Freesurfer

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30089 discussions

power analysis
by John Anderson 11 Dec '17

11 Dec '17

Dear Freesurfer exerts, I read sentences similar to this one in multiple publications (e.g. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3500581/) "Power analyses were carried out using vertex-wise variance estimates from the coregistered cortical thickness maps, systematically varying processing parameters. " Please how can I use freesurfer to do power analysis. Cortical thickness (vertex-based analysis) is very well documented in Freesurfer wiki. How can I use the output of this analysis (i.e. gamma.mgh and the gammavar.mgh ) to measure the power. I highly appreciate any advice. John

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Reset view command in freeview
by Anna Mynick 11 Dec '17

11 Dec '17

Hi all, I’m wondering whether there's a command-line equivalent to the the Reset View tool found in the Freeview GUI when you right-click a volume in 3d view. I tried using the -viewport tag (e.g. freeview -v myvolume.nii.gz -viewport coronal), but the problems with this are: (1) Though the tag does change the viewpoint in which my volume is displayed, which is what I want, it also switches out of the 3d view, and my goal is to maintain the 3d view so I can view my region as an isosurface (2) I’d like the option of choosing between anterior, posterior, superior, inferior, and left and right views, as in the Reset View tool menu, rather than just coronal, sagittal, and axial. In other words, is there a way to open a volume to a specific view from the command line while maintaining 3d view? Thanks for any help! Best, Anna

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[Re] medial wall label in Freesurfer 6
by M del Mar Velasco 11 Dec '17

11 Dec '17

Hi, Have you take a look at our data? Have you find any possible cause? We need to continue with our analysis and it is now stopped. Thanks you in advance, M del Mar

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Postdoc position available at Martinos Center
by Hesheng Liu 11 Dec '17

11 Dec '17

Hi, I am looking for talented postdoc fellows. Please see below for details: Applications are invited for a postdoctoral research fellow position at Hesheng Liu Lab (http://nmr.mgh.harvard.edu/bid/Home.html) Martinos Center for Biomedical Imaging, Massachusetts General Hospital/Harvard Medical School. The research will focus on studying functional network structure in the individual subject’s brain, and understanding the functional organization that differs in individuals with neurological and psychiatric illnesses (e.g. epilepsy, brain tumor, stroke, schizophrenia, or OCD). Requirements: PhD (or MD) in cognitive neuroscience, biomedical engineering, psychology, radiology or a related discipline and a strong research background are required. The ideal candidate will have a background in brain research using MRI or MEG/EEG/ECoG/TMS; research experience with clinical or healthy populations; experience in task design and analysis for cognitive experiments; and good writing skills. We are especially interested in devotion to advanced quantitative data analysis, the ability to program in MATLAB/C and/or to modify existing analysis code will be beneficial. Expertise in analyzing HCP or other open source data is a plus. Interested applicants should email: (a) CV, (b) statement of post-doctoral and career goals, (c) writing sample (e.g., a published manuscript), and (d) letters and/or contact information for three references to Dr. Hesheng Liu (Hesheng(a)nmr.mgh.harvard.edu) A two-year commitment is required. --- Hesheng Liu, Ph.D. Associate Professor, Harvard Medical School & Massachusetts General Hospital Director, Laboratory For the Study of the Brain Basis of Individual Differences http://nmr.mgh.harvard.edu/bid/Home.html

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Job posting: NeuroImaging Research Associate Department of Child and Adolescent Psychiatry Hassenfeld Children’s Hospital at NYU Langone {Disarmed}
by Nath, Tanmay 11 Dec '17

