Freesurfer March 2019

freesurfer@nmr.mgh.harvard.edu

114 participants
172 discussions

PetSurfer
by Shane Schofield 26 Mar '19

26 Mar '19

External Email - Use Caution Hello PetSurfer Developers On the tutorial page, I do not understand this part: --km-hb 11 12 13 50 51 52 specifies the ROIs to use as the high-binding region if using MRTM2. This creates km.hb.tac.nii.gz with the value for the high-binding region for each time point. What exactly is a high-binding region and how do these inputs affect the rest of the estimation? If I do not know what the high binding regions for a tracer are, may I leave this blank? Thank you.

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How to improve recon all on subjets with hight atrophy level like Alzheymer patients?
by Barbara Micaela Duarte Abritta 26 Mar '19

26 Mar '19

External Email - Use Caution Hello everyone, recently I have started to analyze a new sample of subjets which is made up of people with Alzheimer's, due to this pathology several of my subjects have a high level of atrophy in subcortical and temporal areas of the brain, which causes several errors in the pial surface as a wm surface. So to make both surfaces more accurate I tried to put some control points but in many places this solution was not enough due the level of inaccuracy. Is there any solution for this problem? I will appreciate if you could offer any suggestions to solve this problem. Regards Bárbara

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mkanalysis-sess with a customized HRF
by Francesca Strappini 26 Mar '19

26 Mar '19

External Email - Use Caution Dear Freesurfer's experts, I would like to use a customized HRF with mkanalysis-sess. Is there a way to do it? Thanks! Best Francesca -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strappini(a)weizmann.ac.il

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Longitudinal Two Stage Model Question
by Arsenije Subotic 26 Mar '19

26 Mar '19

External Email - Use Caution Hello, I am doing a longitudinal analysis for which I have already qcached my data using the long_mris_slopes command. I am having issues figuring out how to run the mri_glmfit command for my longitudinal two stage model. I'm interested in comparing the spc over time between two groups after controlling for age and gender. The tutorial on the longitudinal two stage model however only shows how to do it for one sample. Am I still expected to use contrasts and make glm directories like the cross-sectional group analysis tutorial suggests? I was just confused because the code is different. I have a longitudinal table so I assumed that would be enough, but do I still need to make a FSGD file that is basically the same as the longitudinal file? Thank you for your help, Arsenije --- Arsenije Subotic | MSc Student Department of Clinical Neurosciences Hotchkiss Brain Institute, University of Calgary | T2N 4N1, Canada Tel: (403) 918-6970 arsenije.subotic1(a)ucalgary.ca

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Re: [Freesurfer] mris_fix_topology stuck running
by Soichi Hayashi 26 Mar '19

