Freesurfer October 2017

freesurfer@nmr.mgh.harvard.edu

119 participants
179 discussions

Original dimension
by Fereshte 10 Oct '17

10 Oct '17

Dear Experts, I've made some volumes from aseg.mgz using mri_binarize and then used mri_convert to make nii files. But when i open these files using Mricro i see the original dimension of the image has changed ( 181,217,181 to 256,256,256). I have no idea what the problem is. I'd appreciate your help. Many thanks in advance Best

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Fwd: Tracula dpath error
by Anna Varghese 10 Oct '17

10 Oct '17

Dear all, I am unable to get the dpath folder after the running the "trac-all path " step, although it shows an information on the terminal as "trac-paths finished without error". Earlier, I had experienced an error with "trac-all bedp" but I ran it locally by directly using the "bedpostx <file path>" command. A dmri.bedpostX folder with all the files have been created . Following this, I encountered the above mentioned problem for pathway reconstruction. I have attached the config file and trac-all.log file. Would appreciate any help.

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Fornix included with hippocampus
by Alexopoulos, Dimitrios 09 Oct '17

09 Oct '17

A quick question re: the hippocampus segmenation using FS 53. Is the Fornix included as as part of the hippocampus segmentation/volume. Looking at the aseg for "bert", it appears not to be included. Jim ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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volumetric atlas to volumetric subject space
by Jonathan Bain 09 Oct '17

09 Oct '17

Dear FreeSurfer community, For a template subject (Colin27), I have a volumetric atlas (nifti file, where each brain region is numbered 1, 2, 3...). I am trying to use FreeSurfer to get the volumetric atlas into volumetric subject space (moving through surface-based registration). I have tried two approaches, but neither has worked satisfactorily. First, I used mri_vol2surf to move from the Colin27 volume to the subject surface. This was problematic because the output contained fractional labels (e.g. 2.33), and the labeled regions also had holes in them. Second, I used mris_sample_parc to move from the Colin27 volume to annotation files. When overlaid atop the FreeSurfer inflated surface, the output regions were not at all where they were supposed to be. I checked the sform of the original nifti and noticed that the first row was negative (flip in the x-direction), but the error persisted when I flipped the data and changed the sform first row to positive. I already have run recon-all for Colin27 and for my subjects. I am using freesurfer-Linux-centos6_x86_64-dev-20160903-5b25567. I have looked through the archive but have not found this question addressed. If you have any suggestions for how to do this, I would greatly appreciate it! Thank you, Jonathan The commands I am using: - First: mri_vol2surf --mov /path/to/Juelich-maxprob-thr0-1mm.nii.gz --trgsubject 002_KM --o /path/to/002_KM/mri/lh.julich_label.mgz --hemi lh --mni152reg --interp nearest - Second: mris_sample_parc -ct /path/to/freesurfer/FreeSurferColorLUT.txt colin27 lh /path/to/Juelich-maxprob-thr0-1mm.nii.gz colinJUE_lh.annot

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Hole in fsaverage Pial?
by Funk, Quentin 09 Oct '17

09 Oct '17

FS Experts, There seems to be a hole in the lh.pial for fsaverage--see the attached screenshot. It doesn't show up when checking the Euler number, but it's definitely a divet in the produced surface that looks a little strange. I searched through the mailing list history and couldn't find anything about it.. Is this a problem with our installation/will it affect any overlays in that area? -qf Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S. News & World Report as the No. 1 hospital in Texas for patient care. Houston Methodist is nationally ranked in 8 specialties and is designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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occiptal flattening
by Patricia Stefancin 09 Oct '17

09 Oct '17

Hello, I have been trying to flatten patches (the occipital cortex) in order to create retinotopic maps. However, when I run mris_flatten, the command window says it cannot read the patch file I have created. I have followed the tutorial page and have included -1 in my command, and still nothing appears to work. What can I do to flatten these patches? Best, Tricia

