Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30132 discussions

Re: [Freesurfer] use of ANTs Denoising in FS 7.1
by Glasser, Matthew 25 Aug '20

25 Aug '20

External Email - Use Caution Perhaps it smooths the data some and that would impair the gradient placement of the final white and pial surfaces? Matt. From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Alexopoulos, Dimitrios" <dimitriosalexopoulos(a)wustl.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Tuesday, August 25, 2020 at 3:56 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] use of ANTs Denoising in FS 7.1 External Email - Use Caution Hi all, In previous datasets, and prior to FS 7, we independently ran ANTs denosing on the input T1s prior to running recon-all, However, FS 7.1 now appears to use the denosing utility in parts of the pipeline. “ANTS denoise is used when creating the orig surface (but not thefinal surfaces)” Does this mean the denoised image is only used in the segmentation part of the pipeline (to generated the aseg.mgz) and does not propagate through to final surfaces? Why not use denoised T1 through the surface-generation phase of the pipeline. Can you provide some further clarification. Thx. Jim ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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FS educ links
by John Absher 25 Aug '20

25 Aug '20

External Email - Use Caution Hi, We're implementing freesurfer and other neuroimaging applications on the High Performance Computing center. To help more users get up to speed quickly, I'm trying to pull together up-to-date freesurfer/freeview educational materials into a single online resource. Is it OK to link directly to available online resources/tutorials/videos/datasets as long as I include appropriate attributions? If not, how do I go about getting permissions? Warm Regards, John R. Absher, MD, FAAN Clinical Associate Professor, University of South Carolina School of Medicine Greenville Department of Internal Medicine, Division of Neurology Clinical Assistant Professor, Clemson University School of Health Research (CUSHR) Graduate Faculty, Clemson University School of Public Health Sciences Prisma Health-Upstate 200 Patewood Drive, Suite 350B Greenville, SC 29615 John.Absher(a)prismahealth.org<mailto:John.Absher@prismahealth.org> or jabsher(a)greenvillemed.sc.edu<mailto:jabsher@greenvillemed.sc.edu> or jabsher(a)clemson.edu<mailto:jabsher@clemson.edu> 864-454-4500 (office) 864-350-6655 (mobile) 864-454-4505 (fax) [cid:image001.jpg@01D67ADF.953C21D0] Inspire health. Serve with compassion. Be the difference. ---------------------------------------------------------------------- CONFIDENTIALITY NOTICE This message is intended only for the use of the individual or entity 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 message is not the intended recipient, you are hereby notified that any dissemination, distribution, or copying of this communication is strictly prohibited by law. If you have received this communication in error, please notify me immediately.

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Full professorship in Neuropsychology and Cognitive Neuroscience at the University of Zurich
by Nicolas Langer 25 Aug '20

25 Aug '20

External Email - Use Caution The University of Zurich invites applications for a professorship in Neuropsychology and Cognitive Neuroscience (chair). The applicant should be an internationally recognized expert in one or several fields of Neuropsychology and Cognitive Neuroscience with a strong record of empirical research. Candidates should hold a PhD degree at the time of application and have an excellent record of academic achievements in the relevant field. The applicant should have acquired international reputation in this field and demonstrated substantial research activities and expertise as documented by publications in high-ranking journals in this field, as well as by successful grant applications. The applicant is expected to have substantial expertise in teaching Neuropsychology and Cognitive Neuroscience. The University of Zurich is an equal opportunities employer and in particular strives to increase the percentage of women in leading positions. Therefore, qualified female researchers are particularly encouraged to apply. The Department of Psychology values transparent, reproducible and replicable research and supports open science practices. Applicants are asked to document how they have pursued open science practices in the past and/or will do so in the future. The Department of Psychology of the University of Zurich with its broad research and teaching spectrum and Zurich as a center for higher education offers a research and teaching environment with plenty of opportunities for scientific exchange and cooperation. The position is a chaired, tenured Professorship at the associate or full professor level and should be filled by August 1, 2022. Teaching may be carried out in English. Non-German speaking candidates are expected to acquire a working knowledge of German within the first three years of appointment. The closing date for applications is 30 September 2020. Details on the application procedure are available on www.phil.uzh.ch/jobs.html. For further information please contact Prof. Klaus Oberauer (k.oberauer(a)psychologie.uzh.ch) https://jobs.uzh.ch/offene-stellen/professorship-in-neuropsychology-and-cog… Nicolas Langer Assistant Professor of Methods of Plasticity Research University of Zurich Andreasstrasse 15 (Office AND.4.56) 8050, Zurich, Switzerland n.langer(a)psychologie.uzh.ch phone: (+41) 44 635 34 14 http://www.psychology.uzh.ch/en/areas/nec/plafor.html