11 Dec '17

[cid:B8DEC9D7-21A7-46E6-9E54-E04F15EBF0CE] NeuroImaging Research Associate Department of Child and Adolescent Psychiatry Hassenfeld Children’s Hospital at NYU Langone Dr. Adriana Di Martino at the Department of Child and Adolescent Psychiatry, Hassenfeld Children’s Hospital at NYU Langone (https://med.nyu.edu/faculty/adriana-di-martino; https://scholar.google.com/citations?user=Fpr79egAAAAJ) invites applicants for the position of NeuroImaging Research Associate. The position is full-time. Our research: The successful candidate will work on NIH-funded studies investigating behavioral and neural correlates of school-age children and preschoolers with neurodevelopmental conditions. Multiple methods of inquiry are used, including functional and structural magnetic resonance imaging (MRI), Diffusion Tensor Imaging (DTI), physiological measures (e.g., heart rate, respiration), computer-based tasks, and clinical questionnaires. Responsibilities: · Assist in collecting neuroimaging data synchronous to behavioral, eye tracking, physiological data during awake and asleep scans · Processing, and analyzing neuroimaging data · Assist in experimental design and coding of stimulus presentation · Maintaining server infrastructure, coordinate usage among other members of the lab Requirements: Interest in Neuroscience, Psychology or related field. Preferably Master’s degree, though a bachelor in computer science or related fields maybe considered. In all cases, strong computer programming skills, particularly with Python, R, MATLAB and shell scripting, are required. Brief Qualifications: Experience with MRI, eye-tracking, and/or psychophysiology research, computer software (Microsoft Office; Adobe Photoshop, Linux/Unix), and data management; experience processing neuroimaging data using relevant software programs (e.g., AFNI, MATLAB, SPM), programming experimental tasks (e.g., using E-prime, Presentation), use of eye-tracking equipment, and/or statistical analysis (e.g., SPSS, SAS, R) is highly desired. Please highlight relevant skills in your cover letter. The ideal candidate will be an independently minded individual with strong programming, analytical and organizational skills. This candidate should possess a keen attention to detail and be an internally motivated problem solver as well as possess a strong willingness to learn and develop additional computer skills related to data management and preparation of data. To apply, please send a 1) cover letter of interest and 2) resume to Dr. Adriana Di Martino (Adriana.DiMartino(a)nyumc.org<mailto:Adriana.DiMartino@nyumc.org>). The position will remain open until filled. The earliest start date will be December 15, 2017. Thank You Tanmay Nath, Ph.D. Assistant Research Scientist Hassenfeld Children’s Hospital at NYU Langone Department of Child and Adolescent Psychiatry Child Study Center One Park Ave 8th Floor, New York, NY 10016 Phone: 646.754.5141 Tanmay.Nath(a)nyumc.org| nyulangone.org<https://urldefense.proofpoint.com/v2/url?u=http-3A__nyulangone.us7.list-2Dm…> facebook.com/nyuchildstudycenter<https://urldefense.proofpoint.com/v2/url?u=http-3A__nyulangone.us7.list-2Dm…> nyulangone.org<https://urldefense.proofpoint.com/v2/url?u=http-3A__nyulangone.us7.list-2Dm…> facebook.com/nyuchildstudycenter<https://urldefense.proofpoint.com/v2/url?u=http-3A__nyulangone.us7.list-2Dm…> ------------------------------------------------------------ This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. =================================

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"Invalid FreeSurfer license key" with v5.3.0-HCP on Opensuse Leap
by Cholewa, John 10 Dec '17

10 Dec '17

We're having difficulties running mri_convert with a freshly-downloaded license key (as well as one that was generated some time ago when this version of Freesurfer was installed. It's version 5.3.0-HCP, running on Opensuse Leap 42.2. A glance at the list suggests that there's a suse-specific problem with version 5.3. Is there any workaround I could apply to get around the issue? Since we're using the Human Connectome Project's version, we can't update to 6.0, and we likely need to use the same version as we have been using to keep our research consistent anyway. Here's the error output: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /nethome/cfales/HCP/pipetests_rTMS/SUBJECTS/23006/T1w/T1w_acpc_dc_restore_1mm.nii.gz... -------------------------------------------------------------------------- ERROR: Invalid FreeSurfer license key found in license file /usr/local/opt/freesurferhcp/.license If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. -------------------------------------------------------------------------- The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege.

