Freesurfer

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30132 discussions

Re: [Freesurfer] lGI permutation and monte-carlo
by Avi Gharehgazlou 12 Jun '20

12 Jun '20

External Email - Use Caution Thank you so much for your input, it was very helpful and I really appreciate it. Regarding your question with relation to my 4th question, when I run the below command line to visualize my results after correcting for multiple comparisons using monte-carlo at 1.3 significance level in this example, I assumed the clusters that appear on freeview are only my significant clusters (clusters that survived monte carlo correction) since I put " cache.th13.abs.sig.cluster.mgh" and then as overlay " cache.th13.abs.sig.ocn.annot " in my command line. If not, will you please tell me how I can see only clusters that are significant after correction for multiple comparisons (at 1.3 sig level in this case)? Also, in my command line, I can put either lh.pial or lh.inflated to see the results//clusters on the pial or inflated surface, respectively. Correct? vglrun freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.pial:overlay=lh.lgi.TD_PTSD_age_SA_IQ_FWHM0.glmdir/group.diff/cache.th13.abs.sig.cluster.mgh:overlay_threshold=1.3,5:annot=lh.lgi.TD_PTSD_age_SA_IQ_FWHM0.glmdir/group.diff/cache.th13.abs.sig.ocn.annot -viewport 3d Thank you so much, Avi

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Matlab runtime installation error for Freesurfer v7.1.0
by Yann Quidé 11 Jun '20

11 Jun '20

External Email - Use Caution Hi team, I am trying to install fs_install_mcr R2014b, but encounter an error just at the end of it: mv: rename /var/folders/1f/4_zl7p9n795c2yq1dgb3hvt40000gq/T/tmp.Xvv7Ku4d/install-target/v84 to /Applications/freesurfer/7.1.0/MCRv84: Permission denied Any idea how I can fix this to finalise the installation? I should have the admin rights on the machine. Thanks, Yann

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Re: [Freesurfer] Regarding installation in CentOS7
by fsbuild 11 Jun '20

11 Jun '20

External Email - Use Caution Hello Rahul, Did you try following the instructions on the wiki pages about how to do an install with the tar archive or RPM ?  Please see links to Linux and/or Mac install and setup, https://surfer.nmr..mgh.harvard.edu/fswiki/rel7downloads -R. On Jun 11, 2020, at 16:25, Rahul Sharma <sharmarahul.26dec(a)gmail.com> wrote:        External Email - Use Caution        Unable to perform installation. Please help me out regarding the same.Regards:Rahul SharmaResearch ScholarNIT Silchar (Assam)9827834360_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Regarding installation in CentOS7
by Rahul Sharma 11 Jun '20

11 Jun '20

External Email - Use Caution Unable to perform installation. Please help me out regarding the same. Regards: Rahul Sharma Research Scholar NIT Silchar (Assam) 9827834360

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Final result of monkey make_averge_subject
by Pam Garcia 11 Jun '20

11 Jun '20

External Email - Use Caution Hi FS developers, I have some questions related to make_average_subject I followed the steps describe here https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates to 1. build a monkey curvature pattern 2. build FS monkey average using 40 subjects I've finished the surface and volume average, but the anatomy of the prefrontal lobe looks rounded and the size of the brain was adjusted to the human MNI. I suppose that this is due to the affine registration. My questions are the follows: 1. Is there some way to avoid the affine registration or only use 3 DOF for registration when the average is built? All the images were previously registered to MNI monkey space 2. In the case that the affine registration can´t be avoided is it correct to use a surface gotten from the template image and next use this as average in mris_preproc?

