Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30081 discussions

Use Hippocampal segmentation sub-nuclei on other brain softwares
by Borghi, G. (Gregorio) 12 Apr '21

12 Apr '21

External Email - Use Caution Dear All, I have been stuck on this issue for quite some time. What I am trying to do is running a segmentation on both amygdala and hippocampus, and then to look at the different activation of the segmented sub-fields of both structures during a social-emotional task. However, despite my efforts I have not been able to find a way for translating either the segmented output files to bring them in a format that can be used by R, FSL, or SPM. Is there anyone who might have an answer on how to do that? Or is there a function in freesurfer that provides the list of voxel coordinates per volume for each hippocampal and amygdala subfields? Kind regards, Gregorio Borghi

2 1

How to edit GM when WM is ok
by Caroline Chwiesko 09 Apr '21

09 Apr '21

External Email - Use Caution Hello Freesurfer experts, i am doing some editing after recon-all. I have the issue that one gyrus is not captured by the pial surface. There is no wm that is wrong and that i could correct. It looks like this gyrus has a weird angle so there is actually no WM visible. How can such an error be corrected? I am happy to send a couple images if needed. Thank you very much in advance for any help! Cheers Carolin

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MRI RA Position at Ohio State
by Hayes, Scott M. 09 Apr '21

09 Apr '21

External Email - Use Caution Research Assistant Position The Buckeye Brain Aging Lab (B-BAL) Department of Psychology The Ohio State University Applications are being sought for a full-time research assistant position in the Buckeye Brain Aging Lab (B-BAL; thebbal.com<http://secure-web.cisco.com/1HjejvxI7VUxlECPLn2YyeI79In8qatKRagfSEjyO8G66zH…>) directed by Dr. Scott Hayes. The B-BAL studies the relationships among aging, physical activity, cognition and the brain [using Magnetic Resonance Imaging (MRI) metrics]. We also examine neural correlates of memory in healthy and clinical populations. The Research Assistant 1 assists in the general coordination and conduct of research in the B-BAL, including administration of neuropsychological tests and/or questionnaires to young and older adults; recruits, screens, and schedules human subjects, including coordination of subject appointments (cognitive, MRI, and physical fitness assessments), subject payments, and submission of IRB amendments; assists with participant recruitment efforts between the laboratory and community partners; assists with research lab purchases and maintains lab supplies; assists with cognitive, MRI, and physical fitness data collection, including obtaining informed consent, cognitive testing (computer and paper and pencil based testing), MRI data acquisition, and record keeping; assists with cognitive and MRI data processing and analyses, supervises undergraduate research assistants. Desired qualifications include: Bachelor's degree in psychology, neuroscience, computer science, engineering, or physics; programming experience in unix, python, matlab, as well as experience in neuroimaging data analyses; knowledge of software packages, such as FreeSurfer, FSL, AFNI, SPM, CONN, R. The position is available for one year with the possibility of extension for additional years based on satisfactory performance and availability of funds. If you are interested in being considered for the position, please apply online at https://secure-web.cisco.com/1sICga4tsxcHZeNaUj6ZIbnSVd8ouX635dTqvkezT0yVfL… Submit a cover letter, writing sample (research paper from course, poster presented at a conference), current CV and arrange to have two reference letters emailed to bbal(a)osu.edu<mailto:bbal@osu.edu> . If you have questions about the position or the lab, please email bbal(a)osu.edu<mailto:bbal@osu.edu> . To build a diverse workforce, The Ohio State University encourages applications from all individuals. Ohio State is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to age, race, color, religion, sex, sexual orientation, gender identity, national origin, disability status, or protected veteran status.

