Freesurfer November 2015

freesurfer@nmr.mgh.harvard.edu

138 participants
239 discussions

Multimodality analysis in FreeSurfer
by Silas 18 Nov '15

18 Nov '15

Dear Freesurfer team, I've scanned a group of subjects and gained structural and myelination data. Then, I've used mris_preproc to map the data onto the surface of fsaverage (and concatenating the data). I would like to investigate the correlation between cortical thickness and myelination by mapping this correlation onto the fsaverage (an one sample group mean analysis) - is this possible? Do you have an existing guide approaching this problem? Thank you! Best, Silas

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Obtaining MNI-305 Coordinates for Destrieux ROIs
by Riley North 18 Nov '15

18 Nov '15

Hello, I was following the conversation (recreated below) about converting the Destrieux ROI labels to MNI-305 coordinates and was wondering if all issues were resolved but not posted to the list. I attempted the same commands as were recommended in the original conversation: *mri_annotation2label --subject fsaverage --hemi lh --annotation aparc.a2009s * followed by *mri_surfcluster --in fsaverage/surf/rh.thickness --clabel my_label.label --sum sum.my_label --centroid --thmin 0 --hemi lh --subject fsaverage --nofixmni * *(where my_label is a given Destrieux ROI)* The 'sum' files returned by the second command all show the same MNI x-y-z coordinates as one another: [-29.4 -22.0 17.4] for lh ROIs and [29.8 -20.7 18.0] for rh ROIs. The original poster also said he observed that the x-y-z coordinates were the same for all of the ROIs for a given hemisphere. Like the original poster, I'm trying to get a single x-y-z MNI305-space coordinate triplet for each Destrieux ROI for use in network display software. Is there a modification to the above command that will return what I'm looking for? The original conversation (italicized) is posted below in chronological order: *Post #1: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg42598.html <https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg42598.html>* *Hi Freesurfer Experts, For the purpose of defining nodes in a graph theory analysis, I would like to generate a list of X Y Z coordinates in MNI space for all the labels in the Destrieux atlas. I came across a previous post with the following steps:* *Step 1: mri_annotation2label --subject fsaverage --hemi lh --annotation aparc.a2009s --outdir /Users/ElijahMak Step 2: mri_surfcluster --in /Applications/freesurfer/subjects/fsaverage/surf/lh.thickness --clabel lh.G_and_S_frontomargin.label --sum sum.lh.G_and_S_frontomargin --centroid --thmin 0 --hemi lh --subject fsaverage Everything went smoothly, but I would like to check my steps with you before I proceed to generate the coordinates individually for each ROI per hemisphere. The output from #2 is sum.lh.G_and_S_frontomargin. When I load it, I see dhcp-172-17-218-173:~ ElijahMak$ cat sum.lh.G_and_S_frontomargin # Cluster Growing Summary (mri_surfcluster) # $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve Exp $ # $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ # CreationTime 2015/08/10-12:29:31-GMT # cmdline mri_surfcluster --in /Applications/freesurfer/subjects/fsaverage/surf/lh.thickness --clabel lh.G_and_S_frontomargin.label --sum sum.lh.G_and_S_frontomargin --centroid --thmin 0 --hemi lh --subject fsaverage # cwd /Users/ElijahMak # sysname Darwin # hostname dhcp-172-17-218-173.eduroam.wireless.private.cam.ac.uk <http://dhcp-172-17-218-173.eduroam.wireless.private.cam.ac.uk/> # machine x86_64 # FixVertexAreaFlag 1 # FixSurfClusterArea 1 # # Input /Applications/freesurfer/subjects/fsaverage/surf/lh.thickness # Frame Number 0 # srcsubj fsaverage # hemi lh # surface white # SUBJECTS_DIR /Applications/freesurfer/subjects # SearchSpace_mm2 65416.6 # SearchSpace_vtx 932 # Bonferroni 0 # Minimum Threshold 0 # Maximum Threshold infinity # Threshold Sign abs # AdjustThreshWhenOneTail 1 # Area Threshold 0 mm^2 # clabelfile lh.G_and_S_frontomargin.label # clabelinv 0 # Overall max 3.33248 at vertex 83949 # Overall min 0 at vertex 0 # NClusters 1 # Total Cortical Surface Area 65416.6 (mm^2) # FixMNI = 1 # # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ NVtxs 1 3.332 83949 82219.39 -29.4 -22.0 17.4 163842 Are those TalX TalY TalZ the values I'm looking for? Many thanks for your time. Best Wishes, Elijah* *Reply to Post #1: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg42656.html <https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg42656.html>* *Those are more-or-less talairach coords, not MNI. If you add --nofixmni, the results will be reported in mni305 coords. - Douglas N Greve* *Post #2: **https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg42693.html <https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg42693.html>* *Hi Douglas, Thanks for the help! However, when I tried the --nofixmni flag, all the ROIs appeared to have identical MNI coordinates. I have pasted the output from 3 ROIS in the LH.* *# ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ NVtxs 1 3.332 83949 82219.39 -29.4 -22.0 17.4 163842 1 3.533 117158 82219.39 -29.4 -22.0 17.4 163842 1 3.170 83424 82219.39 -29.4 -22.0 17.4 163842 The same thing happens to the ROIs on the RH (XYZ: 29.8 29.8 18.0). Best Wishes, * *Elijah * Thanks, Riley

