Freesurfer July 2019

freesurfer@nmr.mgh.harvard.edu

104 participants
165 discussions

make_average_subject error
by Niels Janssen . 31 Jul '19

31 Jul '19

External Email - Use Caution Dear all, I have seen this error mentioned several times on the list but I have never seen a solution posted. It is claimed that there is a patch and a README that explains the patch at: https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/ In this folder there are a bunch of files but there is no README so I am not sure what exactly I need to do. I tried replacing the files in my /usr/local/freesurfer/bin with those in this patch folder but the error remains. This error appears with all my data sets that I have tried. So it doesnt seem to be something specific to my data. Loading aseg from /media/fMRI_21/studyname/freesurfer/avgsub3/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; mghRead(mri/norm.mgz, -1): could not open file ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter Segmentation fault (core dumped) Linux nielsj-XXXYYY 4.18.0-25-generic #26~18.04.1-Ubuntu SMP Thu Jun 27 07:28:31 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux recon-all -s avgsub3 exited with ERRORS at mié jul 31 12:05:20 WEST 2019 -- Niels Janssen Brain Imaging Laboratory Institute of Biomedical Technologies Institute of Neurosciences University of La Laguna Tenerife, Spain https://sites.google.com/view/nielsjanssen/

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Re: [Freesurfer] ppmi
by Tosun, Duygu 30 Jul '19

30 Jul '19

External Email - Use Caution Is this for PPMI project? We can provide total hippo volumes if needed. > On Jul 31, 2019, at 1:48 AM, eric f <ejf(a)icsi.berkeley.edu> wrote: > > I don't think it will take 20h, probably more like 10-12h, so that's > only 1.5 years:). Most people who are running it that many data sets > have access to a computational cluster (on ours it would only take a few > weeks). Alternatively, you can try buying cloud-based computational > power (eg, amazon web services). > >> On 7/30/19 4:56 PM, Jiajun Luo wrote: >> >> External Email - Use Caution >> >> Hi, >> >> Now I have T1 and T2 images (dcm files) and want to calculate the >> hippocampal volume. I find it takes ~20h to run recon-all -all and >> then ~40min to run -hippocampal-subfields-T1. However, I need to >> calculate the hippocampal volume for more than 1,000 individuals >> (which means it may take ~3 years to complete). Do you know how I can >> improve my efficiency? >> >> Thank you! >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.e… > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.e…

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Help for Hippocampal Calculation
by Jiajun Luo 30 Jul '19

30 Jul '19

External Email - Use Caution Hi, Now I have T1 and T2 images (dcm files) and want to calculate the hippocampal volume. I find it takes ~20h to run recon-all -all and then ~40min to run -hippocampal-subfields-T1. However, I need to calculate the hippocampal volume for more than 1,000 individuals (which means it may take ~3 years to complete). Do you know how I can improve my efficiency? Thank you!

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Re: [Freesurfer] mri_curvature_stats: -a parameter has no effect and errors (FACES_aroundVertex_reorder: packed / faces mismatch, and Segmentation fault)
by Maria Kalemanov 30 Jul '19

30 Jul '19

Dear Rudolph, Thanks a lot for your reply! Do you know why does it fail on holes/edges? Does the algorithm require each triangle vertex to have 1-ring neighbours? Also, do you by chance know how to use the -a parameter correctly? I did not observe any difference nor in the results nor in runtime with a call like this: mris_curvature_stats -a 5 -f surface -m -o noisy_sphere_r10_a5.stats -G --signedPrincipals --writeCurvatureFiles noisy_sphere noisy_sphere_r10 Many thanks and best wishes Maria On 30.07.19 18:00, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > Hi Maria -- > > If there are holes/edges in the surface `mris_curvature_stats` it will > fail. -- Maria Kalemanov, M.Sc. PhD student Department Molecular Structural Biology Max Planck Institute of Biochemistry Am Klopferspitz 18 82152 Martinsried Germany Phone:+49 89 8578-2041 External Email - Use Caution

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Postdoctoral Research Associate Position Available
by Shashwath Meda 30 Jul '19