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R: Re: R: Re: R: Re: R: Re: Map of covariance
by stdp82＠virgilio.it 09 Oct '17

09 Oct '17

Thank you very much. Where I should put 0 0 0 0 .25 .25 .25 .25? Which are the contrast reported below that I should modify? C1) gr1-gr2_intercept 1 -1 0 0 0 0 0 0 C2 )gr1-gr2_slope 0 0 0 0 1 -1 0 0 C3) gr1-gr3_intercept 1 0 -1 0 0 0 0 0 C4) gr1-gr3_slope 0 0 0 0 1 0 -1 0 C5) gr1-gr4_intercept 1 0 0 -1 0 0 0 0 C6) gr1-gr4_slope 0 0 0 0 1 0 0 -1 C7) gr2-gr3_intercept 0 1 -1 0 0 0 0 0 C8) gr2-gr3_slope 0 0 0 0 0 1 -1 0 C9) gr2-gr4_intercept 0 1 0 -1 0 0 0 0 C10) gr2-gr4_slope 0 0 0 0 0 1 0 -1 C11) gr3-gr4_intercept 0 0 1 -1 0 0 0 0 C12) gr3-gr4_slope 0 0 0 0 0 0 1 -1 C13) gr1+gr2-vs-gr3+gr4.intercept 0.5 0.5 -0.5 -0.5 0 0 0 0 C14) gr1+gr2-vs-gr3+gr4.slope 0 0 0 0 0.5 0.5 -0.5 -0.5 C15) group.effect.intercept 1 -1 0 0 0 0 0 0 1 0 -1 0 0 0 0 0 1 0 0 -1 0 0 0 0 C16) group.effect.slope 0 0 0 0 1 -1 0 0 0 0 0 0 1 0 -1 0 0 0 0 0 1 0 0 -1 >----Messaggio originale---- >Da: "Douglas Greve" <greve(a)nmr.mgh.harvard.edu> >Data: 3-ott-2017 16.19 >A: <freesurfer(a)nmr.mgh.harvard.edu> >Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: Map of covariance > >probably you want 0 0 0 0 .25 .25 .25 .25 > > > >On 10/3/17 10:10 AM, stdp82(a)virgilio.it wrote: >> Many thank for your response. >> Claryfing my question on point 3, >> When I look in group.effect.slope, the map show the group difference removing >> the effect of the covariate. >> Conversely, I would to obtain the map reporting only the effect of covariate >> on dependent variable (functional connectivity). >> Is possible to look on it? >> Regards >> Stefano >> >> >>> ----Messaggio originale---- >>> Da: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >>> Data: 2-ott-2017 16.58 >>> A: <freesurfer(a)nmr.mgh.harvard.edu> >>> Ogg: Re: [Freesurfer] R: Re: R: Re: Map of covariance >>> >>> >>> >>> On 10/01/2017 05:08 PM, stdp82(a)virgilio.it wrote: >>>> Hi, >>>> on 4 groups, 1 covariate (4GV1) >>>> >>>> I run mri_glmfit using the following .mtx >>>> >>>> C1) gr1-gr2_intercept 1 -1 0 0 0 0 0 0 >>>> C2 )gr1-gr2_slope 0 0 0 0 1 -1 0 0 >>>> C3) gr1-gr3_intercept 1 0 -1 0 0 0 0 0 >>>> C4) gr1-gr3_slope 0 0 0 0 1 0 -1 0 >>>> C5) gr1-gr4_intercept 1 0 0 -1 0 0 0 0 >>>> C6) gr1-gr4_slope 0 0 0 0 1 0 -1 0 >>> should be >>> >>> 0 0 0 0 1 0 0 -1 >>> >>>> C7) gr2-gr3_intercept 0 1 -1 0 0 0 0 0 >>>> C8) gr2-gr3_slope 0 0 0 0 0 1 -1 0 >>>> C9) gr2-gr4_intercept 0 1 0 -1 0 0 0 0 >>>> C10) gr2-gr4_slope 0 0 0 0 0 1 0 -1 >>>> C11) gr3-gr4_intercept 0 0 1 -1 0 0 0 0 >>>> C12) gr3-gr4_slope 0 0 0 0 0 0 1 -1 >>>> C13) gr1+gr2-vs-gr3+gr4.intercept 0.5 0.5 -0.5 -0.5 0 0 0 0 >>>> C14) gr1+gr2-vs-gr3+gr4.slope 0 0 0 0 0.5 0.5 -0.5 -0.5 >>>> C15) group.effect.intercept >>>> 1 -1 0 0 0 0 0 0 >>>> 1 0 -1 0 0 0 0 0 >>>> 1 0 0 -1 0 0 0 0 >>>> C16) group.effect.slope >>>> 0 0 0 0 1 -1 0 0 >>>> 0 0 0 0 1 0 -1 0 >>>> 0 0 0 0 1 0 0 -1 >>>> >>>> Please: >>>> 1) Could you