft_PP.flt.trk dlabel/mni/rh.slft_PP.flt.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.flt.nii.gz dlabel/mni/lh.cst_AS_roi2.flt.nii.gz dlabel/mni/rh.cst_AS_roi1.flt.nii.gz dlabel/mni/rh.cst_AS_roi2.flt.nii.gz dlabel/mni/lh.unc_AS_roi1.flt.nii.gz dlabel/mni/lh.unc_AS_roi2.flt.nii.gz dlabel/mni/rh.unc_AS_roi1.flt.nii.gz dlabel/mni/rh.unc_AS_roi2.flt.nii.gz dlabel/mni/lh.ilf_AS_roi1.flt.nii.gz dlabel/mni/lh.ilf_AS_roi2.flt.nii.gz dlabel/mni/rh.ilf_AS_roi1.flt.nii.gz dlabel/mni/rh.ilf_AS_roi2.flt.nii.gz dlabel/mni/fmajor_PP_roi1.flt.nii.gz dlabel/mni/fmajor_PP_roi2.flt.nii.gz dlabel/mni/fminor_PP_roi1.flt.nii.gz dlabel/mni/fminor_PP_roi2.flt.nii.gz dlabel/mni/lh.atr_PP_roi1.flt.nii.gz dlabel/mni/lh.atr_PP_roi2.flt.nii.gz dlabel/mni/rh.atr_PP_roi1.flt.nii.gz dlabel/mni/rh.atr_PP_roi2.flt.nii.gz dlabel/mni/lh.ccg_PP_roi1.flt.nii.gz dlabel/mni/lh.ccg_PP_roi2.flt.nii.gz dlabel/mni/rh.ccg_PP_roi1.flt.nii.gz dlabel/mni/rh.ccg_PP_roi2.flt.nii.gz dlabel/mni/lh.cab_PP_roi1.flt.nii.gz dlabel/mni/lh.cab_PP_roi2.flt.nii.gz dlabel/mni/rh.cab_PP_roi1.flt.nii.gz dlabel/mni/rh.cab_PP_roi2.flt.nii.gz dlabel/mni/lh.slfp_PP_roi1.flt.nii.gz dlabel/mni/lh.slfp_PP_roi2.flt.nii.gz dlabel/mni/rh.slfp_PP_roi1.flt.nii.gz dlabel/mni/rh.slfp_PP_roi2.flt.nii.gz dlabel/mni/lh.slft_PP_roi1.flt.nii.gz dlabel/mni/lh.slft_PP_roi2.flt.nii.gz dlabel/mni/rh.slft_PP_roi1.flt.nii.gz dlabel/mni/rh.slft_PP_roi2.flt.nii.gz --bmask /media/vivi/images/freesurfer/000000112288Proc/dlabel/mni/aparc+aseg_mask.nii.gz --fa /media/vivi/images/freesurfer/000000112288Proc/dmri/mni/dtifit_FA.flt.nii.gz --ncpts 5 --debug - If I run that command, I get the same (of course): INFO: Rejected 0 streamlines for straying off mask INFO: Rejected 0 streamlines for reversing direction Segmentation fault Can anybody give me an idea of the problem? I run recon-all and finished without errors. I attach the log file, the error file, and my dmrirc file. Please let me know if you need anything else. Thanks in advance! Viviana Siless -- Parietal Team, INRIA Saclay Neurospin, Centre CEA de Saclay 91191 Gif sur Yvette – FRANCE

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Re: [Freesurfer] bbregister for fmri FEAT data
by Erlend Hodneland 25 Apr '12