26 Mar '19

External Email - Use Caution Bruce, I am still going through the wiki, but I found the mri/brainmask.mgz contains a lot of non brain voxels like these.. [image: Screenshot from 2019-03-26 11-56-48.png] Could this be the cause of the problem? Maybe Freesurfer had a problem generating a good brainmask? Does this create the high number of vertices that needs to be corrected? Soichi On Tue, Mar 26, 2019 at 10:46 AM Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > Hi Soichi > > look at the inflated.nofix in the 3D view, not the orig.nofix. You can > check out our tutorial here: > > > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_free… > > > although there may be a better one (hopefully someone else will chime in > if > so) > > cheers > Bruce > > > > On Tue, 26 Mar 2019, Soichi Hayashi wrote: > > > > > External Email - Use Caution > > > > Bruce, > > Thank you for your help. I'd very much appreciate it. > > > > I've looked at rh.orig.nofix / rh.inflated.nofix, but I couldn't really > find anything out of > > ordinary.. from my layman's eyes. > > > > Screenshot from 2019-03-26 10-35-42.png > > > > Could you point me to the wiki you mentioned? > > > > Soichi > > > > On Sun, Mar 24, 2019 at 4:37 PM Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > wrote: > > Hi Soichi > > > > that is too big a defect to expect it to fix - more than half the > number > > of vertices in a typical hemisphere. It means something is badly > wrong > > that you need to correct prior to the topo fixer. You can look at > our > > wiki for this kind of thing, but I would start by looking at the > > rh.orig.nofix and the rh.inflated.nofix. Something big is wrong, > like large > > parts of the skull attached to the surface or something like that > > > > cheers > > Bruce > > > > > > On Sun, 24 Mar 2019, Soichi Hayashi wrote: > > > > > > > > External Email - Use Caution > > > > > > Hello. > > > I am trying to troubleshoot an issue where recon_all is not > finishing after >24 hours. > > It's getting > > > stuck when it tries to run the following command. > > > > > > $ mris_fix_topology -rusage > ./output/touch/rusage.mris_fix_topology.rh.dat -mgz > > -sphere > > > qsphere.nofix -ga -seed 1234 output rh > > > INFO: assuming .mgz format > > > 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 > > > > > > ************************************************************* > > > $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman > Exp $ > > > $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ > > > reading input surface > /home/hayashis/Downloads/output/surf/rh.qsphere.nofix... > > > before topology correction, eno=-696 (nv=191488, nf=384368, > ne=576552, g=349) > > > reading brain volume from brain... > > > reading wm segmentation from wm... > > > 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 9 iterations > > > marking ambiguous vertices... > > > 133741 ambiguous faces found in tessellation > > > segmenting defects... > > > 63 defects found, arbitrating ambiguous regions... > > > analyzing neighboring defects... > > > -merging segment 16 into 0 > > > -merging segment 23 into 0 > > > -merging segment 48 into 0 > > > -merging segment 32 into 22 > > > -merging segment 49 into 47 > > > -merging segment 54 into 51 > > > 57 defects to be corrected > > > 0 vertices coincident > > > Computing Initial Surface Statistics > > > -face loglikelihood: -9.3123 (-4.6561) > > > -vertex loglikelihood: -6.5427 (-3.2713) > > > -normal dot loglikelihood: -3.5794 (-3.5794) > > > -quad curv loglikelihood: -6.0564 (-3.0282) > > > Total Loglikelihood : -25.4907 > > > > > > CORRECTING DEFECT 0 (vertices=65141, convex hull=8287, v0=517) > > > > > > --------------- > > > > > > After displaying the last line, the process seems to be stuck > running with 100% > > cpu (single core) > > > for >24 hours until our batch scheduler kills it. I think the > issue is with my input > > data, but it > > > looks clean and well ACPC aligned, and I don't know what's wrong > with it. The input > > image dimensions > > > are 182 x 218 x 182. > > > > > > Does anyone have any suggestion on how to troubleshoot this > problem? > > > > > > Thank you, > > > > > > Soichi Hayashi > > > Indiana University > > > > > > > > > > > >

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BrainHack Donostia 2nd edition, 5-8 May 2019, San Sebastian
by Stefano Moia 26 Mar '19

26 Mar '19

External Email - Use Caution Dear all, At the Basque Center on Cognition, Brain and Language (BCBL), we are organizing the second edition of Brainhack Donostia ( https://brainhackdonostia.pages.bcbl.eu ), an event focused on neuroimaging and the promotion of open-source resources in an accessible way across disciplines and experience levels. This edition will take place on May 5 -8 at BCBL, where two invited speakers (Prof. Dimitri Van De Ville, EPFL, and Matteo Bastiani, University of Nottingham) and other scientists from BCBL will give talks and develop hands-on tutorials on data handling from several neuroimaging techniques. In particular, we will cover three techniques: Diffusion-Weighted Imaging (DWI), Magnetoencephalography (MEG) and functional Magnetic Resonance Imaging (fMRI). To know more about it, you can c heck the schedule here: https://brainhackdonostia.pages.bcbl.eu/sites/timeline.html We are also going to host a hackaton in parallel, in which the attendants will propose and collaborate on neuroimaging-related projects (e.g., data acquisition, visualization, etc.). Check the project page for more info: https://brainhackdonostia.pages.bcbl.eu/sites/projects.html We encourage you to come and enjoy such an experience with us! Feel free to register here https://brainhackdonostia.pages.bcbl.eu/sites/register.html For any inquiries, please email us at info.bhg-donostia(a)bcbl.eu We hope to see you in May! Stefano Moia --- PhD student @ BCBL www.bcbl.eu Tel: +34 943 309 300 Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer

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Re: [Freesurfer] mris_fix_topology stuck running
by Soichi Hayashi 26 Mar '19