check whether the all .mtx are complete and corrected, in >>>> particular the gr1+gr2-vs-gr3+gr4.intercept and the gr1+gr2-vs-gr3+gr4. >> slope? >>> they look correct, except for the one i noted >>>> 2) Could you explain the meaning of: >>>> gr1+gr2-vs-gr3+gr4.slope - does the average slope of grp1 and grp2 differ >> from that of grp3 and 4 >>>> gr1+gr2-vs-gr3+gr4.intercept - same >>>> group.effect.slope - interaction between group and covariate >>>> group.effect.intercept - is there an effect of group on the inercept >>>> 3) Which is the contrast identifying the effect of covariate on group >>>> differences? >>> not sure what you mean >>>> Thanks >>>> >>>> Best regards >>>> >>>> >>>> Stefano >>>> >>>> >>>> >>>>> ----Messaggio originale---- >>>>> Da: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >>>>> Data: 5-set-2017 22.59 >>>>> A: <freesurfer(a)nmr.mgh.harvard.edu> >>>>> Ogg: Re: [Freesurfer] R: Re: Map of covariance >>>>> >>>>> you would need to create a contrast to look for the interaction. If you >>>>> have four gruops and 1 covariate, then it would be >>>>> >>>>> 0 0 0 0 1 -1 0 0 >>>>> >>>>> 0 0 0 0 1 0 -1 0 >>>>> >>>>> 0 0 0 0 1 0 0 -1 >>>>> >>>>> >>>>> >>>>> On 09/05/2017 04:32 PM, stdp82(a)virgilio.it wrote: >>>>>> Hi, >>>>>> e.g., by considering two or more groups, I would like to map the clusters >>>>>> reporting the covariance between the functional connectivity or cortical >>>>>> thickness (dependent variable) and age, tacking in account the group >>>>>> differences. >>>>>> Instead, I'm not interested to map the group differences, taking in >> account >>>>>> the nuisance factors. >>>>>> Thanks, >>>>>> Stefano >>>>>> >>>>>>> ----Messaggio originale---- >>>>>>> Da: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >>>>>>> Data: 5-set-2017 18.12 >>>>>>> A: <freesurfer(a)nmr.mgh.harvard.edu> >>>>>>> Ogg: Re: [Freesurfer] Map of covariance >>>>>>> >>>>>>> I don't understand what you are asking. can you elaborate? >>>>>>> >>>>>>> >>>>>>> On 08/30/2017 12:50 PM, stdp82(a)virgilio.it wrote: >>>>>>>> Hi list, >>>>>>>> by applying a design e.g. 4GV1 in fsgd I could assess the dependence >>>>>>>> of group differences taking in account the effect of covariate. >>>>>>>> Anyway, where I should look if I want assess the the map showing the >>>>>>>> clusters in which the dependent variable is associated to covariate, >>>>>>>> tacking in account the group difference? Please could you suggest my >>>>>>>> the path? >>>>>>>> Thanks >>>>>>>> >>>>>>>> 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 >>>>>> >>>>>> >>>>> -- >>>>> 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 >>>>> >>>> _______________________________________________ >>>> 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 >>> >> _______________________________________________ >> 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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Fixed effects fMRI {Disarmed}
by Kevin Aquino 09 Oct '17