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non-brain region
by Ramesh Babu 09 Dec '17

09 Dec '17

Dear Experts, I performed recon-all all precess and it finished without any error. However I found some parts of non-brain regions are left over. Should I correct it or I can leave it? Please see the attached file and give your suggestions. Thanks in advance RB

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Re: [Freesurfer] selxavg3-sess problem: SVD input matrix contains NaN
by Mcnorgan, Christopher 08 Dec '17

08 Dec '17

An epiphany lead me to the solution to the problem, which I shall post here since I am apparently due to experience it again in 2019. The NAN values in the GLM matrices were the result of there being a condition that did not appear in any of the .par files across all of the runs. Once these files were edited so that all of conditions 1, 2 and 3 appeared somewhere among these files, selxavg3-sess was able to run. /********************************************** * Chris McNorgan * Assistant Professor * Department of Psychology * University at Buffalo, * The State University of New York * http://ccnlab.buffalo.edu/ <http://ccnlab.buffalo.edu/> * Office: 716.645.0236 * Lab: 716.645.0222 **********************************************/ > Hi Doug et al., > > It appears I've encountered this problem once before: > https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-February/043647… <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-February/043647…> > > Unfortunately there is no record of any resolution (if there was one) in the original thread, and I have no recollection of what the outcome was. Where the thread did leave off was a request for the Xtmp.mat file, so I will include the Xtmp.mat file from the analysis that worked (GoodXtmp.mat) and the one that failed (BadXtmp.mat). > > The error message: > > Creating Design Matrix > ... creation time = 0.019 sec > DoMCFit = 1 > ntptot = 2592, nX = 81, DOF = 2511 > Saving X matrix to /home/chris/SEM/FS_0231/bold/FAM.self.sm4.down.rh/Xtmp.mat > Error using svd > Input to SVD must not contain NaN or Inf. > Error in cond (line 35) > s = svd(A); > Error in fast_selxavg3 (line 279) > XCond = cond(XtX); > > Curiously, unless something was overlooked, the same analysis was carried out on another dataset that went through the same preprocessing steps without incident. > > The Xn matrix in BadXtmp.mat contains 3 columns of NaN (:,[7,8,9]), but without knowing how those values are calculated, I can't take a principled stab at fixing the problem. > > Thanks for your help, > Chris > > <GoodXtmp.mat><BadXtmp.mat> > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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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Postdoc opportunity at MEEI
by Bruce Fischl 08 Dec '17

08 Dec '17

Mass Eye and Ear is looking for a computational postdoc: masseyeandear.org/simonyanlab/jobs

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Using Nifti parcellation with Freesurfer
by Ricardo Valle 08 Dec '17

08 Dec '17

Dear Freesurfer community, I would like to be able to use any preexisting Nifti atlas with Freesurfer’s parcellation methods. As a proof-of-concept, I am attempting to use the parcellation scheme produced by Finn and colleagues (2015) with mris_ca_train and mris_ca_label. I have some questions about this. I wonder whether what I am trying to do makes sense. To train mris_ca_train, I would feed it the Collin MNI template space and Finn’s parcellation scheme (which is registered to Collin MNI as far as I can tell). This is not ideal for two reasons. First, it would be better to train mris_ca_train on a group of subjects. Second, the anatomical data and parcellation data come from two separate data sets. Is my understanding correct so far? On the other hand, the other way I can think of to parcellate an individual’s data based on an atlas is to register the data and the atlas and assign labels from the atlas to the individual where they overlap. This doesn’t seem any better to me. Are there other ways of using atlases to parcellate individual data that I am not aware of? Right now, I am stuck trying to produce an annot file to give to mris_ca_train. I ran mri_vol2surf --src shen_1mm_268_parc.mgz --hemi lh --mni152reg --out_type paint --o ./lh-surf-parc.mgz where shen_1mm_268_parc.mgz is the result of converting the parcellation scheme from nifti to mgz with mri_convert. The resulting mgz file seems reasonable. However, I don’t know how to make an annot file from it. Is there a way to do this? I also attempted the following: mris_sample_parc -ct ./ctab.txt -sdir .. -file ./ctab.txt FS lh shen_1mm_268_parc.mgz lh-parc.annot The results don’t make sense to me and I don’t understand how mris_sample_parc works. What is the purpose of the translation file (-file option)? From what I’ve read on the wiki, mris_sample_parc is used to sample a manual parcellation done on an individual subject’s volume to that subject’s surface. In my case, the “subject” (Collin MNI brain) happens to be aligned with the parcellation. Does it make sense to run mris_sample_parc? Thank you. Best regards, Ruy

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