25 Apr '12

Both the fmri data registered to orig is mismatched, and also the original raw fmri data are mismatched with orig, see the link here showing our raw data (fmri, orig and 152MNI) shown in fslview http://vedlegg.uib.no/?id=297a1242fa82b4b7565b470806254c5a It is orig.nii converted from orig.mgz that we show yes. Erlend What images are mismatched? Specifically, which anatomical image are you loading into fslview? If you have not loaded the orig.mgz (converted to nii), then there will be be a mismatch. doug On 04/24/2012 04:29 AM, Erlend Hodneland wrote: > Hi again, > > We are trying to do the same as was done in Trachtenberg et al 2012 > (Neurobiology of Aging), ie opt.the commonly used FLIRT+FNIRT registration in > FEAT with BBreg: > > "For group analysis, functional data were registered, via the high resolution > anatomical image, to the Montreal Neurological Institute (MNI) standard > brain. Functional data were aligned to the anatomical image initially using > FMRIB's Linear Image Registration Tool, (FLIRT) ([Jenkinson and Smith, 2001] > <http://www.sciencedirect.com/science/article/pii/S0197458010004926#bib27> > and[Jenkinson et al., 2002] > <http://www.sciencedirect.com/science/article/pii/S0197458010004926#bib28>), > then optimized using the Boundary-Based Registration (BBR) approach (Greve > and Fischl, 2009 > <http://www.sciencedirect.com/science/article/pii/S0197458010004926#bib21>). > Registration from anatomical to standard space was carried out using FMRIB’s > Non-Linear Image Registration Tool (FNIRT)." > > > That is, flirt from fmri --> brain, then initializing bbregister fmri --> > brain by the previous flirt registration, then flirt and fnirt from brain --> > standard space and finally fmri --> standard space and putting all these > transformations together. > > > However, our images are orientad as follows from top -> bottom (fmri, orig, > 152MNI): > > http://vedlegg.uib.no/?id=297a1242fa82b4b7565b470806254c5a > > As shown in the previous communication, when we directly apply the images to > the registration the results are oriented incorrectly, as the input images. > > Can you recommend a specific solution to overcome the orientation mismatch in > these images which is compatible with the registration tasks? > > > Thank you for your patience and help! > > > All best > > E.H. > > > Hi Erlend, while the images in the tkregister2 pics are oriented > correctly the registration is way off. What images are you loading into > fslview? You'll need to convert the orig.mgz into nii and load that to > check the registration. > doug > > On 04/22/2012 04:16 AM, Erlend Hodneland wrote: > > Hi again, > > > > the registration looks fine in tkregister2, but is apparently wrong in > > fslview (and also mricron). See the attached files (as link from > > http://vedlegg.uib.no/?id=399ad2cce1a3138f8eb4f6a06f4acfc4) showing > > screenshots of fslview and tkregister2. How can this be explained, and > > how can we visualize the correct orientation in fslview? > > What does this misalignment influence any further processing with > > fnirt and concatenation of the affine transformation fields? > > > > This is our command we run for bbregister: > > > > bbregister --s subj_505 --mov vol0001.nii.gz --reg register-test.dat > > --init-fsl --t2 --o test.nii.gz > > > > where vol0001 is the first volume in the fmri sequence and is flipped > > to align with LAS (as the highres). > > > > Thank you for your kind help, > > > > Erlend Hodneland > > > > ean that it is in the wrong orientation? It should be in > > the same orientation as the anatomical. How does the reg look in > > tkregister2? Note that fslview can display volumes in odd orientations > > even when the orientation is correct. > > doug > > > > On 04/13/2012 03:31 AM, Erlend Hodneland wrote: > > > Hi, > > > > > > we are trying to register fmri FEAT data (example_func.nii) to the > > > anatomical scan (processed in Freesurfer) using bbregister to opt. > > > the affine registration before running FNIRT. > > > > > > However, the orientation of the registered image is flipped around and > > > is incorrect after applying bbregister. > > > > > > We have tried: > > > > > > 1) bbregister --s subj_501 --mov example_func.nii.gz --reg > > > register.dat --init-header --bold --o example_func2highres-fs.nii > > > 2) bbregister --s subj_501 --mov example_func.nii.gz --reg > > > register.dat --init-fsl --bold --o example_func2highres-fs.nii > > > 3) bbregister --s subj_501 --o example_func2highres-fs.nii --feat > > > "myfeatdirectory" > > > 4) tkregister2 --mov example_func.nii --regheader --reg tkreg.dat > > > (this one looks correct) > > > followed by > > > bbregister --s subj_501 --mov example_func.nii.gz --reg register.dat > > > --init-reg tkreg.dat --bold --o example_func2highres-fs.nii > > > > > > 5) reorienting to match the highres: > > > > > > fslorient -swaporient example_func > > > fslswapdim example_func x -y z example_func_swap (correct > > > orientation) > > > > > > followed by > > > bbregister --s subj_501 --mov example_func_swap.nii.gz --reg > > > register.dat --init-fsl --bold --o example_func_swap2highres-fs.nii > > > > > > with the output being flipped in wrong orientation for all options. > > > > > > We would greatly appreciate if you have any suggestions for how to > > > overcome this problem! > > > > > > Cheers/Sincerly/All best > > > > > > Erlend Hodneland > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > 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 Centergr...(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

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Parcellation Colorscale
by Baum, Sarah H 25 Apr '12