09 Oct '17

Hi all, I would like to perform a fixed effects analysis on a small sample of subjects with FS-fast -- where the time series from all subjects are concatenated together and analysed in a large design matrix. Is there an easy way to do this? I don't know if I'm looking in the wrong place but I can't seem to find it. Cheers, *Dr Kevin Aquino* Research fellow, Sir Peter Mansfield Magnetic Resonance Center, The University of Nottingham. Honorary Research Fellow School of Physics, Faculty of Science, University of Sydney *E* Kevin.aquino(a)nottingham.ac.uk, aquino(a)physics.usyd.edu.au | *W* https://kevinaquino.github.io <http://www.physics.usyd.edu.au/~aquino/> ---------------------------------------------- The brain is a wonderful organ. It starts working the moment you get up and does not stop until you get into the office. - Robert Frost CRICOS 00026A This email plus any attachments to it are confidential. Any unauthorised use is strictly prohibited. If you receive this email in error, please delete it and any attachments. Please think of our environment and only print this e-mail if necessary.

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Problem with New Hippocampus/Amygdala Segmentation
by Max Owens 09 Oct '17

09 Oct '17

Hi Freesurfer Experts, I'm trying to run the new version 6.0 hippocampus/amygdala segmentation procedure (https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields) on data from subjects with whom I have already completed recon-all. I have downloaded the newest development version (and license), as well as the required matlab runtime. However, I am getting the following error: “LD_LIBRARY_PATH is .:freesurfer/MCRv80//runtime/glnxa64:freesurfer/MCRv80//bin/glnxa64:freesurfer/MCRv80//sys/os/glnxa64:freesurfer/MCRv80//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:freesurfer/MCRv80//sys/java/jre/glnxa64/jre/lib/amd64/server:freesurfer/MCRv80//sys/java/jre/glnxa64/jre/lib/amd64/client:freesurfer/MCRv80//sys/java/jre/glnxa64/jre/lib/amd64: Registering imageDump.mgz to hippocampal mask from ASEG cp: cannot stat ‘freesurfer/average/HippoSF/atlas/AtlasDump.mgz’: No such file or directory Error using myMRIread (line 16) Error in myMRIread: temporary directory does not exist Error in segmentSubjectT1_autoEstimateAlveusML (line 134) Command exited with non-zero status 255 @#@FSTIME 2017:09:22:15:55:53 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 e 2.85 S 0.11 U 2.85 P 103% M 205292 F 1 R 22759 W 0 c 2477 w 641 I 0 O 63584 L 0.41 0.56 0.64 @#@FSLOADPOST 2017:09:22:15:55:56 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 0.41 0.56 0.64 All done! ” Have you ever seen this error before? If not, can you provide any suggestions for ways that I might troubleshoot it? I have attached the command I used and the error log if this is of help. Thanks very much for your time, Max -- Max Owens, M.S. Graduate Student in Psychology Clinical Neuroscience Lab University of Georgia

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preproc-sess
by Jiahe Zhang 09 Oct '17

09 Oct '17

Dear Freesurfer experts, I have two questions regarding preproc-sess: 1) What is the default algorithm that does the functional-anatomical registration? And is there any way to change the default to other types of registration methods? 2) If I do not want to normalize to template, i.e. I want to keep the image in native space, should I be using -noreg or -noinorm? Thanks, Jiahe -- Jiahe Zhang Ph.D. Candidate Department of Psychology Northeastern University 617-373-4789

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Freesurfer October 2017