Freesurfer November 2015

freesurfer@nmr.mgh.harvard.edu

138 participants
239 discussions

ERROR: Invalid FreeSurfer license key
by Neda Mohammadi 23 Nov '15

23 Nov '15

Dear FreeSurfer experts, I have downloaded and installed FreeSurfer. I am trying to run the installation tests, and a number of them do not work (e.g., tkmedit, recon etc). the error I get is as follows: ERROR: Invalid FreeSurfer license key found in license file /usr/local/freesurfer/.license If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. I recieved the license key 14 hours ago and copy/pasted the 3 lines exactly as sent to me. I would be very grateful if you could help me. Thanks in advance, -- *Best Regards,* *Neda*

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exctracting grey matter
by Sherihane Bensemmane 20 Nov '15

20 Nov '15

Hi, I am using freesurfer for non_human primate. I did the segmentation in freesurfer , at the end i have the wm.mgz but not grey matter since the command to get it during segmentation doesn't work in monkey brain. in the forlder /surf/ i have all files such as lh/rh.pial, curv, sulc, white. Since I am also using SPM and some toolbox to conduct my connectivity data i need good segmentation, so i wanted to use the files in surf, the pial and white to get the grey matter information and then convert it to a volume file. I've been looking for solutions, but didn't find anything, can you help? how shall i proceed to get my grey matter mask from my segmentation, in the native space. Thank you, Best regards, Sherihane KUL

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malloc error running glm_glmfit-sim
by Lawrence Ryner 20 Nov '15

