Freesurfer May 2013

freesurfer@nmr.mgh.harvard.edu

174 participants
299 discussions

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

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

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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

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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

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error in longitudinal processing "dimension mismatch"
by Qi Wu 21 May '13

21 May '13

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?

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Can I mask out NaN vertices for smoothing?
by Glen Lee 21 May '13

21 May '13

[image: Inline image 1] Hi freesurfer experts, > > I'm dealing with an issue with smoothing on surface data that > unfortunately contain 'NaN' in the ventral temporal region (which is a > region that we are interested in). > > This may be due to the slab data acquisition, where the bottom of the > slice meant to be at the bottom of the tomporal lobe for every subject. > Apparently, we didn't quite succeed in this as we saw missing data points > that are filled with 'NaN' during 2D reconstruction in some subjects' 2D > data. > > In the cartoon above, the yellow color depicts vertices with 'NaN' in the > ventral temporal region , and you can easily see how this is affected by > smoothing (4mm FWHM), such that a large swath of ventral regions have NaNs > after smoothing. > > I've tried smoothing both with and without --cortex flag, but the results > were the same regardless. > > So, the best bet would be masking out those NaN vertices before smoothing > and I wonder if there is any way of doing it in freesurfer. > Otherwise, I may need to consider smoothing outside of the freesurfer > using Matlab (but I have no experience about this approach). > > If anyone has previously dealt with this issue (hope I'm not the only one) > and know how to get around with it either inside or outside of the > freesurfer, please help me. > -Glen > > > > > >

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brain parenchymal fraction calculation
by Ritobrato Datta 21 May '13

21 May '13

Hi All, I am using freesurfer 5.1 and I want to compute the brain parenchymal fraction (GM+WM/GM+WM+ventricularCSF). In aseg.stats, I get the whole GM vol and I can also get the total ventricular CSF by adding the vols of different ventricles. But I am confused abt the terminology - CorticalWhiteMatterVol is this volume the total white matter in the brain or does this exclude something ? Please advise. Best Ri

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Autorecon2 missing ribbon.mgz error?
by Jamie Hanson 21 May '13

21 May '13

Hi Freesurfer List- My group just recently installed 5.3.0 and I kept running into the same error during -autorecon2 where mri_segstats could find ribbon.mgz. I was slightly stumped on the issue, as the ReconAllTable says mri_segstats isn't run until autorecon3? I attached my bugr output and also my log file for one subject (I have about 10+ subjects that error in the same way). It looks like -inflate2 finished fine (which was previously one of the last steps in autorecon2). Any thoughts? Any help is greatly appreciated! Thanks much! Best, jamie. -- Jamie L. Hanson Waisman Laboratory for Brain Imaging & Behavior | Child Emotion Research Lab University of Wisconsin - Madison 1500 Highland Avenue Madison, WI 53705 Email: jamielarshanson(a)gmail.com Homepage: http://brainimaging.waisman.wisc.edu/~hanson/ --------------------------------------------------------------------- FREESURFER_HOME: /apps/x86_64_sci6/freesurfer-latest Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 RedHat release: Scientific Linux release 6.2 (Carbon) Kernel info: Linux 2.6.32-279.22.1.el6.x86_64 x86_64 ---------------------------------------------------------------------

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missing DOSS option in QDEC
by Andreas Berger 21 May '13

21 May '13

Hi surfers, as of FreeSurfer version 5.3, i am missing the option to choose between DOSS and DODS design in QDEC. The radiobuttons in the design tab are no longer there. The default behaviour, judging from the results, seems to be DODS. Has this option been removed? regards, Andreas

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question abt optic chaism volume
by Ritobrato Datta 21 May '13

21 May '13

Hi All, I am using freesurfer 5.1 for my analysis. In FS 5.1, does the Supratentorial volume include the Optic chaism volume ? Please let me know. Thanks Ri

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Freesurfer May 2013