30 Jul '19

External Email - Use Caution *Please direct all submission materials and inquiries to Dr. Michal Assaf @ michal.assaf(a)hhchealth.org <michal.assaf(a)hhchealth.org>* *Postdoctoral Research Associate Position * The Olin Neuropsychiatry Research Center is seeking to fill a postdoctoral researcher/fellow position in the area of autism/cognitive neuroscience focusing on imaging data analysis. The fellow will join a lab conducting research using advanced neuroimaging methods (MRI, DTI, fMRI) in both healthy and psychiatric populations. The major focus will be developing and applying statistical analysis methods such as ICA and dynamic Functional Connectivity to neuroimaging data collected in an NIMH funded study, which examines brain function related to social cognition and emotion regulation in individuals with autism spectrum disorder. Applicants should have a Ph.D. in Psychology, Neuroscience, or related field. They should have an understanding of fMRI statistical methods and experimental design, and promising research experience. The ideal candidate will come from a doctoral program that has provided fMRI data analysis skills, solid theoretical understanding of cognitive neuroscience and psychology/psychiatry, and working knowledge of Linux, Matlab (programming experience preferred), and similar systems to conduct fMRI analyses, or to have an existing track record with fMRI analysis. In addition to opportunities to develop their own program of research compatible with the lab mission, the postdoctoral fellow will have access to several large archival neuroimaging datasets, training in sophisticated data analysis techniques (i.e., independent component analysis, multi-modal analysis, etc.), and access to the center’s data collection and analysis resources (e.g., fMRI, sMRI, DTI, EEG, genotyping, neuropsychological assessment). The fellowship is open for an initial two years, with an option to renew. The Olin Center is an established clinical neuroscience center at the Institute of Living/Hartford Hospital and is affiliated with Yale University with over 40 faculty, postdocs and research assistants. Our mission is to conduct cutting-edge clinical and cognitive neuroscience research that can ultimately translate to psychiatric care. The Olin Center is located on the grounds of the Institute of Living, providing access to thousands of psychiatric patients each year treated in numerous clinical programs. This is an exciting opportunity for a clinical or cognitive neuroscience postdoc looking to establish him/herself in the field through productivity, training in advanced analysis techniques, and access to ample scientific resources. If interested, please send a statement of scientific interests, accomplishments and relevant skills, a CV, and contact information for at least 3 academic references to Dr. Michal Assaf, Autism & Functional Mapping lab director, at michal.assaf(a)hhchealth.org

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TRACULA incorporate topup instead of field map?
by Daniel Callow 30 Jul '19

30 Jul '19

External Email - Use Caution Hello, I have previously used field map correction for b0 inhomogeneities when running TRACULA, however my new data set has A>P and P>A encoding. I know that topup has been shown to perform slightly better than filed map correction. I wonder if it would be possible to manually edit the ($dob0) then # B0-inhomogeneity "correction" part of the code and run topup instead of epidewarp.fsl? I am trying to determine how feasible this is and was wondering if this had been tried by others? If not, does it make more sense to process the data with topup separately and then incorporate it into TRACULA? Thank you for any guidance you can provide, *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442(a)gmail.com <ddcc2442(a)gmail.com>* 443-254-6298

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mgz files not being recreated following recon-all
by Charles Tyshkov 30 Jul '19

30 Jul '19

External Email - Use Caution Hello, After running recon-all, and attempting to run freesurfer (using the command "checksurfswmflair") the following error message appears for number of studies: Failed to load MRI /Volumes/MSdata/SAG_3D_BRAVO/MS2030181102/lesion/flair_on_T1.flirt.nii.gz It seems that gz lesion files are not being created/carried-over for these studies after being run through my script (other studies interestingly are opening up successfully using the same script). The successful studies seem to contain the zip file. Any thoughts as to why certain studies which contain nii.gz files are failing to recompress after being processed? Thanks, Charlie

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Re: [Freesurfer] mris_pmake issue
by Rudolph Pienaar 30 Jul '19

