Freesurfer

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30135 discussions

Segmentation of hippocampal subfields with current dev version
by Eric A Nelson 08 Jul '16

08 Jul '16

Hello, I am trying to use the hippocampal subfield segmentation presented in the Iglesias paper. I downloaded and installed the latest available dev version about a week ago, along with FSL and the Matlab 2012b runtime. I attempted to run the pipeline and the hippocampal subfield segmentation together. The primary pipeline ran successfully as indicated by the log as well as manually checking the output in freeview. The hippocampal subfield segmentation did not complete successfully and the subsequent output files are nowhere to be found. I checked the archive and saw that someone had a similar issue back in October. Based on the archive I have done the following trouble shooting steps: 1) I made sure that /Applications/freesurfer/MCRv80/bin/maci64/libmwi18n.dylib does exist. 2) I also tried unsetting the DYLD_LIBRARY_PATH as followed: In bash: unset DYLD_LIBRARY_PATH In (t)csh: unsetenv DYLD_LIBRARY_PATH Then I reran the hippocampal segmentation as follows: recon-all -s [subject] -hippocampal-subfields-T1 Still no success and not sure what else I can do. I am including both the recon-all.log and hippocoampal-subfields-T1.log. Best, Eric Nelson Neuroimaging and Translational Research Lab UAB

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Refining subcortical structures
by Dorsa Haji Ghaffari 08 Jul '16

08 Jul '16

Hi, I want to refine the surface of my segmented subcortical structures such as thalamus. I know -fix is used for refining the cortex surface, but is there any function that refines the subcortical structures? Thank you Dorsa

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qdec error
by shi yao wang 08 Jul '16

08 Jul '16

Dear FS experts: I am trying to qdec to analysis FS results. when I loading qdec.table.dat, it shows cannot open the data (could not fine column name of fsid or ID) Following is my qdec files: /home/Lawrence/Lawrence_data fsid Gender age diagnosis L_frontal_V L_cingulate_V L_occipital_V L_temporal_V L_parietal_V L_insula_V R_frontal_V R_cingulate_V R_occipital_V R_temporal_V R_parietal_V R_insula_V 201 male 26 RT 90473 12084 21898 59241 62664 5899 85844 11010 19002 56413 60214 6085 202 male 21 RT 97466 10844 25305 59970 60806 7282 96692 12076 26222 61450 61593 7172 203 female 27 RT 72102 10805 17281 47113 47328 5990 72102 10805 17281 47113 47328 5990 301 female 19 Control 71977 7757 17074 44763 45861 5627 68432 8775 17099 44247 48478 5407 302 female 21 Control 81139 11166 23599 56458 51749 6361 80712 9279 24278 54830 54307 6596 303 male 20 Control 99284 11845 26018 65006 60851 7058 96242 10520 23110 61714 67203 7235 error message: Loading data table /home/Lawrence/Lawrence_data/qdec/qdec.table.dat... ERROR: QdecDataTable::Load could not find column named 'fsid' or 'ID' in /home/Lawrence/Lawrence_data/qdec/qdec.table.dat! Error loading the data table. Thanks Lawrence

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Fwd: Recon-all exited with errors after mri_nu_correct.mni
by Emeline MULLIER 08 Jul '16

08 Jul '16

Hello FreeSurfer Developers, I have just tried to install FreeSurfer on a new machine and I met a problem with recon-all command. I have tried the tutorial command : recon-all -s bert -all And I have the error message : recon-all -s bert exited with ERRORS. My machine is on Ubuntu 16.04. I installed : freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 I attached my recon-all.log. $FREESURFER_HOME /usr/local/freesurfer I saw a similar problem with virtualbox shared folder but it is not my case here. Do you have an idea of the problem ? Thank you, __ Emeline MULLIER PhD Candidate Department of Radiology Center hospitalier universitaire vaudois (CHUV) and Université de Lausanne (UNIL) Rue du Bugnon 46, CH-1011

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Mri_glmfit-sim hemisphere correction
by Arkadiy Maksimovskiy 08 Jul '16

08 Jul '16

Hi Everyone, I was wondering if someone might know whether it is necessary to use the flag "2spaces" on both the left and the right hemisphere? If I am understanding correctly, this flag corrects for a specific multiple comparison of two hemispheres. Thus, it seems like it would only be necessary to only use it once, because if used on each hemisphere, we would be "penalizing" our results more than necessary- thus being too conservative. If we already correct for using two hemispheres once, then why correct a second time? If it is only necessary to use it on only one of the hemispheres, would this run the risk of unfairly biasing our results (i.e. more conservative on one hemisphere and more liberal on another)? Thank you for your help in clarifying this, - Arkadiy