25 Apr '12

Hi- I'm looking to compare two parcellations (one is a stroke patient with her brain as is, the other is the same subject with the lesion "fixed" run as a separate subject). It would be helpful if the parcellations would color the same area the same color, but currently every single ROI is colored differently than the corresponding parcellation in the other subject's brain. I looked up the color table in the .annot file, and the RGB coordinates listed for each region are exactly the same for each surface volume. Is there any easy way to make the colors the same? If it helps— I use AFNI/SUMA for visualizing data. Thanks in advance, Sarah Sarah H. Baum Ph.D. Candidate, Neuroscience Sarah.H.Baum(a)uth.tmc.edu w: 713.500.5089 c: 571.225.7007

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Re: [Freesurfer] Fwd: Freesurfer Digest, Vol 98, Issue 29
by Andrew C Yourich 25 Apr '12

25 Apr '12

Sadly, I haven't been able to determine the problem yet. I have tested the exact command that was suggested in both the Mac 5.1.0 version as well as the Windows/Ubuntu 5.1.0 virtual machine version, and neither have seemed to expand correctly when viewed in freeview. I won't have access to a machine running Linux natively until tomorrow. A colleague who runs Freesurfer 5.0 and 5.1.0 on a Linux machine is going to work with me to test if he has this issue as well. Do you know if there have been any changes to the code of the mris_expand binary since 4.0.2? If not, we may try using the mris_expand from that version on the recon-all results from a 5.1.0 segmentation to see if the issue truly is the expand binary or not. Any other suggestions you all have would be appreciated. Thanks, Andrew ________________________________________ From: Alexandre Gramfort [gramfort(a)nmr.mgh.harvard.edu] Sent: Tuesday, April 24, 2012 3:24 PM To: Andrew C Yourich Subject: Fwd: Fwd: Freesurfer Digest, Vol 98, Issue 29 hi, have you fixed your problem? I still don't manage to make it work… thanks Alex ---------- Forwarded message ---------- From: Alexandre Gramfort <gramfort(a)nmr.mgh.harvard.edu> Date: Mon, Apr 23, 2012 at 7:10 PM Subject: Re: Fwd: Freesurfer Digest, Vol 98, Issue 29 To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Cc: Nick Schmansky <nicks(a)nmr.mgh.harvard.edu>, ayourich(a)uab.edu, Krish Subramaniam <krish(a)nmr.mgh.harvard.edu>, Ruopeng Wang <rpwang(a)nmr.mgh.harvard.edu> > not sure about the mac, I'll cc Nick, Krish and Ruopeng so that they can > answer. could be due to my update of XCode this morning but things work fine with freeview -f lh.white -v ../mri/T1.mgz on my mac with lion. sorry for the noise > I built my own in ~fischl/dev/freesurfer/bin/freeview. Sure, put the > surfaces somewhere I can look at them and I'll take a look see the files in : /homes/6/gramfort/cluster/work/data/MNE-sample-data/subjects/fsaverage/surf/lh.white.expanded that's the sample data we use for MNE. the log: $ mris_expand -thickness lh.white 0.5 lh.white.expanded using distance as a % of thickness expanding surface lh.white by 50.0% of thickness and writing it to lh.white.expanded reading thickness... ending sse = 4485.856144 nrounds = 6 writing expanded surface to lh.white.expanded... writing group avg surface area 822 cm^2 into surface file surface expansion took 27 minutes and 15 seconds. Alex 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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Fwd: Load Brodmann surface area into inflated surface
by _andreia_＠sapo.pt 25 Apr '12