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recon-all output resolution
by Billah, Tashrif 25 Aug '20

25 Aug '20

Hi all, Is the resolution of mri/*mgz files produced by `recon-all -all` always 1mm^3 regardless of the resolution of my input unless -hires is used? This is what I found in recon-all.log: without --hires: mri_convert 001/mri/rawavg.mgz 001/mri/orig.mgz --conform I believe the `--conform` flag does the resampling for all resolution. with -hires: mri_convert 434/mri/rawavg.mgz 434/mri/orig.mgz --conform_min Best, Tashrif

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Cannot disable the topology correction
by k3ops＠free.fr 25 Aug '20

25 Aug '20

External Email - Use Caution Hi FS team, I am having an error when disabling (-nofix) the topology correction with the recon-all command. The "-nofix" option is skipping the topology correction as expected but then the next step is failing because "?h.orig" file does not exist. When reading the recon-all table here: https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV6.0 it looks like "-fix" step (topology correction) is first copying the following file: "cp ?h.orig.nofix ?h.orig" So if this step is ignored with the "-nofix" option then "?h.orig" files are not created, which is causing a failure with next step (cannot read ?h.orig). Do you have any solution to that? My goal is to run FreeSurfer without topology correction because for some cases it is running in an infinite loop (more than 2 days of processing). Thanks, Florent FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0 Platform: Ubuntu 18.04

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Schwartz atlas reference in recon-all 3T flag
by Hye Min Shin 25 Aug '20

25 Aug '20

External Email - Use Caution Hello, I understand that from a previous FreeSurfer question the Schwartz atlas used in the 3T flag during recon-all is not published yet ( https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg47175.html) Since this question was asked back in 2016 I wanted to double-check if the reference atlas for the Schwartz atlas is still not published yet. Best, Julia Shin

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POSTDOC and PhD POSITION- photoacoustic imaging , machine learning and OCT image analysis
by Nasiriavanaki, Zahra 24 Aug '20

24 Aug '20

Hi all Please see below for available postdoc and PhD positions at the Biomedical Engineering Department, University of Illinois at Chicago. Best, Zahra (Mona) Nasiriavanaki, M.D. Postdoctoral Research Fellow Massachusetts General Hospital 149 13th Street, 149-2615 Charlestown, MA, USA, 02129 We have openings for two postdocs, one with expertise in the area of photoacoustic imaging instrumentation, and the other one in the area of machine learning and OCT image analysis. We also have one Ph.D. position available in the area of photoacoustic imaging. Please share this with your qualified colleagues/friends. See more details at: https://engineering.academickeys.com/seeker_job_display.php?dothis=display&… [http://engineering.academickeys.com/seeker_job_attachments.php?dothis=displ…]<https://engineering.academickeys.com/seeker_job_display.php?dothis=display&…> Two postdoctoral positions and a PhD position at the Biomedical Engineering Department , Biomedical Engineering Department , The University of Illinois at Chicago (UIC)<https://engineering.academickeys.com/seeker_job_display.php?dothis=display&…> Two postdoctoral positions and one PhD position are available in OPIRA lab in the Biomedical Engineering Department, the University of Illinois at Chicago (UIC). 1. The first postdoctoral fellow will contribute to the design, development, and optimizati... engineering.academickeys.com<http://engineering.academickeys.com/>