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Postdoc position available in PET/MRI at Martinos Center, MGH/HMS
by Wey, Hsiao-Ying 10 Jun '20

10 Jun '20

Research Fellow in Simultaneous PET/MR Neuroimaging Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Harvard Medical School We are seeking two postdoctoral fellows to join our team to pursue research in simultaneous PET/MR imaging in neuroscience applications. Our research focuses on developing and applying novel PET/MRI methods to investigate the neurochemical underpinnings of psychiatric and neurological disorders. We have projects and training opportunities in the following area: (1) Quantify neuroreceptor dynamics and functional with pharmacological challenges in animal models and human subjects, with applications in pain, addiction, and psychiatric disorders; and (2) Assess the impacts of neurovascular coupling/function on PET radiotracer kinetics, with applications in neurodegenerative disorders. Our research programs are highly translational spanning from animal models, first-in-human studies, to clinical applications. The appointment as a Massachusetts General Hospital, Harvard Medical School research fellow will be for 1 year with possibility for extension based on performance and the availability of funding. The positions are available immediately. The successful candidate will be a highly motivated researcher with a desire to begin an independent career related to or involving neuroimaging. The position requires a Ph.D. degree in Medical Physics, Biomedical Engineering, Computer Science, Neuroscience or a related field. However, we will consider candidates of any scientific background. This position requires experience in analysis of medical imaging data. Experience with MRI or PET is a plus. Extremely strong candidates with minimal imaging experience are still encouraged to apply. Strong written and oral English communication skills are required. [cid:clip_image001.png]Additional Skills/Abilities/Competencies The job requires a candidate who is mature, responsible and flexible with excellent organizational and people skills. S/He must be able to work with in a fast-paced environment and should be able to problem-solve/troubleshoot, juggle and prioritize multiple tasks and seek assistance when appropriate. Application Interested applicants should send a cover letter describing research interests and experience, an updated CV, and names and contact information of three references to: Hsiao-Ying (Monica) Wey, Ph.D. (E-mail: hsiaoying.wey(a)mgh.harvard.edu) Please contain “Research Fellow Application: Your Name” in the e-mail subject line. The Massachusetts General Hospital and Harvard Medical School are equal opportunity and affirmative action employers. Best, Hsiao-Ying (Monica) ------ Hsiao-Ying (Monica) Wey, Ph.D. Assistant Professor of Radiology, Harvard Medical School Director of Translational Imaging, Chemical Neuroscience Program A. A. Martinos Center for Biomedical Imaging Institute for Innovation in Imaging (i3) Massachusetts General Hospital 149 Thirteenth Street, Room 10.110 Charlestown, MA 02129 Phone: (617) 724-1384 Email: hsiaoying.wey(a)mgh.harvard.edu

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Fwd: Postdoc position available - computational modeling of fMRI/MEG data, and real-time fMRI neurofeedback of language
by Douglas N. Greve 10 Jun '20

