Freesurfer

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30084 discussions

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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geodesic distance calculation
by Silvia Désirée Thielemann 17 Nov '15

17 Nov '15

Dear freesurfer experts, I'm analysing functional data using fsfast running under freesurfer-Linux-centos7_x86_64-dev-20150728. After streaming out the maximal activated cluster using mri_surfcluster, I want to calculate the geodesic distance between these vertices. Can I do this with mris_pmake using sphere.reg as surface? Furthermore, I would like to evaluate symmetry between the hemispheres. I would like to mirror the maximal activated vertice of a special contrast of the left hemisphere to the right hemisphere and calculate the geodesic distance between the mirrored coordinate and the maximal activated vertices of the right hemisphere. Is there a way to do this? Best regards, Desiree

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email
by Jasmin Alves 17 Nov '15

17 Nov '15

jalves(a)usc.edu -- Jasmin Alves Predoctoral Student Medical Biology Graduate Program University of Southern California jalves(a)usc.edu

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recon-all
by John Anderson 17 Nov '15

17 Nov '15

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Error in processing for local gyrification index
by Dr Meenal Yadav 17 Nov '15

17 Nov '15

Hi List, I am getting the following error when running recon-all lgi for local gyrification index. I have changed the script in matlab as we are using matlab 2013b as mentioned in the previous thread. I am attaching the script. Please let me know what else to do. Thanks Regards Meenal Budhiraja PhD student Karolinska Institute Stockholm,Sweden. preparing pial mesh structure ... ...searching for mesh edges...done (349.20 sec). ... creating path file for vertex 1 / 66330 area file for outer ROIs saved at 1 Improper assignment with rectangular empty matrix. Error in dsearchn (line 79) [d(i),t(i)] = min(sum((x-yi).^2,2)); Error in mesh_vertex_nearest (line 29) nearestIndex = dsearchn(vertices,points); Error in reorganize_verticeslist (line 28) [nextindex,nextvalue]=mesh_vertex_nearest(mesh_total.vertices(remaininglist,:),mesh_total.vertices(verticeslist(start_vertex),:)); Error in make_roi_paths (line 93) reorglist = reorganize_verticeslist (mesh_total, A, mesh_outer, perim, verticeslist, step); >> ERROR: make_roi_paths did not complete successfully!

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