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Re: [Freesurfer] extracting beta coefficients and p-values
by Douglas N. Greve 24 Aug '20

24 Aug '20

answers below. also, please remember to post to the list On 8/21/2020 6:52 PM, Rizvi, Batool wrote: > > External Email - Use Caution > > Thank you Dr. Greve! This is very helpful! Just to confirm, similar to > taking the effect of age, if I wanted to get the beta of Parietal WMH > (my main continuous IV), I would just average betas 5-8? > > I forgot to add this in my previous email, but I’m also trying to > extract p-values of all the variables involved, and wasn’t sure how > to. I tried running a couple different commands. > > When I ran this below command, I got a file with 1 column of 8 numbers: > > mri_segstats --i contrasts.sig.mgh --annot fsaverage lh > lh-Avg-long.thickness-spc-Parietal_WMH-Cor/mc-z.abs.th20.sig.ocn.annot > --excludeid 0 --avgwf avgwfsig.dat > where did contrasts.sig.mgh come from? Was this created by QDEC? > > But when I tried the below command, I got a file with 1 number. > > mri_segstats --i lh-Avg-long.thickness-spc-Parietal_WMH-Cor/sig.mgh > --annot fsaverage lh > lh-Avg-long.thickness-spc-Parietal_WMH-Cor/mc-z.abs.th20.sig.ocn.annot > --excludeid 0 --avgwf avgwfsig2.dat > > From the 1^st way (using contrasts.sig.mgh): > > -0.27711 > > -2.51072 > > 0.42697 > > 0.62922 > > -0.85069 > > 0.52623 > > 1.00393 > > -0.42921 > > From the 2^nd way (using sig.mgh) > > -2.51072 > > I’m pasting my fsgd format once more: > > GroupDescriptorFile 1 > > Title ParietalWMH_age_gender_APOe_EC_left > > MeasurementName long.thickness-spc > > Class APOE_statusNO-genderF > > Class APOE_statusYES-genderF > > Class APOE_statusNO-genderM > > Class APOE_statusYES-genderM > > Variables Parietal_WMH age_years Avg_ECthickness > > Input W38284_base APOE_statusNO-genderF 0.732010 85.830000 3.125000 > > .. (only listing the 1^st Input line here) > > My contrast file (C.dat) looks like below: > > 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 > > And I’m trying to find p-values for these variables’ associations w/ > thickness: APOE status, gender, Parietal WMH, Age, Avg EC thickness. > Each contrast will have a sig file. But the command above will compute the average significance, which really does not mean anything > > Thanks so much again for all the help! > > Batool >

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problems with brainmask.mgz and wm.mgz files
by Dalton Bermudez 24 Aug '20

24 Aug '20

External Email - Use Caution For some reason when I ran the recon-all command it generated a brainmask.mgz file which excluded part of the right hemisphere and a wm.mgz which did a horrible job at segmenting gray matter from white matter. The recon-all command later exited with an error. How do I fix the problem? I have attached the recon-all.log file for your reference. Thank you, Dalton

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FreeSurfer6 hires patch for longitudinal output
by Nandita Vijayakumar 24 Aug '20

24 Aug '20

External Email - Use Caution Dear FreeSurfer team, I have processed my data through the longitudinal stream of FreeSurfer6 using the -hires flag. I would like to apply the patch to fix the global metrics, but seem to run into an error when supplying the longitudinal subject directory. I've tried running the following command: recon-all -long sub-001_wave1.long.sub-001 sub-001 -segstats -parcstats -parcstats2 -parcstats3 -wmparc -balabels But get the following error: Unmatched ". The command seems to work fine on the cross-sectional directories. So I'm wondering if the patch can be applied to longitudinal directories? Thanks, Nandi

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