30 Jul '19

OK -- looked again -- and I need to fix the in-line help obviously. Anyway, this works: mris_pmake --subject testSubject \ --hemi lh \ --surface pial \ --curv sulc \ --mpmOverlay euclidean \ --mpmProg pathFind \ --mpmArgs vertexStart:121981,vertexEnd:132633 (obviously use your <subject>) Try that and let me know. Best On Tue, 2019-07-30 at 17:33 +0200, Sebastian Strauss wrote: > External Email - Use Caution > > Dear Rudolph, > Thank you for following up. > I changed flags and tried it again with this command line: > > mris_pmake --subject cvs_avg35_inMNI152_temp --hemi lh -- > surfaceFile pial --curvatureFile > sulc --mpmOverlayArgs euclidean --mpmProgID pathFind --mpmArgs > startVertex:121981,endVertex:132633 > > > There seems to be a similar problem with the flag since message is > the same: > > mris_pmake: unrecognized option `—surfaceFile' > > Any further ideas? > > Thank you for your help! > > > Best > > > > Am 30.07.2019 um 16:53 schrieb Rudolph Pienaar < > > rudolph(a)nmr.mgh.harvard.edu>: > > > > > > Apology if this is a repeat email. I used the wrong email address > > in my > > reply. I was one of the original > > authors of `mris_pmake` although it's been (quite) a few years now. > > I > > do remember that at some point the CLI changed, and given the FS > > release cycle it took a while for this to make it into production. > > > > Anyway, yes, the flags changed and looks like the documentation > > didn't. > > I looked at the code and sort of (rustily) remembered where things > > changed. Try using the flags below instead. You should be able to > > figure out the mapping I think. So what used to be '--surface0' is > > now > > '--surfaceFile'. Similary, the old '--surface1' is now ' > > --secondarySurfaceFile', etc. > > > > Please try with these new flags where appropriate and let us know > > if it > > works. It would also be useful if you posted your full CLI when you > > try > > and run a command. > > > > Best > > > > > > > > startVertex > > endVertex > > surfaceFile > > secondarySurfaceFile > > curvatureFile > > secondaryCurvature > > patchFile > > labelFile > > labelFileAuxSurface > > costFile > > b_labelFile_save > > b_patchFile_save > > b_transitionPenalties > > b_useAbsCurvs > > controlPort > > timeoutSec > > b_syslogPrepend > > userMessages > > sysMessages > > resultMessages > > stdout > > costCurvFile > > b_mpmProgUse > > b_mpmOverlayUse > > mpmProgID > > mpmArgs > > mpmOverlayArgs > > b_exitOnDone > > b_costPathSave > > mpmOverlayID > > > > > > On Mon, 2019-07-29 at 21:36 +0200, Sebastian Strauss wrote: > > > External Email - Use Caution > > > > > > Dear Freesurfers, > > > > > > I am trying to calculate distances using mris_pmake with > > > Freesurfer > > > Version 6.0.0. When using the command line the following error > > > appears: > > > mris_pmake: unrecognized option '—surface0' > > > > > > In January the similar question ( > > > https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg60835.html > > > ) was ask but without any answers. Does anyone have the same > > > problem > > > btw any suggestions? > > > > > > Thank you! > > > > > > Best wishes > > > > > > Sebastian > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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mris_pmake issue
by Sebastian Strauss 30 Jul '19

30 Jul '19

External Email - Use Caution Dear Freesurfers, I am trying to calculate distances using mris_pmake with Freesurfer Version 6.0.0. When using the command line the following error appears: mris_pmake: unrecognized option '—surface0' In January the similar question (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg60835.html) was ask but without any answers. Does anyone have the same problem btw any suggestions? Thank you! Best wishes Sebastian

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mri_curvature_stats: -a parameter has no effect and errors (FACES_aroundVertex_reorder: packed / faces mismatch and Segmentation fault)
by Maria Kalemanov 30 Jul '19

