Freesurfer

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30088 discussions

Re: [Freesurfer] mris_decimate error
by fsbuild 06 Sep '19

06 Sep '19

External Email - Use Caution Hello, On the Mac, we use homebrew to provide some libraries that freesurfer binaries need to link against in order to run, see https://brew.sh/ Once you install homebrew you should have a “brew” command available in the terminal window.  Then to get libglib you could try from the terminal, $ brew install glib … though it may tell you it is already installed.  You could also check that it exists with, $ ls /usr/local/lib/libglib-2..0.0.dylib/usr/local/lib/libglib-2.0.0.dylib@- R. On Sep 6, 2019, at 14:17, rockj5(a)netzero.net wrote:       External Email - Use Caution        When running mris_decimate on macOS High Sierra, I get this error:dyld: Library not loaded: /usr/local/lib/libglib-2.0.0.dylib Referenced from: /Applications/freesurfer/bin/mris_decimate Reason: image not foundAbort trap: 6Is this a library that was supposed to be installed by FreeSurfer? I did not make any changes to the installation so I am not sure why this error is occurring.Thanks to anyone that can help. I really appreciate it._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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mris_decimate error
by rockj5＠netzero.net 06 Sep '19

06 Sep '19

External Email - Use Caution When running mris_decimate on macOS High Sierra, I get this error: dyld: Library not loaded: /usr/local/lib/libglib-2.0.0.dylib Referenced from: /Applications/freesurfer/bin/mris_decimate Reason: image not found Abort trap: 6 Is this a library that was supposed to be installed by FreeSurfer? I did not make any changes to the installation so I am not sure why this error is occurring. Thanks to anyone that can help. I really appreciate it. ____________________________________________________________ $4.95 Natural Painkiller Working "Better Than Oxy" worldhealthlabs.com http://thirdpartyoffers.netzero.net/TGL3231/5d72a2fdd8cab22fd34fbst03duc

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Postdoc positions in cognitive and computational neuroscience
by Ivan Alekseichuk 06 Sep '19

06 Sep '19

External Email - Use Caution Multiple postdoc positions in cognitive neuroscience and computational neuroscience are available in the Opitz Lab, University of Minnesota! The lab works in the field of brain stimulation (with the focus on the transcranial methods – TMS, tACS/tDCS) across multiple levels of investigation. We conduct both computational research (using resources of Minnesota Supercomputing Institute) and human experimental research (EEG, ECoG, functional and structural MRI, psychophysics). In collaboration with other labs at the University of Minnesota, we perform basic research in animal models. Through the direct vicinity to the Medical School and Center for Magnetic Resonance Research, we have several collaborators who study brain stimulation in clinical populations. We are looking for a postdoc to contribute to our ongoing projects: closed-loop TMS-EEG, multiscale modeling of TMS/tACS, human research in neurophysiology of TMS/tACS, cognitive effects of brain stimulation in healthy humans and patients; or develop their own research agendas. Interest and ability to integrate into a multidisciplinary team is essential. The ideal candidate should have Ph.D. in applied quantitative field (Engineering, Physics, or Applied Mathematics) or life sciences (Neuroscience, Human Biology, or Cognitive Science). Strong technical and computational skills are preferred, but candidates with strong human experimental background are also encouraged to apply. The Opitz lab is committed to the career advancement of its members. We offer a diverse and inclusive environment with numerous opportunities for members to develop their own projects and support for fellowships and career development awards. Informal inquiries can be made to: aopitz(a)umn.edu See more on the website: http://opitzlab.umn.edu/join_us

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Re: [Freesurfer] Interruption during data processing
by Троицкий Антон Александрович 06 Sep '19

06 Sep '19

External Email - Use Caution Bruce, could you explain how can I do that? I mean what command should I use and parameters? Best regards, Anton Troitskii

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Question about how to build .gca files from non-human atlas and images
by arsene ella 06 Sep '19