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FSFAST error: ERROR: fast_selxavg3() failed\n
by ERIK JAHNER 08 Jul '16

08 Jul '16

Hello FreeSurfer Developers, This is Erik Jahner, I’m attempting to complete the final step in the tutorial concerning FSFast Functional connectivity walkthrough (http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkth… ), but for I get the following error when I run the following command: selxavg3-sess -s subj439rest -a fc.lpccseed.surf.lh Mon Jul 4 11:01:41 PDT 2016 rawfunc2surf-sess completed ---------------------------------------- Started at Mon Jul 4 11:01:40 PDT 2016 Ended at Mon Jul 4 11:01:41 PDT 2016 preproc-sess done ------------------------------------------- /Applications/freesurfer/LagStructure/subj439rest Mon Jul 4 11:01:41 PDT 2016 anadir = /Applications/freesurfer/LagStructure/subj439rest/rest/fc.lpccseed.surf.lh DoGLMFit = 1 DoContrasts = 1 UpdateNeeded = 1 ------------------------------------------ ------- matlab output -------------------- matlab: Command not found. ------------------------------------------ ERROR: fast_selxavg3() failed\n I've searched the list and no similar errors have been reported. I have tried to reinstall MATLAB; I have tried following the instructions to install the runtime environment; I have tried redoing all analysis from scratch. I have noticed that STEP 5 does not work unless I change the -cfg from “L_Posteriorcingulate.config” to “mean.L_Posteriorcingulate.config”. I don’t think this is the problem, but I thought I would point it out. My session directory is “subj439rest” Instead of titling the sub directory “bold”, I titled it “rest” 1) FreeSurfer version: freesurfer-Darwin-lion-stable-pub-v5.3.0 2) Platform: OSX Yousemite 3) uname -a: Darwin ERIKs-iMac.local 15.5.0 Darwin Kernel Version 15.5.0: Tue Apr 19 18:36:36 PDT 2016; root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64 4) selxavg3-sess-rest-fc.lpccseed.surf.lh-160704110140.log: see attached ___________________________________________________ Here are the command lines I put in for steps 4-8, incase this is of some use: STEP 4 fcseed-config -segid 1010 -fcname L_Posteriorcingulate.dat -fsd rest -mean -cfg mean.L_Posteriorcingulate.config STEP 5 fcseed-sess -s subj439rest -cfg mean.L_Posteriorcingulate.config STEP 6 fcseed-config -wm -fcname wm.dat -fsd rest -pca -cfg wm.config fcseed-sess -s subj439rest -cfg wm.config fcseed-config -vcsf -fcname vcsf.dat -fsd rest -pca -cfg vcsf.config fcseed-sess -s subj439rest -cfg vcsf.config STEP7 mkanalysis-sess -analysis fc.lpccseed.surf.lh -surface fsaverage lh -fwhm 5 -notask -taskreg L_Posteriorcingulate.dat 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -mcextreg -polyfit 5 -nskip 4 -fsd rest -TR 2 -per-run STEP 8 selxavg3-sess -s subj439rest -a fc.lpccseed.surf.lh

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cache.th13.neg.sig.cluster.mgh directionality
by Arkadiy Maksimovskiy 08 Jul '16

08 Jul '16

Hello, I apologize if the questions are trivial- I have checked the archives, but could not find anything on this. I have run a t-test between two groups on cortical thickness, and used mri_glmfit-sim for pos, neg, and abs versions. 1. If my FSGD is organized as: Group 1 Group 2 and my matrix file is 1 -1 Would a blue result in an absolute version indicate that Group 1 < Group 2? 2. When running the command: "less" on "cache.th13.pos.sig.cluster.mgh", I am getting 1 significant cluster, however, when running the same command on the "absolute" version of this file, there is nothing significant. Do you know why this might be the case? Much appreciated, Arkadiy

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Error with MatlabR2016a and LGI
by Mahtab Farahbakhsh 08 Jul '16

08 Jul '16

Dear FreeSurfer, I am trying to calculate LGI for my images, but it seems like that it doesn't work. I have tried everything, but it's still giving me the same error. I'm using FreeSurfer on a mac and my Matlab version is R2016a. When I try to run "recon-all -s <subj> -localGI", I get this error: ERROR: Matlab is required to run mris_compute_lgi!. I have done these so far: PATH=/Applications/MATLAB_R2016a.app/bin/matlab:$PATH export PATH And my $PATH is: /Applications/MATLAB_R2016a.app/bin/matlab:/usr/local/fsl/bin:/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/usr/local/fsl/bin:/Applications/freesurfer/mni/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/opt/X11/bin: No such file or directory And when I write getmatlab, I get this: ERROR: Cannot find matlab. Does not exist or is not in path. My original Matlab is in the /Applications folder and I also have a folder named "matlab" in my FreeSurfer folder. Would you please guide me what I should do? Best Regards, Mahtab.

