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Unknown cortical parcellation in S_calcarine (lh.aparc.a2009s.annot)
by Matthieu Vanhoutte 11 Jan '16

11 Jan '16

Dear FS's experts, Projecting volumic data onto native surface (brain mask: "Unknown_S_calcarine_ROI_mask.jpg"), I observed that a thin region in the S_calcarine was set to 0. I loaded then the inflated left surface and the l.aparc.a2009s.annot ("Unknown_S_calcarine_ROI_annot.jpg") and took into account that this region inside the S_calcarine was set as "unknown" in the parcellation file . So I checked the aseg at the anterior end of the calcarine and see if it incorrectly labeled some voxels there as ventricle. I corrected the aseg and rerun from there with this command : *recon-all -all -sd ${SUBJECTS_DIR} -subjid ${SUBJECT_ID} -nuintensitycor-3T -make all* However, this command exited with errors (please find attached recon-all_log.txt). Thanks in advance far any helping ! Best regards, Matthieu 2016-01-08 10:14 GMT+01:00 Matthieu Vanhoutte <matthieuvanhoutte(a)gmail.com>: > Hi Bruce, > > I erased the false ventricle signal and re-run with -make all option. > > However, Recon-all exited with errors: > > --------------------------------------------------- >> #@# 1/1 Hallaert_Beatrice_M0_2010-12-15 Thu Jan 7 19:46:56 CET 2016 >> -------------- >> ----------------------- >> mri_surf2surf --srcsubject Hallaert_Beatrice_M0_2010-12-15 --srchemi lh >> --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg >> sphere.reg --tval >> ./tmp.mris_preproc.16394/Hallaert_Beatrice_M0_2010-12-15.1.mgh --sval >> /NAS/tupac/matthieu/FS5.3/Hallaert_Beatrice_M0_2010-12-15/surf/lh.volume >> --jac --sfmt curv --noreshape --no-cortex >> Source registration surface changed to sphere.reg >> Target registration surface changed to sphere.reg >> srcsubject = Hallaert_Beatrice_M0_2010-12-15 >> srcval = >> /NAS/tupac/matthieu/FS5.3/Hallaert_Beatrice_M0_2010-12-15/surf/lh.volume >> srctype = curv >> trgsubject = fsaverage >> trgval = >> ./tmp.mris_preproc.16394/Hallaert_Beatrice_M0_2010-12-15.1.mgh >> trgtype = >> srcsurfreg = sphere.reg >> trgsurfreg = sphere.reg >> srchemi = lh >> trghemi = lh >> frame = 0 >> fwhm-in = 0 >> fwhm-out = 0 >> label-src = (null) >> label-trg = (null) >> OKToRevFaceOrder = 1 >> Reading source surface reg >> /NAS/tupac/matthieu/FS5.3/Hallaert_Beatrice_M0_2010-12-15/surf/lh.sphere.reg >> Loading source data >> Reading curvature file >> /NAS/tupac/matthieu/FS5.3/Hallaert_Beatrice_M0_2010-12-15/surf/lh.volume >> ERROR: number of vertices in >> /NAS/tupac/matthieu/FS5.3/Hallaert_Beatrice_M0_2010-12-15/surf/lh.volume >> does not match surface (124822,125094) >> ERROR: reading curvature file >> Linux toto 3.13.0-24-generic #47-Ubuntu SMP Fri May 2 23:30:00 UTC 2014 >> x86_64 x86_64 x86_64 GNU/Linux >> >> recon-all -s Hallaert_Beatrice_M0_2010-12-15 exited with ERRORS at Thu >> Jan 7 19:46:57 CET 2016 >> > > Please find attached the logs. > > Moreover, I visualized aparc.a2009.annot and there's still unknown label > in calcarine. > > Best regards, > Matthieu > > > 2016-01-07 17:52 GMT+01:00 Matthieu Vanhoutte <matthieuvanhoutte(a)gmail.com > >: > >> Hi Bruce, >> >> Thank you I erased false ventricle and rerun recon-all