06 Sep '19

External Email - Use Caution *Dear **Freesurfer experts,* *I’ve built an atlas of structures of a non-human average brain and now **I would like to build **its** .gca files from scratch. **From the Freesurfer mailing list, I saw that this is possible using **rebuild_gca_atlas.csh* *which trains labelled brai**ns (**seg_edited.mgz**) and their intensity volumes (it is said to use the **norm.mgz** for this purpose) from several subjects through **mri_ca_train**. **My questions are :**1) How to normalize my native intensity volume to a **norm.mgz** volume without .gca and .lta files asking by **mri_ca_normalize **?**Y**ou’ve suggested to give **mri_ca_normalize** a flag to tell it to use a manual segmentation instead of the gca by trying **-seg <manual seg volume>**. Then the gca name won't matter - it should ignore it… I tried this as followed :**let : **- **Brain_Template_T1_MPR.mgz ** be my intensity native volume**- **Brain_Cortex_Atlas.mgz* * be my manual segmented volume**- **Brain_Template_T1_MPR_norm.mgz* * be **my **norm** output** volume* *Command lines :**mri_ca_normalize** Brain_Template_T1_MPR.mgz **-seg** Brain_Cortex_Atlas.mgz Brain_Template_T1_MPR_norm.mgz**gave the following error message :**reading 1 input volume**reading atlas from '-seg'...**GCAread(-seg): could not open file**No such file or directory**mri_ca_normalize: could not open GCA -seg.**No such file or directory* *mri_ca_normalize* *-seg ** Brain_Cortex_Atlas.mgz Brain_Template_T1_MPR.mgz Brain_Template_T1_MPR_norm.mgz**gave the following message and stopped:**using segmentation volume /home/arsene/Bureau/FS_GCA/FS_SHEEP_CGA/Brain_Cortex_Atlas.mgz to generate control points...**usage: mri_ca_normalize [<options>] <inbrain1> <inbrain2> ... <atlas> <transform file> <output1> <output2> ...* *What is wrong with theses **mri_ca_normalize* *commands ?* *2) My second question is to know how to transfert labels from my* *manual seg**mented** volume **(ex : **atlas.mgz**) to each single image volume (ex : vol1**.mgz**) ?**You’ve suggested to use **mri_label2label**, but **I didn’t see anything allowing me to do a **volume_to_volume** transfert **from **its **–help**…** If I got it wrong, could you suggest a command ?* *cheers* *Arsene*

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Morphological Features, Description & References
by Loske, Philipp 06 Sep '19

06 Sep '19

External Email - Use Caution Hello FreeSurfer Developers, I have a question about references and descriptions to all the morphological features available in aparc.stats, extracted from structural MRI. I am using all the different features (SurfArea, GrayVol, ThickAvg, ThickStd, MeanCurv, GausCurv, FoldInd, CurvInd) for the 68 cortical regions available from the Desikan Kiliany atlas. I have been trying to find references to how these features are measured or derived, but couldn't find a proper list of references to each of the features. I a lot of references here https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferMethodsCitation, with detailed descriptions on surface reconstruction and how cortical thickness is measured, but couldn't find a detailed explanation on the other features, especially curvature values. I think I have been able to find out what each of the measurements mean and how they are calculated in principle, through searching the internet a lot, but with no direct link to FreeSurfer. For instance, I know you can calculate the curvature values from the principle curvatures, but how does FS estimate those form the reconstructed Surface? And which one of the two surfaces does it use? White-pial or pial-csf surface? I found https://brainder.org/ really helpful, but it says for example that a new way of measuring cortical volume was implemented in FS 6.0.0, so does that mean for previous versions FS uses the Thickness x SurfaceArea method? Would be great if you can help me with this, or point me to the correct website I might just have missed during my search. Best wishes Philipp The University of Aberdeen is a charity registered in Scotland, No SC013683. Tha Oilthigh Obar Dheathain na charthannas clàraichte ann an Alba, Àir. SC013683.

