Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30096 discussions

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. >>>> >>>> >>>> >> >> >> > >

1 0

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

2 3

mri_glmfit application in the two-stage longitudinal approach
by Qi Wu 21 May '13

21 May '13

Hi Martin, Now I move onto the mri_glmfit step (still within the two stage method). The on-line tutorial for doing this is not very clear. "The output of the first stage is stored in the subject-template (base), already in fsaverage space. Simply replace the thickness file with your long.thickness-pc1fit (etc) and run your analysis. " For the normal group analysis, one mgh file (the stacked image for all subject for each hemisphere) is created under the SUBJECT folder after the mri_prepro, and the mri_surf2surf steps. However, I assume that after the long_mris_slopes command, the mgh file (lh.long.thickness-spc.fwhm5.fsaverage.mgh, etc.) saved within each subject's base/surf folder is just for that subject. Right? My question is: what is the right way to process these subject specific mgh files within mri_glmfit? How to design the FSGD file for this particular glmfit? I appreciate your clarification on this issue, and I do believe that it would be very helpful if you could add your clarification onto the online tutorial for the two stage method ( http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel) Many thanks Keith On Wed, May 8, 2013 at 4:28 PM, Martin Reuter <mreuter(a)nmr.mgh.harvard.edu>wrote: > Hi Keith, > > your longitudinal qdec file looks OK. Something must have gone wrong > before (in the processing, e.g. maybe the base was reprocessed and the > longs were not updated or things were renamed?) > > I would create a new directory with only this subject, then start from > scratch. create both cross (kp5 and kp5b), the base (kp5_base) and both > longs with the correct naming . Then check if the long_mris_slopes command > still fails. > > Best, Martin > > > On 05/01/2013 12:11 PM, Qi Wu wrote: > > Dear Freesurfer experts, > > I have a dataset of 2 time points. I ran into problems when I tried to use > the two-stage approach to pull out statistics such as the rate of change in > Freesurfer 5.1. > > I could not even get the first stage working. The error messages I got > were “ERROR: MRISar1: Surf/Src dimension mismatch” “ERROR -11 : mri_glmfit > did not work?” > > I did further trouble-shooting for this particular message "nv1 = 140942, > nv1 = 143525", and I found out that "143525" was in the "base" folder > (kp5_base), and "140942" was for the two longitudinally registered images > (kp5.long.kp5_base, and kp5b.long.kp5_base). > > The command line I used was : “long_mris_slopes --qdec > ./qdec/AS_long_qdec.dat --meas thickness --hemi lh --do-avg --do-rate > --do-pc1 --do-spc --do-stack --do-label --time weeks –nosmooth”. > > The first three lines in the qdec file: > > “fsid fsid-base weeks age sex FSS avgPain > > kp5 kp5_base 0 48 0 4.1 7 > > kp5b kp5_base 20 48 0 8.6 6” > > This error was similar to what was in a previous post ( > https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-June/024576.html… joost janssen Jun 29, 2012). I tried to fix any similar problems, but > still wasn’t able to get it working. > > What else could I have been doing wrong? > > The on screen error output is provided as follows > > Many thanks > > Keith > > Postdoctoral fellow > Toronto Western Hospital > Toronto, Ontario > Canada > > *********************************** > > Parsing the qdec table: ./qdec/AS_long_qdec.dat > > Working in SUBJECTS_DIR: > /data/keith/freesurferdata/subjects_longitudinal_5.1_old > > Subject-Template: kp5_base > > INFO: 2 TPs in kp5_base , mean age: 10.0 > > =============================================================================== > > > SUBJECT kp5_base Intersecting Within-Subject Cortex Label > > cp > /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5.long.kp5_base/label/lh.cortex.label > /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/label/lh.long.cortex.label > > > mris_label_calc intersect > /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5b.long.kp5_base/label/lh.cortex.label > /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/label/lh.long.cortex.label > /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/label/lh.long.cortex.label > > > LabelWrite: saving to > /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/label/lh.long.cortex.label > > =============================================================================== > > > SUBJECT kp5_base Stackinbg Within-Subject Maps > > mri_concat > /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5.long.kp5_base/surf/lh.thickness > /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5b.long.kp5_base/surf/lh.thickness > --o > /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/surf/lh.long.thickness-stack.mgh > > ninputs = 2 > > Checking inputs > > nframestot = 2 > > Allocing output > > Done allocing > > nframes = 2 > > Writing to > /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/surf/lh.long.thickness-stack.mgh > > =============================================================================== > > > SUBJECT kp5_base Running Within-Subject GLM > > Writing ./tmp-kp5_base_lh_thickness_6PR2rH/X-long.mat ... > > mri_glmfit --y > /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/surf/lh.long.thickness-stack.mgh > --X ./tmp-kp5_base_lh_thickness_6PR2rH/X-long.mat --allow-zero-dof > --no-contrasts-ok --surf kp5_base lh --label > /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/label/lh.long.cortex.label > --glmdir ./tmp-kp5_base_lh_thickness_6PR2rH/glm > > Reading source surface > /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/surf/lh.white > > Number of vertices 143525 > > Number of faces 287046 > > Total area 91438.851562 > > AvgVtxArea 0.637094 > > AvgVtxDist 0.873064 > > StdVtxDist 0.245806 > > $Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $ > > cwd /data/keith/freesurferdata/subjects_longitudinal_5.1_old > > cmdline mri_glmfit --y > /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/surf/lh.long.thickness-stack.mgh > --X ./tmp-kp5_base_lh_thickness_6PR2rH/X-long.mat --allow-zero-dof > --no-contrasts-ok --surf kp5_base lh --label > /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/label/lh.long.cortex.label > --glmdir ./tmp-kp5_base_lh_thickness_6PR2rH/glm > > sysname Linux > > hostname davissvr1.uhnres.utoronto.ca > > machine x86_64 > > user qwu > > FixVertexAreaFlag = 1 > > UseMaskWithSmoothing 1 > > OneSampleGroupMean 0 > > y > /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/surf/lh.long.thickness-stack.mgh > > logyflag 0 > > X ./tmp-kp5_base_lh_thickness_6PR2rH/X-long.mat > > usedti 0 > > labelmask > /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/label/lh.long.cortex.label > > maskinv 0 > > glmdir ./tmp-kp5_base_lh_thickness_6PR2rH/glm > > IllCondOK 0 > > ReScaleX 1 > > DoFFx 0 > > Creating output directory ./tmp-kp5_base_lh_thickness_6PR2rH/glm > > Loading y from > /data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/surf/lh.long.thickness-stack.mgh > > Saving design matrix to ./tmp-kp5_base_lh_thickness_6PR2rH/glm/Xg.dat > > Normalized matrix condition is 1 > > Matrix condition is 10 > > Found 131455 points in label. > > ERROR: mri_reshape: number of elements cannot change > > nv1 = 143525, nv1 = 140942 > > Pruning voxels by thr: 0.000000 > > Found 134956 voxels in mask > > Saving mask to ./tmp-kp5_base_lh_thickness_6PR2rH/glm/mask.mgh > > Reshaping mriglm->mask... > > ERROR: mri_reshape: number of elements cannot change > > nv1 = 140942, nv1 = 143525 > > search space = 91439.090793 > > DOF = 0 > > Starting fit and test > > Fit completed in 0.0042 minutes > > Computing spatial AR1 on surface > > ERROR: MRISar1: Surf/Src dimension mismatch. > > ERROR -11 : mri_glmfit did not work? > > > > _______________________________________________ > Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- > Dr. Martin Reuter > 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. >