with option -make >> all. >> >> Is there any mean to prevent this problem ? >> >> Best regards, >> Matthieu >> >> ------------------------------------- >> Matthieu Vanhoutte, MSc >> Research Engineer - Department of Neuroradiology >> Regional University Hospital, Lille, France >> http://www.ci2c.fr >> >> 2016-01-07 16:21 GMT+01:00 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>: >> >>> it's the bit of ventricle at e.g. 150, 117, 76 in the aseg. This should >>> be unknown instead. You can erase it all from the aseg.mgz, then rerun >>> recon-all -make all I think >>> >>> Bruce >>> On Thu, 7 Jan 2016, matthieuvanhoutte(a)gmail.com wrote: >>> >>> Matthieu (matthieuvanhoutte(a)gmail.com) has uploaded some files for you >>>> at the Martinos Center FileDrop: >>>> >>>> + T1.mgz (3.89 MiB) < >>>> http://gate.nmr.mgh.harvard.edu/filedrop2/?u=83wgnvpqp7q&f=1qg3sxihniv> >>>> + aseg.mgz (230.42 KiB) < >>>> http://gate.nmr.mgh.harvard.edu/filedrop2/?u=83wgnvpqp7q&f=41rb99vxdza> >>>> + aparc.a2009s+aseg.mgz (406.09 KiB) < >>>> http://gate.nmr.mgh.harvard.edu/filedrop2/?u=83wgnvpqp7q&f=b68kofegemp> >>>> >>>> Also, they left this message for you: >>>> Hi Bruce, >>>> >>>> I couldn't see what you've explained to me. I attached the T1 and aseg >>>> files, could you please give me coordinates of this phenomen ? >>>> >>>> Once problem have been seen, what is the process to follow for >>>> correcting aseg labels and re-run recon-all at which step ? >>>> >>>> Thanks in advance ! >>>> >>>> Best regards, >>>> Matthieu >>>> >>>> >>>> Hi Matthieu >>>> >>>> check the aseg at the anterior end of the calcarine and see if it >>>> incorrectly labels some voxels there as ventricle. The bit of WM that >>>> separates ventricle from calcarine at the posterior horn of the >>>> ventricle >>>> is thin and sometimes quite dark, and if we lose that the ventricle >>>> label >>>> can extend incorrectly into calcarine, in which case we think it isn't >>>> cortex. If you correct the aseg and rerun from there it should fix it. >>>> >>>> cheers >>>> Bruce >>>> >>>> >>>> On Thu, 7 Jan 2016, >>>> Matthieu Vanhoutte wrote: >>>> >>>> Dear FS's experts, >>>>> >>>>> Projecting volumic data onto native surface (brain mask: >>>>> "Unknown_S_calcarine_ROI_mask.jpg"), I observed that a thin region in >>>>> the >>>>> S_calcarine was set to 0. >>>>> >>>>> I loaded then the inflated left surface and the l.aparc.a2009s.annot >>>>> ("Unknown_S_calcarine_ROI_annot.jpg") and took into account that this >>>>> region >>>>> inside the S_calcarine was set as "unknown" in the parcellation file . >>>>> >>>>> What does it mean and is this possible to correct for this ? >>>>> >>>>> Best regards, >>>>> Matthieu >>>>> >>>> >>>> Please be aware, your upload will expire on December 31st. If you'd >>>> like to download these files, feel free to use the link below: >>>> >>>> http://gate.nmr.mgh.harvard.edu/filedrop2/?u=83wgnvpqp7q >>>> >>>> Cheers, >>>> The Martinos Center Web Team >>>> >>>> >>>> >>>> >>> >>> The information in this e-mail is intended only for the person to whom >>> it is >>> addressed. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to you >>> in error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. >>> >>> >> >