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direction for restart in the middle
by Krieger, Donald N. 18 Nov '15

18 Nov '15

I have run freesurfer 6Beta on the scan with very large CSF spaces With flags: -bigventricles and -notal-check . I used the latter flag per suggestions in the log as the first run failed on a talaraich check. This second run appears to be hung as it has not written anything new into the recon-all.log file for 7 hours. I would like to restart this at a reasonable point rather than at the beginning. Can you recognize where it is and what is are suggested restart flags? Here are the files which have appeared in the mri directory. aseg.auto.mgz aseg.presurf.mgz brainmask.mgz error.log mri_nu_correct.mni.log.bak nu_noneck.mgz orig_nu.log segment.dat talairach.log transforms wm.mgz aseg.auto_noCCseg.label_intensities.txt brain.finalsurfs.mgz brain.mgz filled.mgz norm.mgz orig orig_nu.mgz T1.mgz talairach_with_skull_2.log v.mgz wm.seg.mgz aseg.auto_noCCseg.mgz brainmask.auto.mgz ctrl_pts.mgz mri_nu_correct.mni.log nu.mgz orig.mgz rawavg.mgz talairach.label_intensities.txt talairach_with_skull.log wm.asegedit.mgz Here are the last 50 lines or so of the log file: ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2 ion: 3.10.73-1.el6.elrepo.x86_64 CompilerName: GCC CompilerVersion: 40400 ...skipping... mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 201 lh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.767.2.2 2015/07/06 21:59:21 greve Exp $ before topology correction, eno=-510 (nv=99342, nf=199704, ne=299556, g=256) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 10 iterations marking ambiguous vertices... 111330 ambiguous faces found in tessellation segmenting defects... 38 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 13 into 0 -merging segment 23 into 0 -merging segment 29 into 0 -merging segment 32 into 0 -merging segment 36 into 0 -merging segment 16 into 12 -merging segment 15 into 14 31 defects to be corrected 0 vertices coincident reading input surface /oasis/scratch/comet/donkri/temp_project/subjects/201/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.2710 (-4.6355) -vertex loglikelihood: -8.2866 (-4.1433) -normal dot loglikelihood: -3.4816 (-3.4816) -quad curv loglikelihood: -6.0138 (-3.0069) Total Loglikelihood : -27.0531 CORRECTING DEFECT 0 (vertices=53053, convex hull=8873) Thanks for your direction on this. - Don

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Hippocampal Subfields 6.0 with 5.3 recons
by O'Shea,Andrew 18 Nov '15

18 Nov '15

Hello all, I was wondering if anyone with knowledge of the new hippocampal subfield segmentation that is going to be released with version 6.0 could answer a quick question. We have previously processed subjects in v5.3 and would like to use the new hippocampal seg algorithm. How "standalone" is the new process? Does the new process use any inputs from the recon-all stream which have changed in the upcoming version? Thanks! -Andrew

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Issue with Talairach - mritotal
by Amlung, Michael 18 Nov '15

18 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)

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How to edit the corpus callosum segmentation
by UQAM 18 Nov '15

18 Nov '15

Hi, I would like to segment the corpus callosum into *twelve* even lenght segments instead of the five segments that freesurfer identifies by default. - First I ran a mri_cc on subject e0070: mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.12segmentsCC.mgz -d 12 e0070 - Then I edited the ColorLUT.txt file and renamed it CColorLUT.txt (see attachment, segments 251 to 262). - Finally I ran a mri_segstats to compute the statistics on segmented volumes. mri_segstats seg $SUBJECTS_DIR/e0070/mri/aseg.12segmentsCC.mgz --ctab $SUBJECTS_DIR/CColorLUT.txt --nonempty --excludeid 0 sum --e0070_CC12.aseg.stats The e0070_CC12.aseg.stats file still displays only five segments of the corpus callosum. Any tips or clues on how I could do things differently to get 12 segments? Thanks in advance, Geneviève

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-hippocampal-subfields-T1
by Daniele Orlandi 18 Nov '15

18 Nov '15

dear all, I'm running analysis with the new FS-v6.0 using the flag -hippocampal-subfields-T1 and I get the following error: none Matrix: -3.00003 0 0 0 0 -3.00003 0 3.00003 0 Offset: [-34.0783, 128.423, -71.9905] Center: [0, 0, 0] Translation: [-34.0783, 128.423, -71.9905] Inverse: -0.33333 0 0 0 0 0.33333 0 -0.33333 0 Singular: 0 I am WriteImage and I'm running! Wrote image to file asmr2.mgz This file does not contain MRI parameters Error using zeros NaN and Inf not allowed. Error in segmentSubjectT1_autoEstimateAlveusML (line 1396) MATLAB:nonaninf How I can solve it? Best, Daniele