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Re: [Freesurfer] {Filename?} Hippocampal subfields --> Can't find a *ctf file?
by pierre deman 08 Jul '16

08 Jul '16

Thanks ! Cheers, Pierre On Jul 8, 2016 1:14 PM, "Iglesias, Eugenio" <e.iglesias(a)ucl.ac.uk> wrote: I think I identified the problem; hopefully this will be sorted out very soon. Cheers, Eugenio Juan Eugenio Iglesias Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On 7 Jul 2016, at 19:23, Perea Camargo, Rodrigo Dennis < RPEREACAMARGO(a)mgh.harvard.edu> wrote: *Warning: This message has had one or more attachments removed (recon-all.cmd). Please read the "UCL-Attachment-Warning.txt" attachment(s) for more information.* Hi all, I am currently trying to run hippocampal subfields in a couple of my participants using FreeSurfer6.0 (located at *nmr*:/usr/local/freesurfer/stable6). It did run successfully for many of my subjects earlier in the year but some of them only had a let hemisphere segmentation. So I decided to re-run them using launchpad and also my local nmr computer. Now, none of the hippocampal sufields segmentations appear (no rh/lh.hippoSfLabels-T1-T2.*.mgz appears). I looked at <FSSUBJECT>/scripts/scripts/hippocampal-subfields-T1T2.log and the error I get is: Error:Cannot find CTF archive /autofs/cluster/freesurfer/centos6_x86_64/stable6/bin/segmentSubjectT1T2_autoEstimateAlveusML.ctf Could a missing *.ctf cause the error? (btw, the re-run happened after the major hardware crash). Thanks in advance for your help, Rodrigo PS: I am attaching the *log files as suggested in the bug reporting page. --- Rodrigo Dennis Perea Research Fellow Department of Radiology Athinoula A. Martinos Center Massachusetts General Hospital rpereacamargo(a)mgh.harvard.edu This is a message from the E-Mail Virus Protection System at UCL ---------------------------------------------------------------------- The original e-mail attachment (recon-all.cmd) is on the list of unacceptable attachments for UCL and has been replaced by this warning message. This constraint is in place to protect users from viruses and other malware. If you think this attachment is a legitimate file and you wish to receive it, please ask the sender to rename the file extension (eg rename file.exe to file.ex_) and resend it to avoid this constraint. On receiving the file you will have to save it and rename it back to its original extension. Reference: 1bLDxs-0003ZW-3F -- UCL E-mail Virus Protection System Servicedesk(a)ucl.ac.uk Internal phone: 25000 <hippocampal-subfields-T1T2.log><recon-all.log> _______________________________________________ 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 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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PhD/Postdoc positions in Neuroscience of Autism/Dyslexia, Max Planck Institute, Leipzig
by Katharina von Kriegstein 08 Jul '16

08 Jul '16

Applications are welcomed for two researcher positions at doctoral or postdoctoral level at the Max Planck Institute for Human Cognitive and Brain Sciences (MPI-CBS) in Leipzig, Germany, in the Neural Mechanisms of Human Communication group led by Katharina von Kriegstein. PhD student or Postdoctoral Position in Neuroscience of Developmental Dyslexia: The objective of the research project is to use functional and structural magnetic resonance imaging (MRI) and behavioural intervention training to understand the role of auditory and visual sensory processing in populations with developmental dyslexia. Further information on the position can be found here: http://www.cbs.mpg.de/489916/job_full_offer_10626437?c=7390 PhD student or Postdoctoral position in Neuroscience of Autism Spectrum Disorder: The objective of the research project is to use high-resolution functional and structural magnetic resonance imaging (MRI) and behavioural tests to understand the role of auditory and visual sensory processing in populations with Autism Spectrum Disorder. Further information on the position can be found here: http://www.cbs.mpg.de/490195/job_full_offer_10626459?c=7390 Both positions are funded by an ERC-Consolidator grant. --- Katharina von Kriegstein Max Planck Research Group Leader Max Planck Institute for Human Cognitive and Brain Sciences Stephanstr. 1A, 04103 Leipzig, Germany Professor of Cognitive and Clinical Neuroscience Humboldt University of Berlin Rudower Chaussee 18, 12489 Berlin, Germany Phone +49 (0) 341-9940-2476 Fax +49 (0) 341-9940-2448 http://www.cbs.mpg.de/independent-research-groups/human-communication

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