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Postdoctoral positions available -- San Diego
by Ruth Carper 08 Jan '16

08 Jan '16

The Brain Development Imaging Laboratory (BDIL) at the Dept.of Psychology, San Diego State University (SDSU), is offering 1-2 postdoctoralpositions in diffusion-weighted and other anatomical MRI techniques. Job Description Post-doctoral positions will be supported by several newlyfunded NIH projects examining brain structure and network organization acrossthe lifespan in autism spectrum disorders (ASD) including a study of toddlersand a study of older adults. New projects will implement multi-shell diffusionweighted imaging (i.e. multiple b-values, appropriate for calculation of ODFs, tractography,examination of neurite density in gray and white matter), multi-modalneuroanatomical imaging (e.g. combined T1, T2, DWI), and simultaneousmulti-slice fMRI. The postdoctoral scholar will be responsible for implementationof new analysis pipelines for diffusion weighted and/or anatomical MRI incollaboration with faculty and support staff, for assessment and mitigation ofartifacts, and for continuing analysis of our existing database of multimodalMRI data. Fellow will assist in supervision/training of graduate students andresearch assistants and in the preparation of manuscripts for publication. Thepostdoctoral fellow will regularly interact with collaborating faculty and willhave access to the rich San Diego Neuroscience and Cognitive Sciencecommunities. Requirements · PhD in Neuroscience, CognitiveScience, Psychology, Biomedical Engineering, or other relevant field. · Experience in data acquisition, preprocessing,and analysis of MRI data, with particular focus on diffusion and/or anatomicalMRI. · Preference will be given toapplicants with: o Experiencewith multiple analysis methods/toolkits in the relevant modality. o Experiencein multiple imaging modalities (e.g. both diffusion and functional imaging). o Experiencewith ASD, other developmental disorders, or normal aging. Brain Development Imaging Lab &Research Facilities BDIL (www.sci.sdsu.edu/bdil)is a diverse and collaborative research group with 3 faculty members andmultiple PhD and Master’s students in Psychology, Cognitive Science, ClinicalPsychology, and BioInformatics from both SDSU and University of California, SanDiego (UCSD). Research applies multiple imaging modalities (e.g. DWI,anatomical MRI, fMRI, functional connectivity MRI, MR spectroscopy) as well asbehavioral and neuropsychological measures to investigate the brain bases ofASD and age-related change across the lifespan (1-65 years). BDIL collaborateswith experts in MR physics, Radiology, EEG, MEG, and Bioinformatics toimplement innovative imaging and analysis techniques (e.g., simultaneousfMR/EEG recording, combined MEG and MRI). BDIL maintains close ties withfaculty at UCSD Center for Functional MRI (CFMRI) where imaging is performed andwith affiliated faculty at UCSD School of Medicine. BDIL researchers have fullaccess to CFMRI (http://fmri.ucsd.edu/),a research dedicated facility with two 3T human research scanners (8 & 32channel head coils), led by top experts in radiology physics, and supported byengineering staff. To Apply Please e-mail CV, research statement, reprints, and 3 lettersof recommendation to Ralph-Axel Mueller at: rmueller(a)sdsu.edu.

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amygdala nuclear subregions
by Dorit Kliemann 08 Jan '16

08 Jan '16

Hi Heidi, segmentation of amygdalar subregions is currently not yet implemented in FreeSurfer, but we are working on including this feature soon. Best, Dorit ----------------------------- Message: 9 Date: Fri, 8 Jan 2016 13:21:48 +0000 From: "Jacobs H (NP)" <h.jacobs(a)maastrichtuniversity.nl> Subject: [Freesurfer] amygdala nuclear subregions To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <D2B5767A.155A7%h.jacobs(a)maastrichtuniversity.nl> Content-Type: text/plain; charset="iso-8859-1" Dear FreeSurfer developers, In the FreeSurferColorLut file I see labels for the subregions of the amygdala. Is it possible to extract the volumes for these regions? And how can I do this? I don't see them in the aseg or aparc stat files. Many thanks! Heidi

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Gray Matter Errors, Ignored Areas
by Julio Alberto González Torre 08 Jan '16

08 Jan '16

Hi everyone. I have a little trouble. First of all, I performed the recommended reconstruction. When I inspect the results, the boundaries of white matter are correct, but the Gray Matter is incorrectly understimated. As I show in the attached file, large parts of gray matter were ignored on the pial surface. It is extrange, because when I inspect the aseg file, the voxels of those areas are correct classified as cortex. I have been searching how to fix it, but I was unable to find how to do it on the troubleshooting tutorials. When this problem appears in white matter tissue, can be corrected with control points. What can I do when the same problem is in gray matter? Thanks.[image: Imágenes integradas 1]

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Re: [Freesurfer] malloc error with mri_glmfit-sim
by Antonin Skoch 08 Jan '16

