Freesurfer July 2020

freesurfer@nmr.mgh.harvard.edu

96 participants
160 discussions

FS 7.1.0 - Editing intensity values for WM
by Nils Böer 29 Jul '20

29 Jul '20

External Email - Use Caution Hello everyone, I just have a short question, because I can't find anything helpful in the tutorials. In my MRI scans freesurfer includes areas to the white matter, even though visual inspection concludes that the area should be grey matter. Is there a possibility to change the value at which freesurfer includes areas to the WM, which i can just change? For example freesurfer includes areas to the WM with intensity values below 85 and i want to change that. I'd be thankful for any feedback/links to guides. Best regards, Nils -- Nils Böer Research Assistant with Bachelor Degree (WHB) *Psychology and Movement* University of Paderborn Department of Sports and Health Warburger Str. 100 33098 Paderborn Room: Sp 1.401 Email: nils.tobias94(a)gmail.com / nboeer(a)mail.uni-paderborn.de <nils.tobias94(a)gmail.com> Web: https://sug.uni-paderborn.de/en/sport/sportpsychologie/team/ https://sug.uni-paderborn.de/department/it/ <https://sug.uni-paderborn.de/en/sport/sportpsychologie/team/> <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> Virenfrei. www.avast.com <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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Re: [Freesurfer] Coregistration to MNI
by Douglas N. Greve 29 Jul '20

29 Jul '20

Here is the command mri_cvs_register --mov $subject --mni --openmp N This command can take a very long time to run. The --openmp N indicates the number of processors to use if you have a multiprocessor system. Even with N=3, it can take 18 hours. On 7/29/2020 12:35 AM, Camargo, Aldo wrote: > > External Email - Use Caution > > Hi Douglas, > > I don't have the folder cvs and I don't have the files bellow: > > cvs/final_CVSmorph_tocvs_avg35_inMNI152.m3z > $FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri.2mm/register.lta > > How can I get these files, > > Aldo > > ------------------------------------------------------------------------ > *From:* Camargo, Aldo <ACamargo(a)som.umaryland.edu> > *Sent:* Monday, July 27, 2020 11:46 PM > *To:* Douglas N. Greve <dgreve(a)mgh.harvard.edu> > *Subject:* Re: [Freesurfer] Coregistration to MNI > Thanks a lot Douglas for your great input, > > Aldo > ------------------------------------------------------------------------ > *From:* freesurfer-bounces(a)nmr.mgh.harvard.edu > <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Douglas N. Greve > <dgreve(a)mgh.harvard.edu> > *Sent:* Monday, July 27, 2020 10:46 AM > *To:* freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> > *Subject:* Re: [Freesurfer] Coregistration to MNI > This command will allow you to have a registration file and sample > into MNI152 2mm space > > mri_vol2vol --gcam pet.nii.gz register.dof6.lta > $SUBJECTS_DIR/$subject/cvs/final_CVSmorph_tocvs_avg35_inMNI152.m3z > $FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri.2mm/register.lta 0 1 > pet.cvs.2mm.sm00.nii.gz > > you can get the registration file with > mri_coreg --mov pet.nii.gz --s $subject --reg register.dof6.lta > > > > On 7/26/2020 9:19 AM, Zollei, Lilla,Ph.D. wrote: >> Hi Aldo, >> If you have a recon-ned structural MRI corresponding to your PET scan >> then the answer is yes. >> Lilla >> ------------------------------------------------------------------------ >> *From:* freesurfer-bounces(a)nmr.mgh.harvard.edu >> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> >> <freesurfer-bounces(a)nmr.mgh.harvard.edu> >> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Camargo, >> Aldo <ACamargo(a)som.umaryland.edu> <mailto:ACamargo@som.umaryland.edu> >> *Sent:* Saturday, July 25, 2020 12:19 AM >> *To:* Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> >> <mailto:freesurfer@nmr.mgh.harvard.edu> >> *Subject:* [Freesurfer] Coregistration to MNI >> >> External Email - Use Caution >> >> Hi Freesurfer experts, >> >> I want to coregister a PET image to the MNI space, can I use >> mri_cvs_register ? >> >> Thanks a lot, >> >> Aldo Camargo >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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7.1 require experts opts for hires?
by Salvatore Torrisi 28 Jul '20