20 Nov '15

Hi, I'm a new FS user just trying to run through the tutorials. In the Group Analysis tutorial, doing the multiple comparisons correction, when I run mri_flmfit-sim I get a malloc() memory corruption error. The output is below. I am running the VirtualBox Xubuntu 12.04 Freesurfer 5.3.0 version on a PC with 64-bit Windows 7 and 3472 MB of RAM (assigning more RAM than that causes the VirtualBox to crash). I setup a shared folder on my E: drive to store the buckner tutorial data. Had to add fsuser to vboxsf using usermod to be able to access the data from xubuntu. Also can't setup symbolic links on a shared folder so I had to copy the fsaverage dataset to the E: drive. Not sure if that is a good way to set things up but I couldn't find much guidance on the best way to do this. Found lots of mailing list threads related to this error, but none of them actually seem to provide a solution. Any help would be appreciated. ********* mri_glmfit-sim \ > --glmdir lh.gender_age.glmdir \ > --cache 4 neg \ > --cwpvalthresh 0.05 \ > --2spaces cmdline mri_glmfit --y lh.gender_age.thickness.10.mgh --fsgd gender_age.fsgd dods --C lh-Avg-thickness-age-Cor.mtx --surf fsaverage lh --cortex --glmdir lh.gender_age.glmdir SURFACE: fsaverage lh log file is lh.gender_age.glmdir/cache.mri_glmfit-sim.log cd /media/sf_Data/tutorial_data/buckner_data/tutorial_subjs/group_analysis_tutorial/glm /usr/local/freesurfer/bin/mri_glmfit-sim --glmdir lh.gender_age.glmdir --cache 4 neg --cwpvalthresh 0.05 --2spaces $Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $ Wed Nov 18 13:15:50 EST 2015 Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 20:41:14 UTC 2012 i686 i686 i386 GNU/Linux fsuser setenv SUBJECTS_DIR /media/sf_Data/tutorial_data/buckner_data/tutorial_subjs/group_analysis_tutorial FREESURFER_HOME /usr/local/freesurfer Original mri_glmfit command line: cmdline mri_glmfit --y lh.gender_age.thickness.10.mgh --fsgd gender_age.fsgd dods --C lh-Avg-thickness-age-Cor.mtx --surf fsaverage lh --cortex --glmdir lh.gender_age.glmdir DoSim = 0 UseCache = 1 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = 13.914377 CSD /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm14/neg/th40/mc-z.csd mri_surfcluster --in lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh --csd /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm14/neg/th40/mc-z.csd --mask lh.gender_age.glmdir/mask.mgh --cwsig lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.cluster.mgh --vwsig lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.voxel.mgh --sum lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.cluster.summary --ocn lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.ocn.mgh --oannot lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.ocn.annot --annot aparc --csdpdf lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.pdf.dat --cwpvalthresh 0.05 --o lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.masked.mgh --no-fixmni --bonferroni 2 --surf white Creating CDFs from CSD files csd->threshsign = -1 thsign = neg, id = -1 version $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve Exp $ hemi = lh srcid = lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh srcsubjid = fsaverage srcsurf = white srcframe = 0 thsign = neg thmin = 4 thmax = -1 fdr = -1 minarea = 0 Bonferroni = 2 xfmfile = talairach.xfm nth = -1 outid = lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.masked.mgh MGH ocnid = lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.ocn.mgh MGH sumfile = lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.cluster.summary subjectsdir = /media/sf_Data/tutorial_data/buckner_data/tutorial_subjs/group_analysis_tutorial FixMNI = 0 Found 149953 vertices in mask Found 149953 vertices in mask Found 149953 points in clabel. ------------- XFM matrix (RAS2RAS) --------------- /media/sf_Data/tutorial_data/buckner_data/tutorial_subjs/group_analysis_tutorial/fsaverage/mri/transforms/talairach.xfm 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; ---------------------------------------------------- Reading source surface /media/sf_Data/tutorial_data/buckner_data/tutorial_subjs/group_analysis_tutorial/fsaverage/surf/lh.white Done reading source surface Reading annotation /media/sf_Data/tutorial_data/buckner_data/tutorial_subjs/group_analysis_tutorial/fsaverage/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Computing metric properties Loading source values number of voxels in search space = 149953 Done loading source values (nvtxs = 163842) overall max = 3.62547 at vertex 153106 overall min = -11.4482 at vertex 134036 surface nvertices 163842 surface area 65417.097656 surface area 65416.648438 Computing voxel-wise significance CSDpvalMaxSigMap(): found 94908/163842 above 0 Adjusting threshold for 1-tailed test. If the input is not a -log10(p) volume, re-run with --no-adjust. Searching for Clusters ... thmin=4.000000 (3.698970), thmax=-1.000000 (-1), thsignid=-1, minarea=0.000000 Found 32 clusters Max cluster size 7917.266602 Pruning by CW P-Value 0.05 Saving thresholded output to lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.masked.mgh Saving cluster numbers to lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.ocn.mgh Saving cluster pval lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.cluster.mgh Constructing output annotation Writing annotation lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.ocn.annot mri_segstats --seg lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.ocn.mgh --exclude 0 --i /media/sf_Data/tutorial_data/buckner_data/tutorial_subjs/group_analysis_tutorial/glm/lh.gender_age.thickness.10.mgh --avgwf lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.y.ocn.dat --sum /tmp/mri_glmfit-sim.junk.4706 $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --seg lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.ocn.mgh --exclude 0 --i /media/sf_Data/tutorial_data/buckner_data/tutorial_subjs/group_analysis_tutorial/glm/lh.gender_age.thickness.10.mgh --avgwf lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.y.ocn.dat --sum /tmp/mri_glmfit-sim.junk.4706 sysname Linux hostname xubuntu-VirtualBox machine i686 user fsuser UseRobust 0 Loading lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/cache.th40.neg.sig.ocn.mgh Loading /media/sf_Data/tutorial_data/buckner_data/tutorial_subjs/group_analysis_tutorial/glm/lh.gender_age.thickness.10.mgh Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 22 segmentations Computing statistics for each segmentation 1 1 8074 8074.000 2 2 17658 17658.000 3 3 3247 3247.000 4 4 388 388.000 5 5 2404 2404.000 6 6 1596 1596.000 7 7 911 911.000 8 8 937 937.000 9 9 450 450.000 10 10 1002 1002.000 11 11 1084 1084.000 12 12 1010 1010.000 13 13 451 451.000 14 14 483 483.000 15 15 441 441.000 16 16 565 565.000 17 17 246 246.000 18 18 184 184.000 19 19 235 235.000 20 20 386 386.000 21 21 203 203.000 Reporting on 21 segmentations Computing spatial average of each frame 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20*** glibc detected *** mri_segstats: malloc(): memory corruption: 0x2e90cb88 *** ********************** -Lawrence This email and/or any documents in this transmission is intended for the addressee(s) only and may contain legally privileged or confidential information. Any unauthorized use, disclosure, distribution, copying or dissemination is strictly prohibited. If you receive this transmission in error, please notify the sender immediately and return the original. Ce courriel et tout document dans cette transmission est destiné à la personne ou aux personnes à qui il est adressé. Il peut contenir des informations privilégiées ou confidentielles. Toute utilisation, divulgation, distribution, copie, ou diffusion non autorisée est strictement défendue. Si vous n'êtes pas le destinataire de ce message, veuillez en informer l'expéditeur immédiatement et lui remettre l'original.