08 Jan '16

Dear FreeSurfer experts, I am getting the same error with malloc(): memory corruption on mri_segstats invoked within mri_glmfit-sim. Apart from Frances, the process continues forever without any output after error message (i.e. without "Writing to..." and "Abort..." line). My commandline is: mri_glmfit-sim --glmdir . --cache 2 abs --cwp 0.05 --2spaces My version is also v5.3.0, Ubuntu, 32bit. With some data or some parameters of --cache it works OK. I do not get this error at 64bit version with the data and parameters which caused the error in 32bit version. Here is full relevant output of mri_segstats. $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --seg ./lh-diff-C-PL-intercept-pial_lgi/cache.th20.abs.sig.ocn.mgh --exclude 0 --i /dataStrojovna2_1/ansk/ADHD/cortical/C_PN_PL_porovnani/qdec/pial_lgi_5_lh_dg_age/y.mgh --avgwf ./lh-diff-C-PL-intercept-pial_lgi/cache.th20.abs.y.ocn.dat --sum /tmp/mri_glmfit-sim.junk.8273 sysname Linux hostname aglaia4 machine i686 user ansk UseRobust 0 Loading ./lh-diff-C-PL-intercept-pial_lgi/cache.th20.abs.sig.ocn.mgh Loading /dataStrojovna2_1/ansk/ADHD/cortical/C_PN_PL_porovnani/qdec/pial_lgi_5_lh_dg_age/y.mgh Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 4 segmentations Computing statistics for each segmentation 1 1 2542 2542.000 2 2 2426 2426.000 3 3 1738 1738.000 Reporting on 3 segmentations Computing spatial average of each frame 0 1 2*** glibc detected *** mri_segstats: malloc(): memory corruption: 0x2f80d4b0 *** Regards, Antonin Skoch

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amygdala nuclear subregions
by Jacobs H (NP) 08 Jan '16

08 Jan '16

Dear FreeSurfer developers, In the FreeSurferColorLut file I see labels for the subregions of the amygdala. Is it possible to extract the volumes for these regions? And how can I do this? I don't see them in the aseg or aparc stat files. Many thanks! Heidi

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R: R: Re: FDR correction
by stdp82＠virgilio.it 08 Jan '16

