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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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License files with FreeSurfer 5.2.0
by Mike Schmidt 09 Oct '17

09 Oct '17

I am re-running some old scans on current hardware to do comparisons with 5.2.0 output from old hardware, 5.2.0 output from current hardware, and current 6.0.0 output, all of the same input image. I am aware that FreeSurfer 5.2.0 is deprecated and don't intend to use its output, per se. My problem is that I have copied a .license file (from February 2017) that works successfully with version 6.0.0 (known-good) into FreeSurfer 5.2.0's FREESURFER_HOME and FreeSurfer 5.2.0 finds the file, but says it is invalid. Renaming the .license file to license.txt resulted in it not being found at all. I've even retrieved an old license file (from prior to April 2015) from backup that I used to use (email address no longer exists), thinking I had used it with 5.2.0 in the past, but it is also reported as invalid. I've read in this forum that 6.0.0 uses a different license file format due to libcrypt changes. But I can't seem to get new or old licenses to work. Is it possible to register for a replacement old-style license? Or is there another way to get 5.2.0 to work? I have not applied for a new license as I have one that already works with 6.0.0 and have assumed another new one will work the same. Thank you for any assistance, Mike Schmidt

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Re: [Freesurfer] qdec.table_ref
by Martin Reuter 09 Oct '17

09 Oct '17

Hi Amy, please send your questions to the freesurfer email list . Try replacing ID with fsid , also you may need to fix the white spaces (replace multiple spaces with a single space or tab). Best, Martin > On 9. Oct 2017, at 03:09, 田阿敏 <237416567(a)qq.com> wrote: > > > Hi~ > > I am Amy from Zhejiang University in China. When I run QDEC to load the file qdec.table.dat, I always get this info: > > Loading data table /Applications/freesurfer/subjects/qdec/qdec.table.dat... > ERROR: QdecDataTable::Load did not find a column named 'fsid', 'ID', or 'Subject' in the first column of /Applications/freesurfer/subjects/qdec/qdec.table.dat! > Error loading the data table. > > > Attached are the files that I made to load the subjects information. > What's wrong? > ------------------ > 田阿敏 Tian Amin > 13071892606 > amintian(a)zju.edu.cn, 237416567(a)qq.com <mailto:237416567@qq.com> > Master Degree Candidate, > Zhejiang University Interdisciplinary Institute of Neuroscience and Technology, ZIINT. > Huajiachi Campus, No. 268 Kaixuan Road, Jianggan District, Hangzhou, Zhejiang Province, China, 310029. > > > <qdec.table_ref.dat><qdec.table_ref2.dat><qdec.table.dat>

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qdec.table_ref
by 田阿敏 08 Oct '17

08 Oct '17

Hi~ I am Amy from Zhejiang University in China. When I run QDEC to load the file qdec.table.dat, I always get this info: Loading data table /Applications/freesurfer/subjects/qdec/qdec.table.dat... ERROR: QdecDataTable::Load did not find a column named 'fsid', 'ID', or 'Subject' in the first column of /Applications/freesurfer/subjects/qdec/qdec.table.dat! Error loading the data table. Attached are the files that I made to load the subjects information. What's wrong? ------------------ 田阿敏 Tian Amin 13071892606 amintian(a)zju.edu.cn, 237416567(a)qq.com Master Degree Candidate, Zhejiang University Interdisciplinary Institute of Neuroscience and Technology, ZIINT. Huajiachi Campus, No. 268 Kaixuan Road, Jianggan District, Hangzhou, Zhejiang Province, China, 310029.

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recon-all exits with errors
by Ali Radaideh 07 Oct '17

07 Oct '17

Dear FreeSurfer Experts, I have just launched a new project and collected new T1 weighted images (as my previous ones) and started processing them using FreeSurfer. Unfortunaely non of them works with FreeSurfer. When I run recon-all -autorecon-all -s subjecname, I get the following error: #@# Talairach Fri Oct 6 09:20:02 EEST 2017 /home/ali/processing/Farah_hospital/MR.BASHEER_IGIAM/mcropped_noor/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz Linux ali-XPS-L501X 4.8.0-54-generic #57-Ubuntu SMP Wed May 24 10:21:44 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s mcropped_noor exited with ERRORS at Fri Oct 6 09:20:05 EEST 2017 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting I have checked my images and they look fine and they are similar to the ones I have processed a year ago. I have searched for a solution to this error but unfortunately I did not find any. Could you please help me on this? Thanks alot in advance, Ali -- *Ali M. Al-Radaideh. PhDDepartment of Medical ImagingFaculty of Allied Health SciencesThe Hashemite University, Zarqa, JordanW.phone +962 5 3903333 ext.5422, 5355, 5364Email: ali.radaideh(a)hu.edu.jo <ali.radaideh(a)hu.edu.jo>* *webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM= <http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=>*

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Fw: Re: 1 mistake in FreeSurfer
by 田阿敏 07 Oct '17

07 Oct '17

------------------ 田阿敏 Tian Amin 13071892606 amintian(a)zju.edu.cn, 237416567(a)qq.com Master Degree Candidate, Zhejiang University Interdisciplinary Institute of Neuroscience and Technology, ZIINT. Huajiachi Campus, No. 268 Kaixuan Road, Jianggan District, Hangzhou, Zhejiang Province, China, 310029. ------------------ Original ------------------ From: "ltirrell";<ltirrell(a)nmr.mgh.harvard.edu>; Date: Sat, Oct 7, 2017 07:26 AM To: "田阿敏"<237416567(a)qq.com>; Subject: Re: 1 mistake in FreeSurfer Hello, This seems to be a problem with the version of python you're using. If you can use python 2.7, the issue should go away. If you continue to run into any issues, you should contact the freesurfer mailing list (freesurfer(a)nmr.mgh.harvard.edu) and they may be able to help. Best, Lee On Fri, 6 Oct 2017, ?????? wrote: > > Hi~ > > > Here is error report when I run aparcstats2table. Maybe adding the missing parentheses could solve the > problem. Thanks~ > > > > tianamindeMacBook-Pro:subjects amytian$ aparcstats2table -s subj1 --hemi lh > > File "/Applications/freesurfer/bin/aparcstats2table", line 156 > > print 'ERROR: atleast 1 subject must be provided' > > ^ > > SyntaxError: Missing parentheses in call to 'print' > > > > > ------------------ > ?????? Tian Amin > 13071892606 > amintian(a)zju.edu.cn, 237416567(a)qq.com > Master Degree Candidate, > Zhejiang University Interdisciplinary Institute of Neuroscience and Technology, ZIINT. > Huajiachi Campus, No. 268 Kaixuan Road, Jianggan District, Hangzhou, Zhejiang Province, China, 310029. > > > > 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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Descriptions of regions in Yeo 2011 Network atlases
by Mehta, Chintan 06 Oct '17

06 Oct '17

Dear Freesurfer users, I am examining the Yeo 2011 17 Network atlases in Freesurfer 6.0. The regions are labeled 1 through 17. Is there a reference table mapping these numbers with the names of cognitive networks described by Yeo, et al. (2011) (<https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3174820/>https://www.ncbi.nlm.nih.gov/pubmed/21653723)? For example, would network 1 correspond to visual networks? I cannot find descriptions in the readme files except the color look-up table. Thank you. Best, Chintan

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