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freesurfer vs ITK build from sources on ubuntu(LUCID)
by Nedialko I. Krouchev 17 Nov '15

17 Nov '15

I'd be very grateful for any help provided on this matter. It has been close to three weeks since I started trying to compile freesurfer from its sources (CSV stable5) on 32bit ubuntu ver. 10.04. I followed to the letter the recipe outlined in: http://surfer.nmr.mgh.harvard.edu/fswiki/DevelopersGuide To do so I found additional prerequisite sources in: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/fs_supportlibs/src/ mni.srcbuild.June2015.tgz 12.0 MB 6/19/15, 8:51:00 PM mni.srcbuild.README.txt 6.5 kB 2/25/09, 12:00:00 AM tcltktixblt-8.4.6.tgz 11.4 MB 7/26/10, 12:00:00 AM vtk-5.2.1.tar.gz 16.2 MB 2/26/10, 12:00:00 AM vxl-1.13.0.zip 34.0 MB 2/26/10, 12:00:00 AM and then (when I'd have almost given up) the "Hacks" in: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-April/029159.ht… In addition, overcame the complex VTK structure of includes ... Finally, to find I am still missing ITK, which is barely mentioned elesewhere. Please correct me if I am wrong, but I assume it is all about the National Library of Medicine's Insight Segmentation and Registration Toolkit (ITK). Then which version of ITK goes with the rest of freesurfer (as described above)? http://www.itk.org/ITK/resources/legacy_releases.html

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Advice for FreeSurfer developers
by Gronenschild Ed (NP) 17 Nov '15

17 Nov '15

Hi Doug, Yes, I know. It’s the hippocampal subfields segmentation that needs matlab runtime. Cheers, Ed On 17 Nov 2015, at 18:00, freesurfer-request(a)nmr.mgh.harvard.edu<mailto:freesurfer-request@nmr.mgh.harvard.edu> wrote: Message: 8 Date: Mon, 16 Nov 2015 12:52:20 -0500 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] Advice for FreeSurfer developers To: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Message-ID: <564A17D4.6090707(a)nmr.mgh.harvard.edu<mailto:564A17D4.6090707@nmr.mgh.harvard.edu>> Content-Type: text/plain; charset=windows-1252; format=flowed Do you know what command was looking for matlab? On 11/12/2015 02:10 AM, Gronenschild Ed (NP) wrote: Hi Doug, I used mostly the default options, nothing special: recon-all -autorecon1 -clean-tal -expert my_options.txt -hires where the file my_options.txt contains some options for nu_correct. Then I entered recon-all -autorecon2 -autorecon3 -hippocampal-subfields-T1 -hires The error occurred with the last recon-all command. BTW, I really don't know if the -clean-tal option is needed with FS v6. Cheers Ed On 11 Nov 2015, at 18:00, <freesurfer-request(a)nmr.mgh.harvard.edu<mailto:freesurfer-request@nmr.mgh.harvard.edu> <mailto:freesurfer-request@nmr.mgh.harvard.edu>> wrote: Message: 9 Date: Wed, 11 Nov 2015 11:08:46 -0500 From: Douglas Greve <greve(a)nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] Advice for FreeSurfer developers To:freesurfer@nmr.mgh.harvard.edu<http://nmr.mgh.harvard.edu/> <mailto:freesurfer@nmr.mgh.harvard.edu> Message-ID: <5643680E.1030800(a)nmr.mgh.harvard.edu<mailto:5643680E.1030800@nmr.mgh.harvard.edu> <mailto:5643680E.1030800@nmr.mgh.harvard.edu>> Content-Type: text/plain; charset=windows-1252; format=flowed Hi Ed, generally recon-all does not need matlab. Are you running the gyrification analysis? That should be the only thing that needs matlab. doug On 11/11/15 6:14 AM, Gronenschild Ed (NP) wrote: Dear developers, Is it possible to check the presence of Matlab runtime right at the start of recon-all in FreeSurfer v6 instead of a long way down in the pipeline. After 36 hours for a high-res data processing I got this unexpected error message. Thanks in advance. Cheers Ed _______________________________________________ Freesurfer mailing list

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travel grants for April workshop
by Jasmin Alves 17 Nov '15

17 Nov '15

Hello, Are there possibly any travel grants available to attend the Freesurfer workshop in April? It would greatly benefit my PhD studies to attend this workshop to learn more about structural techniques, however my PI does not have sufficient funds to send me. Thanks, Jasmin -- Jasmin Alves Predoctoral Student Medical Biology Graduate Program University of Southern California jalves(a)usc.edu

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Freesurfer November 2015