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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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Question about QDEC Design Tab Measurement Parameter
by Sonya Gupta 27 Jul '20

27 Jul '20

External Email - Use Caution Hi, Hope you are having a wonderful morning! In QDEC in the Design tab under the measurement parameter, there are a variety of options (thickness, area, area.pial, volume, sulc, curv, white.K, white.H, w-g.pct.mgh, intensity.deep, intensity.superficial, intensity.deep.mgz, and intensity.superficial.mgz). I was wondering, what is the difference between these measurement options? I couldn't find much documentation online. Thank you! Sincerely, Sonya

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local gyrification index unit
by Backhausen, Lea 27 Jul '20

27 Jul '20

External Email - Use Caution Hi FreeSurfer experts, I have recently been wondering about the correct unit for curvature and local gyrification index. For curvature I find inconsistent information like: mm^-2 (https://onlinelibrary.wiley.com/doi/epdf/10.1002/ima.20138, page 47), but also that curvature values are expressed in degrees (https://www.sciencedirect.com/science/article/pii/S1053811905006543, page 1125). For local gyrification index these papers make it seem like there is just not unit: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5397412/#:~:text=A%20large%20G…. https://www.jneurosci.org/content/jneuro/31/19/7174.full.pdf Which are the correct units? Happy to get some expert input on this, thank you so much! Best, Lea ------------------------------ Lea Backhausen Ph.D. Student (M.Sc. Psychology/Neuroscience) Department of Child and Adolescent Psychiatry, Faculty of Medicine of the TU Dresden, Germany http://www.uniklinikum-dresden.de<http://www.uniklinikum-dresden.de/>

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Working with cortical surface area - parcellation size?
by Yash Patel 27 Jul '20

27 Jul '20

External Email - Use Caution Hi Freesurfer colleagues, I want to analyze regional profiles of differences in cortical surface area (SA). However, SA and its group differences in SA depend on parcellation size. In order to mitigate this effect, should I create a parcellation that has roughly equal area per ROI in FSaverage space, or equal number of vtx per ROI in FSaverage space. Looking at smaller ROIs than the DK atlas - so I will be making the parcellation in any case. Thanks - any advice would be much appreciated Yash

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Coregistration to MNI
by Camargo, Aldo 27 Jul '20

27 Jul '20

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

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ISBI 2021 -- Call for Special Sessions
by Zollei, Lilla,Ph.D. 26 Jul '20

26 Jul '20

Hi All, Do you want to organize a special session at #ISBI2021? There is still time to submit your ideas! See details below: https://biomedicalimaging.org/2021/call-for-special-sessions/ Best, Lilla

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Re: [Freesurfer] FW: mri_fieldsign error
by Douglas N. Greve 24 Jul '20