10 Jun '20

-------- Forwarded Message -------- Subject: Postdoc position available - computational modeling of fMRI/MEG data, and real-time fMRI neurofeedback of language Date: Wed, 10 Jun 2020 10:54:03 +0000 From: Narly Golestani <Narly.Golestani(a)unige.ch> To: Narly Golestani <Narly.Golestani(a)unige.ch> External Email - Use Caution Dear Colleagues, I would be grateful if you could please circulate the below job advertisement to anyone who may be interested. Many thanks in advance and best wishes, Narly. ****************************************** With the launch of a new ‘NCCR Evolving Language’ (http://www.snf.ch/SiteCollectionDocuments/nfs/Faktenblatt_NCCR_evolvinglang…) which involves nearly 40 different research groups from a large variety of disciplines across Switzerland, we seek to fill a *Postdoc position for a four-year project* starting in September 2020, or at the selected candidate’s earliest convenience. Our goal is to make progress in understanding *the importance of prosody in language processing*. To this end, we plan to carry out a set of studies involving both *computational modeling of fMRI *and/or of*MEG data *and*real-time fMRI neurofeedback *to understand the *mechanisms whereby prosody and rhythm support linguistic processing per se*. The computational modeling work will be an extension of our recent work on the neural encoding of acoustic information in speech sounds (https://www.ncbi.nlm.nih.gov/pubmed/31285622) The research will be done in the group of Narly *Golestani*in Geneva (www.brainandlanguagelab.org <http://www.brainandlanguagelab.org>), in collaboration with researchers in Switzerland and abroad (Elia *Formisano*in Maastricht, and Frank *Scharnowski*in Vienna). Applicants should hold a degree in *Cognitive Neuroscience*, *Biomedical Engineering, Computational Neuroscience, or a related field*, and should have solid experience in *human brain imaging *and*programming*, and ideally also *in computational modelling (i.e. encoding / decoding) of fMRI *and/or of*MEG data, real-time fMRI based neurofeedback, machine learning and statistics*. Knowledge of French would be an asset. The NCCR places great emphasis on gender diversity and we particularly encourage women to apply. To apply, please send a cover letter, CV, names and contact information of 2-3 references as well as any other relevant documents to Narly.Golestani(a)unige.ch <mailto:Narly.Golestani@unige.ch>. Feel free to contact me should you have any questions. *Deadline for application: June 30^th 2020.* *-----------------------------------------------------------------------------------------------------------------------------------------------------------------* *Brain and Language Lab* **Prof. Narly GOLESTANI* * Department of Psychology Campus Biotech *9 Chemin des Mines, * *1202 Genève* *+41 22 379 53 52* <https://outlook.unige.ch/owa/redir.aspx?SURL=5WTo-p-J-W9FrDydU-0WU4PdMytUGs…>http://www.brainandlanguagelab.org https://twitter.com/brain_lang_lab *-----------------------------------------------------------------------------------------------------------------------------------------------------------------* <https://outlook.unige.ch/owa/redir.aspx?SURL=5WTo-p-J-W9FrDydU-0WU4PdMytUGs…>

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Unmatched error
by COLLEEN PLETCHER 09 Jun '20

09 Jun '20

External Email - Use Caution Hello, I am currently attempting to run a brain through the longitudinal stream after performing edits on the longitudinal brain, using the command recon-all -long timepoint1 base -autorecon2-wm -autorecon3. I am getting an error that says Unmatched ". All of the data for both timepoint 1 and the base is there and readable. I am using version 6.0. Any advice on how to fix this problem? Thank you!

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Re: [Freesurfer] recon-all -long erros
by Hoopes, Andrew 09 Jun '20

09 Jun '20

As for the --preserve=timestamps error, this is a bug on osx. This will be fixed in the next 7.1 patch, but in the meantime, you can fix this manually via: cd $FREESURFER_HOME/bin sudo rm rca-long-tp-init sudo curl https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/rca-lon… -o rca-long-tp-init sudo chmod +x rca-long-tp-init best Andrew On 6/9/20, 7:36 AM, "Martin Reuter" <mreuter(a)nmr.mgh.harvard.edu> wrote: Hi Jieyin, a couple things I noticed: 1) you call this: recon-all -long P0567/tp4 P0567/tpm -all this is not the way recon-all should be called. You need to specify a SUBJECTS_DIR under which all your time points exists usually you would have $SUBJECTS_DIR/me_tp1 $SUBJECTS_DIR/me_tp2 $SUBJECTS_DIR/me_tpm # (the base or subject-template) $SUBJECTS_DIR/me_tp1.long.me_tpm # (output of long stream) $SUBJECTS_DIR/me_tp2.long.me_tpm # (output of long stream) $SUBJECTS_DIR/you_tp1 $SUBJECTS_DIR/you_tp2 ... If you want a separate directory for each subject, you would need to specify that dir in SUBJECTS_DIR and then the names would just be tp1 tp2 tpm tp1.long.tpm etc. It could be that the / in the subject name messes things up! 2. The command that fails is: /Users/jif19007/Documents/PLING_dataset/MRI_raw/pilot_data/output_P0567 /tp4.long.tpm/mri cp -f --preserve=timestamps /Users/jif19007/Documents/PLING_dataset/MRI_raw/pilot_data/output_P0567 /tpm/mri/brainmask.mgz ./brainmask_tpm.mgz cp: illegal option -- - maybe the mac has problems with the --preserve flag? I don't know when this was added and whether it is really necessary. Currently I don't even know where this is called. Can't find it in recon-all. Maybe some sub-script? Best, Martin On Wed, 2020-05-20 at 19:28 -0400, Jieyin Feng wrote: > External Email - Use Caution > Dear FreeSurfer experts, > > I am running longitudinal processing with FreeSurfer 7.1.0 on MacOX > Catalina. > The dataset is 5 time points with T1 data. I tried to run a single > subject. So far it succeeded on Step 1 (recon-all at each time > point), and Step 2 (-base to build the template), all of them > reported successfully. But I failed at step3, recon-all -long, to > compare each timepoint with the template. > The log file is attached. > I tried to run several times with different timepoints data, all > reported the same stuff. My guess is at the last 9 row, reported that > the cp command incorrectly. But I still have no idea to fix it, or > maybe I need to go to freesurfer's script file? I have no idea... > > Thanks for you time and help in advance! > Stay safe and sound! > > Best, > Jieyin > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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lGI permutation and monte-carlo
by Avi Gharehgazlou 09 Jun '20