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longitudinal recon-all
by Lisa Delalande 20 Nov '15

20 Nov '15

Hi, I would like to know if, in doing a longitudinal study (i.e. 2 or 3 MRI each subjects), this is usual to have many file for one subject (see the picture, 5 file for one subject with two MRI : a0009_1 = MRI 1 and a0009_2 = MRI 2) ? Because in the future I will have around 100 subjects with 3 MRI each so I will have a lot of file to handle with ... Thanks in advance ! Friendly Lisa

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Error message with lh.BA1.label
by BAUTISTA-PERPINYA Maximilia (ETU VIE) 20 Nov '15

20 Nov '15

Dear all, I get the same error when running any subject. I think it may be related to the step concerning: fsaverage/label/lh.BA1.label. I cannot detect where the problem is coming from. I thought that it was an issue with my environment, because there is a double slash in FREESURFER_HOME and all the other environments: FREESURFER_HOME /usr/local//freesurfer FSFAST_HOME /usr/local//freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local//freesurfer/subjects MNI_DIR /usr/local//freesurfer/mni but I just saw that this shouldn't be a problem (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2009-December/012860…) Could you help me identify this error? I copy-pasted the output of bugr and other information. You will find attached also the recon-all.log of one of the subjects. output of bugr: --------------------------------------------------------------------- FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 RedHat release: CentOS release 6.7 (Final) Kernel info: Linux 2.6.32-573.7.1.el6.x86_64 x86_64 --------------------------------------------------------------------- 1) subject name: it happens with any subject 2) the entire command-line executed recon-all -autorecon1 -autorecon2 -autorecon3 -i $g -s $subjid where: $g = /path/to/nii/file and $subjid = subject ID 3) the error message generated from the recon-all.log: SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local//freesurfer Loading source label. Invalid argument ERROR reading /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label Linux biosrv1 2.6.32-573.7.1.el6.x86_64 #1 SMP Tue Sep 22 22:00:00 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux recon-all -s B_LU_02_MRI_E_T0 exited with ERRORS at Sat Nov 14 06:33:30 CET 2015 from the recon-all.error: $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ /usr/local//freesurfer/bin/recon-all PWD /usr/local/freesurfer/subjects/B_LU_02_MRI_E_T0/label CMD mri_label2label --srcsubject fsaverage --srclabel /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label --trgsubject B_LU_02_MRI_E_T0 --trglabel ./lh.BA1.label --hemi lh --regmethod surface Best regards, Max -- Maximilià Bautista-Perpinyà, BSc Master student at Joint Master in Neuroscience (JMN) Université de Strasbourg (in partnership with Universität Freiburg and Universität Basel) & Master Intern at Biological and Personality Psychology Laboratory Department of Psychology, Universität Freiburg maximila.bautista-perpinya(a)etu.unistra.fr

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Unsupported TransferSyntax in DICOMs: problem with "mri_convert"
by Baker, Justin T.,M.D.,Ph.D. 19 Nov '15