28 Jul '20

External Email - Use Caution Hi there FS gurus- We have fairly standard 7T structural data (0.7mm iso) and are using the -hires flag for recon-all. Per the old-ish page "Recon with native submillimeter resolution" we've also been using a higher mris_inflate value in an expert options file, which seemed to help some with FS6. However, we're not sure if this is still recommended with FreeSurfer 7.1. Is it? The recent release notes indicate "better" surface reconstruction but it's not clear in what way(s). Any tips on other expert options to test *with 7.1* for even further improvements would also be greatly appreciated (assuming MPRAGE or MP2RAGE T1s). Thanks in advance! -Salvatore (Sam) Torrisi Advanced MRI Technologies, LLC Helen Wills Neuroscience Institute University of California, Berkeley

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Longitudinal pipeline question
by Rachel Romeo 28 Jul '20

28 Jul '20

External Email - Use Caution Hi, I am working with some longitudinal data that was originally run through troubleshooting/recon-all in freesurfer 5.3. A lot of time went into the edits, so I definitely do not want to replicate these in freesurfer 6. Do I need to run the postprocessing and statistics also with v5.3? And if so, could you please fix the links for the tutorials on http://surfer.nmr.mgh.harvard.edu/fswiki/Tutorials ? The ones at the bottom of the page for v.5 link to the tutorials with v.6 Thanks! Rachel

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Error in Trac-All Pre-Processing step
by Jocelyn Ra 28 Jul '20

28 Jul '20

External Email - Use Caution Hi all, After running the trac-all command in the pre-processing step in the official TRACULA tutorial, I ran into the following error: WARN: Could not find satisfactory control point fit - try 4718 Writing output files to /home1/jr2359/diffusion_tutorial_april2018/diffusion_tutorial/elmo.2005/dlabel/mni/rh.cst_AS_avg33_mni_bbr_* Writing spline volume to /home1/jr2359/diffusion_tutorial_april2018/diffusion_tutorial/elmo.2005/dlabel/mni/rh.cst_AS_avg33_mni_bbr_cpts_6.nii.gz Segmentation fault The "WARN" message repeated several times before this final message, making me believe the issue is with the control points. For reference, I am using the tutorial data set, "set ncpts = (6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5)" for the control points, and LINUX. Has anyone else run into this error, and could someone please help me with this issue? Thank you in advance! Sincerely, Jocelyn

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Re: [Freesurfer] Freesurfer 7.1.0 VirtualBox password
by fsbuild 28 Jul '20

28 Jul '20

External Email - Use Caution Hello Joseph, I will sent the password directly to your email shorty.. - R. On Jul 28, 2020, at 17:59, Joseph Mewse <josephmewse(a)gmail.com> wrote:        External Email - Use Caution        I see that other users have come across this problem also… I hope this has not been formally adressed somewhere already.I would like to request the login password for the ‘development’ user as i can not seem to find it in any of the documentation. Best regards, Joseph Mewse_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer 7.1.0 VirtualBox password
by Joseph Mewse 28 Jul '20

28 Jul '20

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Reposting a Question RE: Hippocampal/Amygdala subfield segmentation - Medial Nucleus Errors
by Angel Hammond 28 Jul '20

28 Jul '20

External Email - Use Caution Hello Freesurfer Experts, I wanted to re-post a portion of a question that a previous team member posted on June 20th, 2019 (See: Reposting a Question RE: Hippocampal/Amygdala subfield segmentation - Anterior Amygdala Area / Medial Nucleus Errors) We have visually checked 133 subjects that have been processed using Freesurfer's latest hippocampal/amygdala subfield segmentation algorithm (Development version 20180518 <https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAm…>) and came across a few cases that had questionable segmentation. The T1s had were processed using FS 5.3, and we used the command "segmentHA_T1.sh" from the latest Dev version. -We have come across about 5 subjects' medical nuclei masks that are located in the Putamen region (more superior/detached from the rest of the amygdala) on one side of the brain (in some cases just the right side, in other cases just the left side). In all of the other subjects, we don't see that same detached looking segmentation into the putamen on one side as these few show. I will attach screenshots to show this. -I have checked the aseg for these subjects as suggested in the previous question, and the hippocampus, amygdala, and putamen all look fine there. I have also checked the output volumes for the medial nucleus of these subjects and the numbers all look fine. -So, my main question is: If the placement of the medial nucleus is wrong in the segmentation (detached/in the putamen as shown) but the aseg looks correct, can we still use those values reliably? Thank you! Angel Hammond Research Specialist Center for Healthy Minds University of Wisconsin-Madison

