Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

fMRI maps without clusters on ventricle
by stdp82＠virgilio.it 23 Nov '15

23 Nov '15

Hi list,I'm performing fcMRI-seed based by FS-FAST.After group comparison and Monte Carlo correction I obtained cortical and subcortical clusters in pos and neg maps.On subcortiacal maps, significant clusters at grf.th1.3.pos.sig.cluster.nii.gz showed some voxels on ventricle or white matter. At 3.pos.sig.cluster.nii.gz the maps are clearly defined.Thus, I'd like to delete voxel on white matter or ventricle to shows activation only on grey matter from grf.th1.3.pos.sig.cluster.nii.gz.Is it possible to do it?Thanks Stefano

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sheered CT in tkregister2
by Borzello, Mia 23 Nov '15

23 Nov '15

Hi Freesurfers, I am trying to coregister with a high-res CT, but for some reason am getting a very sheered image when I am in tkregister. Should I use another CT? Thank you! 1) MG93 2)tkregister2 --s MG93_SurferOutput --mov ct.mgz --reg spm.reg.dat --surf orig 3) no error message, just a sheered image FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0 'build-stamp.txt file does not exist! This appears to be a very old version of FreeSurfer! RedHat release: CentOS release 6.7 (Final) Kernel info: Linux 2.6.32-573.3.1.el6.x86_64 x86_64 NMR Center info (/space/freesurfer exists): machine: huygens SUBJECTS_DIR: /autofs/space/huygens_001/users/mia/subjects PWD: /autofs/space/huygens_001/users/mia/subjects/MG93_SurferOutput/mri ssh huygens setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects cd /autofs/space/huygens_001/users/mia/subjects/MG93_SurferOutput/mri

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creating ROIs for cortical thickness measurements
by Elissa Ash 23 Nov '15

23 Nov '15

Dear Freesurfers, I am new to freesurfer and I am trying to understand how to best perform a cortical thickness analysis for an ROI that is not pre-defined in freesurfer, such as the IFJ or V5. Should I create a surface ROI label using tksurfer (or freeview) or should I create an ROI in volume space? What is the difference? Which way is methodologically correct? Can I obtain the average cortical thickness for my ROI if it is created as a label? Also, is there a tutorial explaining how to draw an anatomical ROI that is not designated in either atlas, either as a label or as a volume? I would like to compare cortical thickness of my ROI to a behavioral measure in a group of subjects that were treated with TMS to this ROI. I have looked through the listserve and tutorials but I have not found my answer. Thank you, Elissa -- Elissa Ash, MD, PhD Director, Center for Memory and Attention Disorders Department of Neurology Tel Aviv Sourasky Medical Center 6 Weizmann St. Tel Aviv 64239, Israel 972-3-6973698 fax: 972-3-695-0365

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How to create a 3g4v matrix
by nellie 23 Nov '15

23 Nov '15

Hi Freesurfer Experts, I’m a new user of Freesurfer, and I learn how to use this software mainly through Wiki. When I came to the step of using GLM to compare group differences, I was confused on the design of 3g4v matrix. In my study, there were 3 classes (A / B / C group) and 4 concomitant variables (gender, age, education, and Moca test score). It’s supposed to be 15 regressors in this design, but I don’t know how to use the numbers (like 1, -1, 0, 0.5, -0.5, etc.) to create a correct matrix. I wonder if you could provide a 3g4v matrix in detail for me. I’ll be grateful if you can help. I hope I’m not bothering you too much, and I’m looking for your reply. Best wishes, Li

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Re: [Freesurfer] Issue with Talaraich in recon-all
by Amlung, Michael 23 Nov '15

23 Nov '15

We are getting an error with recon-all at the stage of Talairach slignment. The error is the one described on the known issues: Can't locate shellwords.pl in @INC. We are running perl5.18, so I downloaded and installed perl5.12 and changed the first line of mritotal as indicated on the ReleaseNotes. We are now getting a different error (pasted below). It appears I need to do manual Talairach alignment, but not entirely sure how to proceed with that (is there documentation available)? Any other suggestions? #@# Talairach Failure Detection Mon Nov 16 12:48:42 EST 2015 /Users/PBCAR/neuro/TNE/freesurfer_data/309/mri \n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach recon-all -s 309 exited with ERRORS at Mon Nov 16 12:48:42 EST 2015 ******************************************** Michael Amlung, Ph.D. Assistant Professor Department of Psychiatry and Behavioural Neurosciences DeGroote School of Medicine McMaster University Peter Boris Centre for Addictions Research 100 West 5th Street Hamilton, Ontario L8N 3K7 Canada Telephone: (+1) 905-522-1155, ext. 39014 Email: amlungm(a)mcmaster.ca Web: http://fhs.mcmaster.ca/psychiatryneuroscience/AmlungMichael.html Lab Website: Cognitive Neuroscience of Addictions Laboratory (CNALab) -----Original Message----- From: Amlung, Michael Sent: Monday, November 23, 2015 9:03 AM To: 'freesurfer(a)nmr.mgh.harvard.edu' Subject: Issue with Talaraich in recon-all I was hoping someone could help with this issue... ******************************************** Michael Amlung, Ph.D. Assistant Professor Department of Psychiatry and Behavioural Neurosciences DeGroote School of Medicine McMaster University Peter Boris Centre for Addictions Research 100 West 5th Street Hamilton, Ontario L8N 3K7 Canada Telephone: (+1) 905-522-1155, ext. 39014 Email: amlungm(a)mcmaster.ca Web: http://fhs.mcmaster.ca/psychiatryneuroscience/AmlungMichael.html Lab Website: Cognitive Neuroscience of Addictions Laboratory (CNALab)

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Issue with Talaraich in recon-all
by Amlung, Michael 23 Nov '15

23 Nov '15

I was hoping someone could help with this issue... ******************************************** Michael Amlung, Ph.D. Assistant Professor Department of Psychiatry and Behavioural Neurosciences DeGroote School of Medicine McMaster University Peter Boris Centre for Addictions Research 100 West 5th Street Hamilton, Ontario L8N 3K7 Canada Telephone: (+1) 905-522-1155, ext. 39014 Email: amlungm(a)mcmaster.ca Web: http://fhs.mcmaster.ca/psychiatryneuroscience/AmlungMichael.html Lab Website: Cognitive Neuroscience of Addictions Laboratory (CNALab)

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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*

2 1

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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