24 Jul '20

A few more questions 1. How much memory do you have on your system? You can find it from the first line of /proc/meminfo It should be something like "MemTotal: 131781468 kB" 2. What environmental limits do you have? Send the result of the "limit" unix command 3. I put a new version of mri_fieldsign here https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_fieldsign. Can you run this version and send me the terminal output? Also, if you can run it outside of your bash script, it would be better. On 7/24/2020 9:44 AM, Xiaomin Yue wrote: > > External Email - Use Caution > > Hi Doug, > > Here is output of uname -a: Linux thalamos.nimh.nih.gov > 3.10.0-1127.13.1.e17.x96-64 #1 SMP 2020 x86-64 x86-64 GNU/Linux. For > the second command: Centos Linux release 7.8.2003 (Core). > > My system has the newest AFNI installed, do you think that could be > the cause of the problem? > > Thanks for your help! > > Xiaomin > > *From: *Douglas N. Greve <mailto:dgreve@mgh.harvard.edu> > *Sent: *Thursday, July 23, 2020 11:00 AM > *To: *Xiaomin Yue <mailto:yuexm@hotmail.com> > *Subject: *Re: FW: [Freesurfer] mri_fieldsign error > > No, sorry, When I run it on my system it works. If I can't replicate > the problem, I can't fix it. I don't know why you get it and I don't. > Can you send me your system specs, ie, > - run uname -a > - the contents of /etc/redhat-release (if it exists) > > > > > On 7/23/2020 9:42 AM, Xiaomin Yue wrote: > > * External Email - Use Caution * > > Any ideas? > > Thanks, > > Xiaomin > > *From: *Xiaomin Yue <mailto:yuexm@hotmail.com> > *Sent: *Tuesday, July 21, 2020 12:36 PM > *To: *Freesurfer support list <mailto:freesurfer@nmr.mgh.harvard.edu> > *Subject: *Re: [Freesurfer] mri_fieldsign error > > * External Email - Use Caution * > > I tried on our Linux: Centos Linux 7 (core), ID_like = ‘rhel > fedora’ with the same “segmentation fault (core dumped)” error. > > Thanks, > > Xiaomin > > *From: *Xiaomin Yue <mailto:yuexm@hotmail.com> > *Sent: *Friday, July 17, 2020 6:07 PM > *To: *Freesurfer support list <mailto:freesurfer@nmr.mgh.harvard.edu> > *Subject: *Re: [Freesurfer] mri_fieldsign error > > * External Email - Use Caution * > > Yes. I will try it on a real Linux box and let you know. > > Thanks, > > Xiaomin > > *From: *Douglas N. Greve <mailto:dgreve@mgh.harvard.edu> > *Sent: *Friday, July 17, 2020 5:32 PM > *To: *Xiaomin Yue <mailto:yuexm@hotmail.com>; Freesurfer support > list <mailto:freesurfer@nmr.mgh.harvard.edu> > *Subject: *Re: [Freesurfer] mri_fieldsign error > > No, it does not. The only other problem I can think of is that it > has something to do with WSL. Do you have a real linux box you can > try it on? > > On 7/17/2020 5:24 PM, Xiaomin Yue wrote: > > * External Email - Use Caution * > > HI Doug, > > Sorry for the slow response. I got the same “segmentation > fault (core dumped)” error when running the left hemi. I > tested it multiple times. Does this function create a > detailed log I can send to you? > > Thanks, > > Xiaomin > > *From: *Douglas N. Greve <mailto:dgreve@mgh.harvard.edu> > *Sent: *Friday, July 17, 2020 1:07 PM > *To: *freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > *Subject: *Re: [Freesurfer] mri_fieldsign error > > I was not able to replicate this on my CentOS7 linux box. You > sent me left hemi data, so I ran the command below > > mri_fieldsign --fs fieldsign.71.nii.gz --polar > LOO.wedge.polar.lh.real.nii.gz LOO.wedge.polar.lh.imag.nii.gz > --eccen LOO.ring.eccen.lh.real.nii.gz > LOO.ring.eccen.lh.imag.nii.gz --s LOO --hemi lh --sphere > > But I also noticed that the command that you gave below is for > the right hemi. Do you know if the left hemi works? > > > On 7/11/2020 1:43 PM, Xiaomin Yue wrote: > > * External Email - Use Caution * > > Hi