09 Jun '20

External Email - Use Caution Hi experts, Upon reading your 2018 paper (cited below) and following threads on the archives, I am aware that I should use permutation testing for lGI analyses rather than monte carlo at p<0.05. However, I have a few questions below that I would really appreciate your input on: 1. For permutation testing on lGI data, what are the CFT and cwp levels you recommend? Would it be appropriate for me to use CFT=1.3 and cwp=0.05? 2. Will you confirm my interpretation for permutation command line below? mri_glmfit-sim --glmdir lh.lgi.TD_PTSD_age_SA_IQ_FWHM0.glmdir --perm 1000 2 abs --perm-resid --cwp 0.05 --2spaces --bg 1 Above command indicates that I used a cluster-forming threshold of p<0.01 and a cluster-wise significance threshold of p<0.05 - meaning that clusters are initially obtained using p<0.01 (CFT) but I report them in my paper if they meet additional cluster-wise probability of p<0.05 (cwp). Both are two-tailed (since I am using abs). Is this interpretation correct? 3. Would it be okay to correct with monte carlo using CFT=3 and cwp= 0.05 (below command line) instead of permutation testing for lGI data? mri_glmfit-sim --glmdir lh.ASDvsADHD.glmdir --cache 3 abs --cwp 0.05 --2spaces 3. I am not smoothing my lGI data (as lGI is a relatively smooth measure and to keep this consistent with the literature I have reviewed), however, after reading your 2018 paper, I wanted to ask if this is appropriate? Your paper recommends CFT<0.001 and FWHM>10mm for surface area analyses. Do I have to smooth lGI when doing a) permutation testing or b) monte carlo correction (steps 1 and 3 above)? If yes, what level of smoothness do you recommend? 4. After correcting with monte-carlo at p<0.05 - When I use the below command line to see my corrected results in freeview, I notice the significant cluster is gray rather than blue (I know it should be blue because I've ran this same analysis using QDEC). In order to see this cluster's true colour (and thus be able to interpret my results) do I have to change the threshold by clicking ‘show outline overlay’ then clicking ‘configure’ and setting the min value to 1.3? Is this the correct way of visualizing my corrected results? vglrun freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.pial:overlay=lh.lgi.TD_PTSD_age_SA_IQ_FWHM0.glmdir/group.diff/cache.th13.abs.sig.cluster.mgh:overlay_threshold=1.3,5:annot=lh.lgi.TD_PTSD_age_SA_IQ_FWHM0.glmdir/group.diff/cache.th13.abs.sig.ocn.annot -viewport 3d reference Greve DN & Fischl B. 2018. False positive rates in surface-based anatomical analysis. NeuroImage. Thank you so much, Avi

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