30 Jul '19

Hello FreeSurfer developers, I have three issues with mris_curvature_stats: 1. I attempted to compute curvature on a *noisy sphere* surface (attached) using different -a parameter values, integers from 0 to 10, like this: mris_curvature_stats -a 5 -f surface -m -o noisy_sphere_r10_a5.stats -G --signedPrincipals --writeCurvatureFiles noisy_sphere noisy_sphere_r10 However, there is no slight difference between the curvatures in the output files. Also the runtimes do not vary. Am I calling the function wrong? Attached is also the ".stats" output in case it's of any use. 2. When running the same command as in 1. (without -a parameter) on a *noisy cylinder *surface (attached), I got the following standard output with errors: Outputting results using filestem [ noisy_cylinder_r10_h25.stats ] Toggling save flag on curvature files [ ok ] Toggling 'signedPrincipals' flag ON [ ok ] Toggling save flag on curvature files [ ok ] Setting surface [ noisy_cylinder/noisy_cylinder_r10_h25.surface ] Reading surface... [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [#FACES_aroundVertex_reorder: packed / faces mismatch; vertex = 94, faces = 4, packed = 2 No such file or directory FACES_aroundVertex_reorder: packed / faces mismatch; vertex = 106, faces = 4, packed = 2 No such file or directory ##################FACES_aroundVertex_reorder: packed / faces mismatch; vertex = 1344, faces = 3, packed = 2 No such file or directory FACES_aroundVertex_reorder: packed / faces mismatch; vertex = 1346, faces = 3, packed = 2 No such file or directory FACES_aroundVertex_reorder: packed / faces mismatch; vertex = 1347, faces = 3, packed = 2 No such file or directory FACES_aroundVertex_reorder: packed / faces mismatch; vertex = 1348, faces = 3, packed = 2 No such file or directory FACES_aroundVertex_reorder: packed / faces mismatch; vertex = 1350, faces = 3, packed = 2 No such file or directory FACES_aroundVertex_reorder: packed / faces mismatch; vertex = 1351, faces = 3, packed = 2 No such file or directory FACES_aroundVertex_reorder: packed / faces mismatch; vertex = 1352, faces = 3, packed = 2 No such file or directory FACES_aroundVertex_reorder: packed / faces mismatch; vertex = 1354, faces = 3, packed = 2 No such file or directory FACES_aroundVertex_reorder: packed / faces mismatch; vertex = 1356, faces = 3, packed = 2 No such file or directory FACES_aroundVertex_reorder: packed / faces mismatch; vertex = 1389, faces = 4, packed = 2 No such file or directory FACES_aroundVertex_reorder: packed / faces mismatch; vertex = 1393, faces = 3, packed = 2 No such file or directory FACES_aroundVertex_reorder: packed / faces mismatch; vertex = 1394, faces = 3, packed = 2 No such file or directory FACES_aroundVertex_reorder: packed / faces mismatch; vertex = 1395, faces = 4, packed = 2 No such file or directory FACES_aroundVertex_reorder: packed / faces mismatch; vertex = 1398, faces = 3, packed = 2 No such file or directory #] [ ok ] FACES_aroundVertex_reorder: packed / faces mismatch; vertex = 1399, faces = 3, packed = 2 Determining KH curvatures... [FACES_Hcurvature_determineSign: During call 2, the passed faces do not share an edge 3. When running the same command as in 1. (without -a parameter) on a *smooth cylinder* surface (attached), I got the following standard output with an error: Saving surf/smooth_cylinder_r10_h25.surface as a surface Outputting results using filestem [ smooth_cylinder_r10_h25.stats ] Toggling save flag on curvature files [ ok ] Toggling 'signedPrincipals' flag ON [ ok ] Toggling save flag on curvature files [ ok ] Setting surface [ smooth_cylinder/smooth_cylinder_r10_h25.surface ] Reading surface... [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [run_freesurfer_curvature.sh: line 10: 24318 Segmentation fault (core dumped) mris_curvature_stats -f surface -m -o ${BASE}.stats -G --signedPrincipals --writeCurvatureFiles $SUBJECT $BASE I've searched the list and no similar errors have been reported. Does anyone know why the errors happen? Can it be because the cylinder surfaces are open and have edges? 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Platform: SUSE Linux Enterprise Server 12 SLES 12 SP 1 3) uname -a: Linux hpcl5004 3.12.74-60.64.40-default #1 SMP Wed May 10 05:07:16 UTC 2017 (4eb35ec) x86_64 x86_64 x86_64 GNU/Linux Thanks and best regards Maria External Email - Use Caution

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Freesurfer July 2019