19 Nov '15

Hi FreeSurfer list, Lately, we have noticed that a bunch of DICOMs obtained on our 3T Tim Trio (at McLean Hospital) are getting labeled with TransferSyntax IDs that are causing DICOM unpacking scripts (like mri_convert) to fail. In particular, the offending TransferSyntaxIDs appear to be "1.2.840.10008.1.2.4.90" and "1.2.840.10008.1.2.4.91", according to what we can glean from the DICOM headers. It seems like the "JPEG Lossless Only" syntax is the real problem, but in any case, we are not finding any suitable workarounds for this issue. Any advice on how to proceed would be much appreciated. We are hoping that a patch to "mri_convert" would solve the problem. Best, Justin

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Generating a correlation map from a functional contrast ...
by Joseph Andreano 19 Nov '15

19 Nov '15

Hi Freesurfer experts, I'd like to generate a correlation map showing the strength of correlation between a behavioral value and the value of a functional contrast between two conditions. >From previous cortical thickness analysis, I know that if I use the -notask tag on mkanalysis, I can use a file that includes all of my behavioral values and correlate them with, say, a thickness value. But when I use -notask, I can't specify a paradigm file, without which I can't specify contrasts. Is there a way to make this correlation map versus a functional value drawn from a contrast? This seems simple, conceptually, but I haven't been able to implement it. Thanks in Advance, Joe _________________________________ Joseph M. Andreano, PhD Postdoctoral Researcher Interdisciplinary Affective Science Laboratory Massachusetts General Hospital _________________________________

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modify QDEC smoothing options
by Hirsch, Gabriella 19 Nov '15

19 Nov '15

Hey Freesurfer experts, I had a quick question. Is there any way to modify QDEC in such a way to have other options other than 0, 5, 10, 15, 20 etc, for smoothing? I know I would also have to -qcache the data for the desired smoothing too but I was wondering if anyone had done this before? Any ideas would be appreciated! Thanks, Gabriella * Confidentiality Notice: If you have received this e-mail in error, please immediately notify the sender by replying to this e-mail, keeping the original message intact. Please do not "Reply All." After replying to the sender, please delete this e-mail from your files. Information contained in this e-mail is only for the use of the individual(s) or entity for whom it is intended, even if addressed incorrectly.

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Skullstripping leaves a little bit of dura
by Guido Orlando Pascariello 19 Nov '15

19 Nov '15

Hi Experts I'm using Freesurfer to quantify some subcortical volumes and cortical areas. I have been preprocessing my data using 'recon-all autorecon1' I have a question About Skullstripping. It is leaving a little bit of dura behind the head. I found '-gcut' which is useful to solve it but it has some cons. I don't want to view the data, I just want to get the quantifications, so I wonder if this pices of dura could affect the '-tessellate' step. I'll be grateful if you can help Being all for now, I await a reply Guido PASCARIELLO Facultad de Ingeniería - Universidad Nacional de Entre Ríos Argentina

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FSFAST First-Levels: Fast_selxavg3() ERROR
by Afzal, Afsana 19 Nov '15

19 Nov '15

Hi, I'm doing first level analysis in FSFAST and I'm consistently getting the following error when running fast_selxavg3(): Saving to /autofs/space/lilli_002/users/DARPA-FAST/hc016/msit/msit.analysis.sm04.b0dc.mni305/rho1mn.sm.nii.gz SmoothOnly requested, so exiting now Found 0 voxels with corrected AR1 > 0.90 Whitening Attempted to access indedge(0); index must be a positive integer or logical. Error in fast_histeq (line 53) if(indedge(end) ~= ny) indedge = [indedge ny]; end Error in fast_selxavg3 (line 640) [edge bincenter binmap] = fast_histeq(nrho1mn.vol(indmask), flac0.acfbins); >> ------------------------------------------ ERROR: fast_selxavg3() failed\n I'm only getting the error for mni305 (lh and rh analyses are completing without a hitch). I have re-preprocessed and attempted to run the analysis several times, but without any success. It's not clear what the error means or what's causing it. Thank you for any help, Afsana ______________________________ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences 149 13th St, Room 2612 Charlestown, MA 02129 Phone: 617-643-5129 Fax: 617-726-4078

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Freesurfer November 2015