1 0

MCSRCH error using sample data (001.mgz and 002.mgz)
by Yoonho Hwang 09 Apr '21

09 Apr '21

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to compute cortical thickness and to analyze it between groups. So I perform "recon-all", but rather than using recon-all -all, some problems arise while performing each of the steps in it. These problems are as follwing. *sample-001.mgz and sample-002.mgz in /usr/local/freesurfer/**subjects/ are used. What is this problem happening? * *IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010* *Resulting transform:* * 1.09487 -0.03668 0.00057 -10.07315;* * 0.03682 1.10413 0.22705 -54.96997;* *-0.00899 -0.18307 0.95770 22.82867;* * 0.00000 0.00000 0.00000 1.00000;* 1) FreeSurfer version: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 2) Platform: Ubuntu release 18.04.1 3) uname -a: Linux LABPC 5.4.0-70-generic #78~18.04.1-Ubuntu SMP Sat Mar 20 14:10:07 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached Thank you very much. Sincerely, Yoonho -- *Hwang, Yoonho* *Medical Image Processing Laboratory (MIPL),* *Department of Biomedical Engineering, Yonsei University.* *#218 Sanhak-Kwan, 1, Yeonsedae-gil, Heungeop-myeon, Wonju,* *Gangwon-do, 26493, Republic of Korea.* *Office: +82-33-760-2499* *Email: ken.lmstar11(a)gmail.com <ken.lmstar11(a)gmail.com>*

2 1

Assistant Professor Position in Cognitive Neurosciences of Language - University of Geneva Switzerland
by Narly Golestani 09 Apr '21

09 Apr '21

External Email - Use Caution Dear all, An Assistant Professor Position in Cognitive Neuroscience of Language is available at the University of Geneva, Switzerland. The position will be in the Psychology section of the Faculty of Psychology and Education Science https://secure-web.cisco.com/1Hn_XNE0p1RKSeisul8uuWPjqFsyEgiu5lMCeaHhECmbSV…, with access to Campus Biotech Facilities "https://secure-web.cisco.com/1T_pbFAMOQE6rzfyb3YUonEwo8892rX5KOMFJx0YbtN0GP…". This position is opened in the context of the NCCR (National Center of Research Competence) "Evolving Language" - http://secure-web.cisco.com/1EWS_y03OVjFu46pudQ4_4N5frGWZHwtV250Dr-BazQ5r_f…. The whole application process can be carried in English. It is required that the successful candidate acquire a working command of French within the first two years in the position. The application deadline is on May 19th, 2021 - please see https://secure-web.cisco.com/1CDMYP8n3cNlL1DfRxXDUt3T2Rps02kJ9kWAYpxlTVcYAo… for more information. We would be most thankful if you could distribute widely. Thanks in advance, and best wishes, Narly Golestani. ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Brain and Language Lab Prof. Narly GOLESTANI Department of Psychology Campus Biotech 9 Chemin des Mines, 1202 Genève +41 22 379 53 52 <https://secure-web.cisco.com/1dinoEmfX1o7ZFkPOcSggpavzSzXiCY2uRru-c5xw5IuM6…>http://secure-web.cisco.com/1y3jxPvURbRT3R3lkfnmhThYAOCwHy0AdTX2xoqOS-umHjg… https://secure-web.cisco.com/1UIgPKfsx4cUK4nmQkVjd2UWtKIAXemv5JGehU-Zt0LIHz… ----------------------------------------------------------------------------------------------------------------------------------------------------------------- <https://secure-web.cisco.com/1dinoEmfX1o7ZFkPOcSggpavzSzXiCY2uRru-c5xw5IuM6…>