25 Apr '12

(sorry, here it is for the list again) ----- Mensagem encaminhada de Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> ----- Data: Mon, 23 Apr 2012 15:30:17 -0400 (EDT) De: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Assunto: Re: [Freesurfer] Load Brodmann surface area into inflated surface Para: _andreia_(a)sapo.pt Hi Andreia, can you cc the list so others can answer? I just took a look and label_area is so old that is uses ?h.smoothwm without any ability to change it. I think there are probably other tools around that will do it, but someone else will know. If not I'll fix label_area to be less obstinate. cheers Bruce On Mon, 23 Apr 2012, _andreia_(a)sapo.pt wrote: > Hi Bruce, > > Thanks for the help! How do I know from which surface, i.e. pial or > wm is the command label_area getting the value? I compared V1 > surface area given in the BA.stats and the one I get with the > command, and the late is higher (V1 from BA.stats= 2081 and from > label_area = 2592.272). > > Now, imagine the follwing: I have no differences in cortical > thickness (CT) and surface area of this BA but the volume is > different (with p values near 0.04...). Also, other BA shows no > differences in CT neither in volume, but with differences showing up > in the surface area (with lower p value here). Since the values for > volume and surface are computed in different ways, can this account > for these odd results? > > Thanks! > Andreia > > > Citando Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>: > >> Hi Andreia, >> >> yes, they will always shrink since the label contains every point that >> could possibly be in the BA, no matter how unlikely. I'll try to find time >> to automatically threshold the BAs so that they have the average area of >> the individual examples, but for now V2 is probably around .7 and MT around >> .4 I think. And yes, I would use ?h.sulc as the background gray scale. The >> volume of the BAs would be computed using both surfaces, but the surface >> area can be from either one. I think we use the white by default, but you >> can use label_area to measure on whatever surface you want. >> >> cheers >> Bruce >> >> >> On Mon, 23 Apr 2012, >> _andreia_(a)sapo.pt wrote: >> >>> (forgot to do answer all, here it goes for the list too) >>> >>> >>> Citando _andreia_(a)sapo.pt: >>> >>>> Hi Bruce, >>>> >>>> The ideia is to show one control subject vs. one patient inflated surface >>>> with BA surface (not volume, sorry) to show the difference >>>> (reduced surface >>>> area in one patient). Loading the relevant labels worked (I have the >>>> statistics shown in bar graphs, the images are only for visualizing the >>>> difference between controls and patients). When I threshold the labels in >>>> the subject's inflated surface they shrink a lot, is this supposed to >>>> happen? >>>> >>>> The BA are V1, V2 and MT. What is the thresghold for V2? >>>> >>>> And is it correct to load ?h.sulc in a gray scale to have the usual cortex >>>> representation, or I should do it other way? >>>> >>>> >>>> And getting back to my previous email: >>>> >>>> Another question is, how is the volume of the BA calculated? Is it >>>>>> from the surface-based stream? >>>>>> >>>>>> And, which surface area is the on in the output of the BA stats? Is it >>>>>> the pial or wm? >>>> >>>> Thanks, >>>> Andreia >>>> >>>> >>>> Citando Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>: >>>> >>>>> Hi Andreia >>>>> >>>>> sorry, I don't understand. What do you mean when you say you want to " >>>>> show the resulting Brodmann area (only 3 BA) volume in the inflated >>>>> surface of my subjects". Do you mean just to show what portion of the >>>>> surface is in each of 3 Brodmann areas? That you would do by loading the >>>>> relevant labels, although you will probably want to threshold them >>>>> differently (e.g. V1 you could threshold at .9 which is 90% and it would >>>>> have about the surface area of an individual, while MT would need to be >>>>> closer to .4 or .5). Or do you actually mean the volume of gray matter >>>>> within each BA? If the latter, it's just 3 numbers/subject, so I would >>>>> think you would want a scatter plot or something, not a map on the >>>>> surface. >>>>> >>>>> cheers >>>>> Bruce >>>>> >>>>> >>>>> On Mon, 23 Apr 2012, _andreia_(a)sapo.pt wrote: >>>>> >>>>>> Hi all, >>>>>> >>>>>> I'm sorry if these questions have already been covered here, but I've >>>>>> looked into the archives and still can't do what I need (and since I'm >>>>>> running out of time for this task I decided to post here): >>>>>> >>>>>> I'm using version 5.0.0. >>>>>> >>>>>> I want to show the resulting Brodmann area (only 3 BA) volume in the >>>>>> inflated surface of my subjects to show the differences between >>>>>> patients and controls (for visualization purpose only). I've managed >>>>>> to overlay the volume in the curvature menu but this is for the entire >>>>>> cortex and I can't show the values bar. How can I show the volume of >>>>>> only 3 BAs and have the scale bar? >>>>>> >>>>>> Another question is, how is the volume of the BA calculated? Is it >>>>>> from the surface-based stream? >>>>>> >>>>>> And, which surface area is the on in the output of the BA stats? Is it >>>>>> the pial or wm? >>>>>> >>>>>> Thanks in advance, >>>>>> Andreia >>>>>> >>>>>> _______________________________________________ >>>>>> 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 > > > ----- Fim de mensagem reenviada -----

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labels export
by Gabriel Gonzalez Escamilla 25 Apr '12

25 Apr '12

4 7

Running Tracula -bedpostx and -path
by Richard Binney 24 Apr '12

24 Apr '12

Hi Anastasia, I ran bedpost directly: bedpostx dmri It seemed to run fine, not exiting with any errors. the only thing that concerned me was that the last output in the terminal was 50 slices processed [when I have 54] queing post-processing stage then it exited. It seemed to run rather quicker than I expected and I expected it to at least output "all slices processed" and/or something after queing post Is there any reason to be concerned? Furthermore, in running the -path, the terminal window constantly outputting... ERROR: Degenerate spline segment 58 81 24 56 69 24 ...... ERROR: Degenerate spline segment ...... but it seems to continue on without exiting. Is there any reason to be concerned about this? what doe sit mean? Thanks for your help R

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