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FreeSurfer 7.1.0 tkmedit not opening - please help
by Nils Böer 27 Jul '20

27 Jul '20

External Email - Use Caution Hello everyone, I'm having a problem with tkmedit on the pre-installed Freesurfer 7.1.0 version for as Ubuntu guest on a Windows 10 host (via Oracle VM). I did work with the 6.0 version before but changed to Freesurfer 7.1 and used the .vdi for Oracle VM where Freesurfer is pre-installed. I did run recon-all for all my data and now wanted to start to check the surfaces with tkmedit. When I try running tkmedit (tkmedit P_01 brainmask.mgz -aux T1.mgz -surfs) it shows me, that it Converted the surfaces but no window is opening. When I'm closing the console it shows me, that there is a process running in the background but the tkmedit window is missing. I hope someone knows how to solve the problem. Best regards, Nils -- Nils Böer Research Assistant with Bachelor Degree (WHB) *Psychology and Movement* University of Paderborn Department of Sports and Health Warburger Str. 100 33098 Paderborn Room: Sp 1.401 Email: nils.tobias94(a)gmail.com / nboeer(a)mail.uni-paderborn.de <nils.tobias94(a)gmail.com> Web: https://sug.uni-paderborn.de/en/sport/sportpsychologie/team/ https://sug.uni-paderborn.de/department/it/ <https://sug.uni-paderborn.de/en/sport/sportpsychologie/team/> <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> Virenfrei. www.avast.com <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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Postdoctoral position in the Haber laboratory at McLean Hospital/Harvard Medical School
by Yendiki, Anastasia 27 Jul '20

27 Jul '20

Dear all - Please see below for a unique opportunity to join the Haber lab in Boston. While the amazing work of the Haber lab speaks for itself, I will also add here the questionable perk that you might have me as a collaborator. If interested, please contact Dr. Haber directly (see below). Best, Anastasia. Postdoctoral position in the Haber laboratory at McLean Hospital/Harvard Medical School The Haber laboratory at McLean Hospital seeks a postdoctoral fellow with a background in neuroscience with a particular interest in circuitry. We are a translational neuroscience laboratory that uses a multidisciplinary approach to: 1) delineate anatomic connections of prefrontal cortex and basal ganglia that underlie motivation and decision making, 2) and link the neurocircuits to structural and functional networks, 3) use this data to develop connectivity profiles in the human brain to determine how circuit abnormalities in obsessive compulsive disorder, addiction, and depression are related to specific connections, and 4) in collaboration with clinical groups, identify potential targets for invasive and non-invasion circuit-based therapeutic approaches. We use a combination of anatomic tracing data, computational tools, and imaging (diffusion MRI, and resting state MRI in both animals and humans) to model neural network interactions. The successful applicant will join a vibrant and collaborative laboratory and scientific community at McLean Hospital. (S)he will have full access to the diverse research, financial, and career development opportunities offered through both McLean Hospital and Harvard Medical School as a Research Fellow in the Department of Psychiatry at Harvard Medical School. McLean Hospital is a comprehensive psychiatric hospital committed to providing easy access to superior quality, cost-effective mental health services in the Boston area, Massachusetts and beyond. Since 1811, McLean Hospital has been a world leader in the treatment of mental illness and chemical dependency, research into the cause of mental illness and the training of generations of mental health care providers. McLean's multidisciplinary programs treat a broad range of psychiatric illnesses across the full continuum of care. There are many opportunities for education and growth in our multidisciplinary, collaborative research environment at McLean Hospital that brings together a diverse group of neurobiologists, clinicians, psychologists and statisticians. Please see https://www.mcleanhospital.org/research Job description: Major job duties may include microscopic, diffusion and/or resting state MRI analyses, and computer analyses. Qualifications: PhD or MD/PhD in neuroscience or related discipline, as well as good computer skills. The following experience is preferred: - Circuitry - Computational neuroscience - Imaging (Diffusion MRI and/or Functional MRI) How to apply: Interested applicants should send a cover letter, CV, and contact information (including phone numbers, email addresses) for three reference letters to shaber(a)mclean.harvard.edu. The position is full-time with excellent benefits. Salary will be commensurate with experience and follow NIH guidelines.

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Freesurfer July 2020