08 Jan '16

Hi list, I have resolved my issue on the previous point 2 by downloading matlab file on: https://sites.google.com/site/kittipat/mvpa-for-brain- fmri/convert_matlab_nifti after the command that you suggest: fdrthresh = fast_fdrthresh(p,0.05); the script produce p=0.053 Therefore, coming back to my answer I guess that no setting of the FDR threshold to 0.05/3 is requested in order to correct for multiple comparison (right and left hemispheres + subcortical). Is it correct? On the previous point 4 my answer remains open. I have used this command line: >mri_surfcluster --in sig.nii.gz --hemi rh --sign abs --no-adjust --fdr 0.05 -- >minarea 5 --sum summaryfile --subject fsaverage --annot aparc but I have difficulty to undestand which is the option to visualize the map corrected by mri_surfcluster. Additionally, from --help I do not understand the use of --ocn and --cst options. Best regards, Stefano >----Messaggio originale---- >Da: stdp82(a)virgilio.it >Data: 7-gen-2016 15.40 >A: <freesurfer(a)nmr.mgh.harvard.edu> >Ogg: [Freesurfer] R: Re: FDR correction > >Thanks. > >- on question 2: >I have run >rh = MRIread('sig.mgh'); >but this error occur >Undefined function 'MRIread' for input arguments of type 'char'. >no help is permitted on MRIread > >-on question 3: >I'm using this command line to visualize the map describing the functional >connectivity form seed to cortex > >tksurfer fsaverage rh inflated -aparc -overlay R_seed/my-glm.wls/group. >diff/sig.nii.gz -fminmax 1.3 3 >tksurfer fsaverage lh inflated -aparc -overlay L_seed/my-glm.wls/group. >diff/sig.nii.gz -fminmax 1.3 3 > >in this way I visualize correctly for right and left hemisphere the >connectivity from ipsilateral seed. >If I would visualize the the connectivity from contralateral seed, how can I >do? > >If I use >tksurfer fsaverage lh inflated -aparc -overlay R_seed/my-glm.wls/group. >diff/sig.nii.gz -fminmax 1.3 3 >tksurfer fsaverage rh inflated -aparc -overlay L_seed/my-glm.wls/group. >diff/sig.nii.gz -fminmax 1.3 3t > >-on question 4: >I have resolved with this command line: >mri_surfcluster --in sig.nii.gz --hemi rh --sign abs --no-adjust --fdr 0.05 -- >minarea 5 --sum summaryfile --subject fsaverage --annot aparc > >but I have difficulty to undestand which is the option to visualize the map >corrected by mri_surfcluster. >Additionally, from --help I do not understand the use of --ocn and --cst >options. > >Best regards, > > >Stefano > > > > > >>----Messaggio originale---- >>Da: greve(a)nmr.mgh.harvard.edu >>Data: 7-gen-2016 0.34 >>A: <freesurfer(a)nmr.mgh.harvard.edu> >>Ogg: Re: [Freesurfer] FDR correction >> >> >> >>On 01/06/2016 11:00 AM, stdp82(a)virgilio.it wrote: >>> Hi list, >>> >>> I would like to ask you a number of questions regarding the FDR which >>> is performed following seed-based fcMRI using FS-FAST. >>> 1-In the previous mail you have suggested me to use mir_fdr command >>> line (version 6.0). Because I have some problem with new version >>> license (as reported in previous mail) and, overall I have run my data >>> using version 5.3, I would ask you whether FDR integrated in tksurfer >>> (version 5.3) is however reliable as the FDR included in 6.0? >>Yes, they call the same code. >>> >>> 2-Becouse the FDR analysis was performed separately for the right and >>> left hemispheres and the subcortical structures, should I set the FDR >>> threshold to 0.05/3 in order to correct for multiple comparison? (I >>> have one group) >>I'm not sure. You can try to run both hemispheres in matlab, somethiing like >>lh = MRIread('sig.lh.mgh'); >>lhp = 10^-abs(lh.vol); >>rh = MRIread('sig.rh.mgh'); >>rlhp = 10^-abs(rh.vol); >> >>p = [lhp rhp]; >>fdrthresh = fast_fdrthresh(p,fdr); >> >>> >>> 3- Is easy for me to follow the guidelines and visualize the cortical >>> areas which are functionally connected with the omolateral seed. How >>> can I do to visualize also the the cortical areas which are >>> functionally connected with the controlateral seed? If change only the >>> rh/lh in command line the visualization of the results is wrong. >>I don't understand. >>> >>> 4- I'd like to perform mri_surfcluster on a group to eliminate cluster >>> < 5 >>> voxels from sig.nii.gz after FDR correction. I'm running >>> mri_surfcluster --in >>> sig.nii.gz --hemi rh --sign abs --fdr 0.05 --minarea 5 --sum >>> summaryfile --ocn >>> ocnid >>> but --subject ... must be included. >>> How should do I do? I would like to run my analysis on group results, >>> not on a single subject. >>If this is from a group analysis, the subject is probablly fsaverage >>> >>> Thanks for your work. >>> Regards, >>> >>> >>> Stefano >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >>-- >>Douglas N. Greve, Ph.D. >>MGH-NMR Center >>greve(a)nmr.mgh.harvard.edu >>Phone Number: 617-724-2358 >>Fax: 617-726-7422 >> >>Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >>_______________________________________________ >>Freesurfer mailing list >>Freesurfer(a)nmr.mgh.harvard.edu >>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >>The information in this e-mail is intended only for the person to whom it is >>addressed. If you believe this e-mail was sent to you in error and the e- mail >>contains patient information, please contact the Partners Compliance HelpLine >at >>http://www.partners.org/complianceline . If the e-mail was sent to you in >error >>but does not contain patient information, please contact the sender and >properly >>dispose of the e-mail. >> >> >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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Control points on noisy scans
by zalewk＠u.washington.edu 07 Jan '16

07 Jan '16

Good afternoon Freesurfer team, I have a small data set with some exceptionally noisy scans resulting in a mix of hyper and hypo-intense striations in the sagittal plane. Ideally I'd like to conserve as much data as possible considering the small number of subjects despite the quality of the scans. The control points added seem to be able to correct only hyper or hypo-intense artefacts alone, but not both in the same scan. Are there any parameters I could alter to correct such large mis-segmentations over a specific area? (Examples are attached in this email) Best, Kody Zalewski

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MPRAGE Data
by Scott E 07 Jan '16

07 Jan '16

Hi folks, Hopefully I'm not asking this question in the wrong place -- please let me know if I am! I have a T1 MPRAGE data file which I'm trying to process into images. I can't, however, figure out how this data is organized within the file. The manufacturer can't provide me details of how to decode the data without a research agreement, and as I don't own the MRI machine itself, I cannot enter into such an agreement. Does anyone have experience decoding raw MPRAGE data? Thanks! Scott

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Recon-all get stucked without error during processing
by Matthieu Vanhoutte 07 Jan '16

07 Jan '16

Dear FS epxerts, I have launched a recon-all process on a subject. Unfortunately, I tried two times but the process get stucked at the same step without error. Please found the recon-all.log associated attached to this mail. Thanks in advance for helping ! Best regards, Matthieu

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