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mri_glmfit error
by Gwang-Won Kim 06 Sep '19

06 Sep '19

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qcache after running recon-all post correction processing
by Swanson,Clayton 06 Sep '19

06 Sep '19

External Email - Use Caution Hi FreeSurfer folks, I searched through the archives and was unable to find the answer I was looking for. I have recently run recon-all on all our subjects (55 participants separated into two groups), then went through and corrected, saved and re-ran recon-all using the following command “recon-all -autorecon2-cp -autorecon3 -subjid Subj_020”. I neglected to add one additional command, the -qcache command for the second round of recon-all’s which I have already run for all participants. Because I am going to be comparing the two groups and doing group analysis what is the most appropriate way to proceed? Should I re-run the participants again although this time with the -qcache command? Or, what would be the most logical and efficient next step? Thanks for the help, Clayton ________________________________ Clayton Swanson MS Graduate Research Assistant & PhD Student Sensorimotor Neuroimaging Laboratory Colorado State University Office: (970) 491-6160 Clayton.Swanson(a)colostate.edu<mailto:Clayton.Swanson@colostate.edu>

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ERROR reading /<my data path>/fsaverage/label/lh.BA1_exvivo.label with recon-all.log
by liuxingze1993 06 Sep '19

06 Sep '19

External Email - Use Caution Hello，Dear FreeSurfer Developers, Hi, I'm attempting to follow the steps descripted on ‘Practice Working with Data’ (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Practice) with our own data, but I’ve met the same problem several times when I programing the command ‘recon-all -all’: SUBJECTS_DIR /media/dell/AA32E/Data_prac/220liujiayue/20181217 FREESURFER_HOME /usr/local/freesurfer Loading source label Invalid argument ERROR reading /media/dell/AA32E/Data_prac/220liujieyue/20181217/fsaverage/label/lh.BA1_exvivo.label I've searched the ‘lh.BA1_exvivo.label’ file in the related path and no such file here. Maybe I need to reinstall the freesurfer? 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Platform: Ubuntu14.04 LTS 3) uname -a: Linux dell 3.13.0-24-generic #46-Ubuntu SMP Thu Apr 10 19:11:08 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached Thank u for viewing, and I will be waiting here for your professional advice !

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qdec contrast and data extraction
by Maximo, Jose Omar 06 Sep '19

06 Sep '19

External Email - Use Caution Hi, Which specific file should I load? I see cluster.mgh, cluster.summary, sign.ocn.annot, sig.ocn.mgh, sig.vertex.mgh, and pdf.dat. How can I extract the values from fsaverage space? Basically, what is the correct way to extract values from these significant clusters? Many thanks, Omar Date: Tue, 3 Sep 2019 15:15:02 +0000 From: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu> Subject: Re: [Freesurfer] qdec contrast and data extraction To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <2286f9bf-37a4-1be9-2252-0bccc833a218(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" You might have done something wrong along the way. When you run the montecarlo correction, it will create a file with the thickness values in it for each cluster. the first thing to do is to load that and see if you see the expected differences. The other thing is to not go back into native space to extract the numbers. There are several operations that happen as it moves into fsaverage space and in preparation for group analysis (interpolation, and smoothing); sometimes these make a big difference. if the ROI is small, it may not map accurately back into the native space (and you should not need to draw it in the first place) On 8/30/2019 11:36 AM, Maximo, Jose Omar wrote: External Email - Use Caution Hi, I have a question: My design is 2 groups (HC and Patients in that respective order) and 2 nuisance factors (age and eTIV). When I look at the average volume difference between the 2 groups, I get blue and red clusters. I presume the color coding is where each group is greater than the other (Blue = Patients > HC and Red = HC > Patients). Then, I processed to extract individual values from each cluster in order to plot them. When I extract data from the blue clusters and plot them, the two groups show no difference in thickness at all, whereas when I look at volume, HC show more than patients in blue clusters (see attached figure). I would assume that both figures would show patients > HC based on the negative statistic. Am I interpreting the colors wrong? Or am I doing something wrong? These are my steps 1) After applying montecarlo correction, I drew my ROIs to extract the data from; 2) map it onto every single subject; and then 3) used mris_anatomical_stats to extract the data from each subject. Any suggestions are welcome. Best, Omar Jose O. Maximo, Ph.D. | Postdoctoral Fellow Department of Psychiatry & Behavioral Neurobiology UAB School of Medicine University of Alabama at Birmingham Cell Phone: (619) 252-3492 Email: jomaximo(a)uabmc.edu<mailto:jomaximo@uabmc.edu>

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