26 Mar '19

External Email - Use Caution Bruce, Thank you for your help. I'd very much appreciate it. I've looked at rh.orig.nofix / rh.inflated.nofix, but I couldn't really find anything out of ordinary.. from my layman's eyes. [image: Screenshot from 2019-03-26 10-35-42.png] Could you point me to the wiki you mentioned? Soichi On Sun, Mar 24, 2019 at 4:37 PM Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > Hi Soichi > > that is too big a defect to expect it to fix - more than half the number > of vertices in a typical hemisphere. It means something is badly wrong > that you need to correct prior to the topo fixer. You can look at our > wiki for this kind of thing, but I would start by looking at the > rh.orig.nofix and the rh.inflated.nofix. Something big is wrong, like > large > parts of the skull attached to the surface or something like that > > cheers > Bruce > > > On Sun, 24 Mar 2019, Soichi Hayashi wrote: > > > > > External Email - Use Caution > > > > Hello. > > I am trying to troubleshoot an issue where recon_all is not finishing > after >24 hours. It's getting > > stuck when it tries to run the following command. > > > > $ mris_fix_topology -rusage > ./output/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere > > qsphere.nofix -ga -seed 1234 output rh > > INFO: assuming .mgz format > > 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 > > > > ************************************************************* > > $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ > > $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ > > reading input surface > /home/hayashis/Downloads/output/surf/rh.qsphere.nofix... > > before topology correction, eno=-696 (nv=191488, nf=384368, ne=576552, > g=349) > > reading brain volume from brain... > > reading wm segmentation from wm... > > 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 9 iterations > > marking ambiguous vertices... > > 133741 ambiguous faces found in tessellation > > segmenting defects... > > 63 defects found, arbitrating ambiguous regions... > > analyzing neighboring defects... > > -merging segment 16 into 0 > > -merging segment 23 into 0 > > -merging segment 48 into 0 > > -merging segment 32 into 22 > > -merging segment 49 into 47 > > -merging segment 54 into 51 > > 57 defects to be corrected > > 0 vertices coincident > > Computing Initial Surface Statistics > > -face loglikelihood: -9.3123 (-4.6561) > > -vertex loglikelihood: -6.5427 (-3.2713) > > -normal dot loglikelihood: -3.5794 (-3.5794) > > -quad curv loglikelihood: -6.0564 (-3.0282) > > Total Loglikelihood : -25.4907 > > > > CORRECTING DEFECT 0 (vertices=65141, convex hull=8287, v0=517) > > > > --------------- > > > > After displaying the last line, the process seems to be stuck running > with 100% cpu (single core) > > for >24 hours until our batch scheduler kills it. I think the issue is > with my input data, but it > > looks clean and well ACPC aligned, and I don't know what's wrong with > it. The input image dimensions > > are 182 x 218 x 182. > > > > Does anyone have any suggestion on how to troubleshoot this problem? > > > > Thank you, > > > > Soichi Hayashi > > Indiana University > > > >

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recon from 7T data
by Barletta, Valeria 26 Mar '19

26 Mar '19

Dear Freesurfers, I am trying to perform the FreeSurfer cortical reconstruction process from my 7 Tesla MEMPRAGE, but am getting very bad results (see first attachment) compared to what I had using the 3 Tesla images (second attachment). Before launching the "recon-all ....... -all" command, I applied the FreeSurfer Gradient non-linearity correction. What can have been the problem? Thank you very much for your help, Valeria

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significant results in FS (CT of ROI values) is not significant in SPSS
by Yali Jiang 25 Mar '19

25 Mar '19

External Email - Use Caution Dear all, I was asked to provide a power calculation of my group comparison results on cortical thickness, so I extracted all clusters with significance in CT into SPSS. but I found the cluster value of CT is not significant in SPSS based on group comparison. so I got a very small effect size although the original ROI was generated by a initial threshold of p < 0.001, and corrected by monte-carlo p < 0.05, two sided. Is this possible? how can I resolve it? best, Yali

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Errors in white matter surfaces from scan collected on 3T Siemens Skyra scanner at .6 mm resolution
by Lalonde, Francois (NIH/NIMH) [E] 25 Mar '19

25 Mar '19

External Email - Use Caution Hi, We collected an MP-RAGE scan at .6mm isotropic resolution with the TR bumped up to TR=5. Subject motion artifacts were mitigated by using a KinetiCor motion correction system. We followed the recommendations for processing submillimeter scans described in the FreeSurfer Wiki i.e. we added the -cm flag to recon-all and included the mris_inflate -n 100 expert option. The attached PDF of the white matter surfaces shows that they appear to be underestimated. The surface estimates fall short of the actual grey/white matter boundary. Arrows point to the most affected areas and the second image is the same as the first but without the yellow white matter surface line. FTP is disabled on my government computer. Please specify the recipient email if I have to transfer the file using FileDrop. Could you suggest other options either at the time of scanning or in running recon-all that could help better segment the white matter? Thanks, François Lalonde, Ph.D. DNU/HGB/NIMH/NIH 10 Center Drive, Room 4D18 Bethesda, MD. 20892 flalonde(a)nih.gov

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Freesurfer March 2019