2 1

usage of mri_segstats
by Fang CAO 21 May '13

21 May '13

Hello list! Can I use the command mri_segstats to calculate the statistics across multiple subjects? If yes, how to do it? Thank you in advance, Fang

2 1

recon-all errors: v5.0.0
by Sudhin A. Shah 21 May '13

21 May '13

1) BEST FITNESS (M) is 984.24263 mri =0.000 curv = 4.318 unmri = -1001.515 ( f=0.00 , v=0.00 , c=4.32 , q= 8.64 ) ( f=0.00 , v=0.00 , c=4.32 , q= 8.64 ) 63 patches have been generated - 38 self-intersected max face = 36973(40653) - loop = 46 (73) - ntries = [27,14799] ERROR: _FindFacePath: could not find path! Linux sudhin-Precision-WorkStation-690 2.6.35-32-generic #67-Ubuntu SMP Mon Mar 5 19:39:49 UTC 2012 x86_64 GNU/Linux recon-all -s xtyzW exited with ERRORS at Tue May 21 05:48:38 EDT 2013 =============== 2)*************************WATERSHED************************** Sorting... mri_watershed Error: Problem in the COG calculation: T1.mgz may not contain properly normalized white-matter. Confirm that T1.mgz has enough white-matter voxels of value 110. If white-matter contains few if any voxels of value 110, try adding wm control-points to nu.mgz, and re-run recon-all. Linux sudhin-Precision-WorkStation-690 2.6.35-32-generic #67-Ubuntu SMP Mon Mar 5 19:39:49 UTC 2012 x86_64 GNU/Linux recon-all -s cbvfB exited with ERRORS at Fri May 17 17:45:23 EDT 2013 ============== 3)CORRECTING DEFECT 2 (vertices=30163, convex hull=6211) error in the retessellation normal vector of length zero at vertex 88778 with 0 faces vertex 88778 has 0 face No such file or directory Linux sudhin-Precision-WorkStation-690 2.6.35-32-generic #67-Ubuntu SMP Mon Mar 5 19:39:49 UTC 2012 x86_64 GNU/Linux recon-all -s ghjG exited with ERRORS at Thu May 16 05:11:49 EDT 2013