1 0

Some func. error during recon-all process
by Yoonho Hwang 09 Apr '21

09 Apr '21

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to compute cortical thickness and to analyze it between groups. So I perform "recon-all", but rather than using recon-all -all, some problems arise while performing each of the steps in it. These problems are as follwing. 1. -whitesurf process is preceded over smooth2 and inflated2 in recon-all file, really it is not. why? 2. This error first started during -cortribbon process, also occurs in other processes such as -cortparc2, -cortparc3, -hyporelabel, -aparc2aseg, and -wmparc. But these process does not ask for a file called aseg as input if you check it on the homepage. Can you tell me how to fix it? error: mghRead(/media/hwang/Disk1/cp2ANZ/FREESURFER/mri/aseg.mgz, -1): could not open file error: cannot compute vol stats without /media/hwang/Disk1/cp2ANZ/FREESURFER/mri/aseg.mgz Command exited with non-zero status 1 1) FreeSurfer version: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 2) Platform: Ubuntu release 18.04.1 3) uname -a: Linux LABPC 5.4.0-70-generic #78~18.04.1-Ubuntu SMP Sat Mar 20 14:10:07 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached Thank you very much. Sincerely, Yoonho -- *Hwang, Yoonho* *Medical Image Processing Laboratory (MIPL),* *Department of Biomedical Engineering, Yonsei University.* *#218 Sanhak-Kwan, 1, Yeonsedae-gil, Heungeop-myeon, Wonju,* *Gangwon-do, 26493, Republic of Korea.* *Office: +82-33-760-2499* *Email: ken.lmstar11(a)gmail.com <ken.lmstar11(a)gmail.com>*

1 0

mri_convert problem
by Pierpaolo Croce 08 Apr '21

08 Apr '21

External Email - Use Caution Dear List, I have installed the ubuntu version of freesurfer (creating the VM as in the tutorial) I would like to run the following command: mri_convert -c -oc 0 0 0 asta.mgh orig.mgz I always get the error in the screen shot. Can someone help me? also using asta.nii format -- Ing. Pierpaolo Croce, PhD. Institute for Advanced Biomedical Technologies - ITAB and Department of Neuroscience and Imaging University of Chieti "G. D'Annunzio" Via dei Vestini, 33 66013 Chieti, Italy

2 1

thalamic nuclei segmentation
by Sara PONTICORVO 08 Apr '21

08 Apr '21

External Email - Use Caution Hi Freesurfer experts, I processed ~150 subjects with freesurfer v6 (recon-all) and I was wondering if it is possible to use the script for the segmentation of the thalamic nuclei on these subjects. I know this part of the processing is now integrated in the v7 of freesurfer, but I'm thinking if there is a way to avoid re-run all the reconstruction with the new version. I looked in the wiki page, and it seems that there was a way to integrate the scripts in the fs-v6, but I don't find any downloadable package or scripts. Thanks for your help, Sara -- Sara Ponticorvo, PhD Department of Medicine Surgery and Dentistry University of Salerno

2 1

Re: [Freesurfer] Virtual Box Account Password
by fsbuild 07 Apr '21

07 Apr '21

External Email - Use Caution Sending this to your posted email address in a few minutes. - R..On Apr 7, 2021, at 05:45, Banu Femir <banu.femir(a)gmail.com> wrote:        External Email - Use Caution        Dear Freesurfer Developers,I downloaded Virtual Box on my Windows following the steps on: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/11Q8tziq_44pDhv3UNtqG-Qaqy_JvvV_aM6BwG…, when I try to turn on the virtual linux, it asks for a password of an account named "developer". I tried to find a password on the internet but could not. This question was asked by someone else on May, 2020, the reply is like " You may check *brain.map* " but I could not find anything about it. I would be so happy if you can help me because I am stuck with my data analysis. I am sending the picture in the attachment. Many thanks!Banu<IMG_3862.jpg>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

Virtual Box Account Password
by Banu Femir 07 Apr '21

07 Apr '21

External Email - Use Caution Dear Freesurfer Developers, I downloaded Virtual Box on my Windows following the steps on: https://secure-web.cisco.com/1CyzUIZtRjJfdg7gYEEp3hkwAuc4pVU2M20x2njsr6thrr… However, when I try to turn on the virtual linux, it asks for a password of an account named "developer". I tried to find a password on the internet but could not. This question was asked by someone else on May, 2020, the reply is like " You may check *brain.map* " but I could not find anything about it. I would be so happy if you can help me because I am stuck with my data analysis. I am sending the picture in the attachment. Many thanks! Banu

1 0

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