Doug, > > I used FS 7.1 under WSL to analyze retinotopy data. Since > the ring and wedge were presented at a different > frequency, the data had to be analyzed separately for each > condition. To get the field sign, I had to use the > mri_fieldsign function to combine polar and eccen data. > However, an error happened with running mri_fieldsign: > “Segmentation fault (core dumped)”. The following is > the command-line output. > > Thanks for your help! > > Xiaomin > > cwd /mnt/d/xyLinuxStaff/projects/wedge_amygdala > > cmdline mri_fieldsign --fs > LOO_xy/bold/rtopy.wedge.self.rh/fieldsign/fieldsign.nii.gz > --polar LOO_xy/bold/rtopy.wedge.self.rh/polar/real.nii.gz > LOO_xy/bold/rtopy.wedge.self.rh/polar/imag.nii.gz --eccen > ../ring_amygdala/LOO_xy/bold/rtopy.ring.self.rh/eccen/real.nii.gz > ../ring_amygdala/LOO_xy/bold/rtopy.ring.self.rh/eccen/imag.nii.gz > --s LOO --hemi rh --sphere > > sysname Linux > > hostname DESKTOP-SVDQE4Q > > machine x86_64 > > user xiaominyue > > eccen real > ../ring_amygdala/LOO_xy/bold/rtopy.ring.self.rh/eccen/real.nii.gz > > eccen imag > ../ring_amygdala/LOO_xy/bold/rtopy.ring.self.rh/eccen/imag.nii.gz > > polar real LOO_xy/bold/rtopy.wedge.self.rh/polar/real.nii.gz > > polar imag LOO_xy/bold/rtopy.wedge.self.rh/polar/imag.nii.gz > > patch (null) > > subject LOO > > hemi rh > > fwhm -1.000000 > > nsmooth -1 > > fieldsign > LOO_xy/bold/rtopy.wedge.self.rh/fieldsign/fieldsign.nii.gz > > usenew 1 > > Reading /mnt/d/xyLinuxStaff/anatMRI_amy//LOO/surf/rh.sphere > > Using spherical coordinates > > Reading > /mnt/d/xyLinuxStaff/anatMRI_amy//LOO/label/rh.aparc.annot > > reading colortable from annotation file... > > colortable with 36 entries read (originally > /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) > > Complex > > Ripping Zeros > > Rot (rad): 0 0 > > surfer: compute_fieldsign2() > > dthresh = 1.5 > > shape = 1 > > nvertices = 153801 > > 0 0 45452 0.03 33.2224 > > 1018 1000 39160 21.33 -18.3959 > > 2055 2000 44734 43.26 33.0783 > > 3148 3000 49793 65.38 0.653687 > > 4344 4000 38626 88.16 16.7555 > > 5529 5000 54149 110.12 -4.90118 > > 6706 6000 61599 133.36 -5.74607 > > 7971 7000 50134 155.88 -17.5589 > > 9165 8000 34182 178.05 -18.9387 > > 10591 9000 59682 200.70 -4.60514 > > 12034 10000 63856 223.18 -4.4884 > > 13297 11000 41007 245.62 27.3489 > > 14938 12000 27365 267.70 -1.40077 > > 16684 13000 23615 289.10 -0.518007 > > 18048 14000 47088 309.37 18.7017 > > 19798 15000 21060 330.11 15.9458 > > 21681 16000 33067 350.27 -11.1953 > > 23173 17000 28744 371.48 -6.18747 > > 25112 18000 27738 392.41 -6.93845 > > 26953 19000 20538 414.47 2.99349 > > 28903 20000 80583 435.98 -0.338512 > > 30319 21000 16251 459.83 -45.2313 > > 32174 22000 17139 483.36 -2.31642 > > 34093 23000 13307 507.02 19.1461 > > 36170 24000 17826 530.65 -10.7575 > > 37683 25000 69324 555.78 -6.17011 > > 39666 26000 14043 583.29 -10.5151 > > 41746 27000 76017 609.92 -0.0112556 > > 43986 28000 84646 636.28 1.24722 > > 46088 29000 9763 664.26 12.7035 > > 48326 30000 92161 694.30 2.03416 > > 50431 31000 99884 724.91 1.20525 > > ./xy_make_wedge_fieldsign.bash: line 21: 22473 > Segmentation fault (core dumped) mri_fieldsign --fs > $line/bold/rtopy.wedge.self.$hemi/fieldsign/fieldsign.nii.gz > --polar > $line/bold/rtopy.wedge.self.$hemi/polar/real.nii.gz > $line/bold/rtopy.wedge.self.$hemi/polar/imag.nii.gz > --eccen > ../ring_amygdala/$line/bold/rtopy.ring.self.$hemi/eccen/real.nii.gz > ../ring_amygdala/$line/bold/rtopy.ring.self.$hemi/eccen/imag.nii.gz > --s $subjname --hemi $hemi --sphere > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > > 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 . 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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