1 0

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

21 May '13

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. >>> >>> >>> > > >

1 0

issue with pial surface in orbitofrontal cortex
by Caspar M. Schwiedrzik 21 May '13

21 May '13

Hi! I am failing to get a proper pial surface in orbitofrontal cortex. See attached screenshot. This is NHP data, processed with version 4.5. I am not sure how to proceed here, as there is no clear with matter. Any advice would be appreciated. Thanks! Caspar

3 21

error: can't allocate region / Cannot allocate memory
by Vincent Koppelmans 21 May '13

21 May '13

Dear FreeSurfer experts, I am trying to create a template for a longitudinal analysis. For each subject I have 7 time points. The resolution of the T1 images is 1.0x0.98x0.98 mm. The first step (i.e. the cross-sectional processing) finished without errors for all participants for all time points. The second step (i.e. the template creation) stopped while processing the third time point (see attached log file). My Machine is running OSX 10.8.3, with FreeSurfer version 5.1.0. I have 16 gb of memory installed. During the run FS was using up only 3gb and there was still 6gb available. How can I solve this problem? Thanks, Vincent LOG FILE: Tue May 7 13:58:41 EDT 2013 /Volumes/Data/tmp/Bedrest/FreeSurfer/8936 /Applications/freesurfer/bin/recon-all -base 8936 -tp 8936_01 -tp 8936_02 -tp 8936_03 -tp 8936_04 -tp 8936_05 -tp 8936_06 -tp 8936_07 -all subjid 8936 setenv SUBJECTS_DIR /Volumes/Data/tmp/Bedrest/FreeSurfer FREESURFER_HOME /Applications/freesurfer Actual FREESURFER_HOME /Applications/freesurfer build-stamp.txt: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 Darwin x.kines.umich.edu 12.3.0 Darwin Kernel Version 12.3.0: Sun Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64 cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited descriptors 256 memorylocked unlimited maxproc 709 PhysMem: 1733M wired, 4205M active, 1281M inactive, 7219M used, 9155M free. (here some stuff happens which I have left out) Finished TP : 2 ===================================================== Working on TP 3 Registration::computeMultiresRegistration - Gaussian Pyramid - Gaussian Pyramid - initial transform: Ti = [ ... 0.9996153712273 0.0026029755827 -0.0276110433042 0.1370086669922 -0.0021083820611 0.9998371005058 0.0179268959910 9.5177154541016 0.0276532080024 -0.0178617853671 0.9994579553604 10.5185699462891 0 0 0 1.0000000000000 ] - initial iscale: Ii =1 Resolution: 4 S( 16 16 16 ) T( 16 16 16 ) Iteration(f): 1 -- diff. to prev. transform: 1.73616 Iteration(f): 2 -- diff. to prev. transform: 0.231302 Iteration(f): 3 -- diff. to prev. transform: 0.247707 Iteration(f): 4 -- diff. to prev. transform: 0.0780292 Iteration(f): 5 -- diff. to prev. transform: 0.0629118 max it: 5 reached! Resolution: 3 S( 32 32 32 ) T( 32 32 32 ) Iteration(f): 1 -- diff. to prev. transform: 1.54023 Iteration(f): 2 -- diff. to prev. transform: 0.389993 Iteration(f): 3 -- diff. to prev. transform: 0.121733 Iteration(f): 4 -- diff. to prev. transform: 0.180449 Iteration(f): 5 -- diff. to prev. transform: 0.0662501 max it: 5 reached! Resolution: 2 S( 64 64 64 ) T( 64 64 64 ) Iteration(f): 1 -- diff. to prev. transform: 0.749486 Iteration(f): 2 -- diff. to prev. transform: 0.0109516 Iteration(f): 3 -- diff. to prev. transform: 0.00196896 < 0.01 :-) Resolution: 1 S( 128 128 128 ) T( 128 128 128 ) Iteration(f): 1 -- diff. to prev. transform: 0.421039 Iteration(f): 2 -- diff. to prev. transform: 0.00943852 < 0.01 :-) Resolution: 0 S( 256 256 256 ) T( 256 256 256 ) Iteration(f): 1 -- diff. to prev. transform: 0.102893 Iteration(f): 2mri_robust_template(40563) 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 228th slice Cannot allocate memory Darwin x.kines.umich.edu 12.3.0 Darwin Kernel Version 12.3.0: Sun Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64 recon-all -s 8936 exited with ERRORS at Tue May 7 14:23:40 EDT 2013 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ---- Vincent Koppelmans, PhD University of Michigan School of Kinesiology Neuromotor Behavior Lab 401 Washtenaw Ave. Ann Arbor, MI 48109-2214 email: vkoppel(a)umich.edu phone: 734-615-5155

3 3

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer