Freesurfer November 2018

freesurfer@nmr.mgh.harvard.edu

121 participants
189 discussions

Extra-axial CSF and TCV GM
by Crocetti, Deana 19 Nov '18

19 Nov '18

External Email - Use Caution Hi Folks, 1) Can I derive a measure of extra-axial CSF. I realize this must be generated in order to create the boundary between the skull and dura but not sure if this is saved in as one of the labels. 2) To generate a measure for Total Cerebral Volume Gray Matter would I combine the following labels? lhCortex + rhCortex + SubCortGray + CerebellumGM Thank you, Deana ---------------------------------------------------------------------- Disclaimer: The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

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FDR correction
by Laura Ferrero 19 Nov '18

19 Nov '18

External Email - Use Caution Hi, I performed an statistical analysis comparing autism group with control group using volume/area and thickness measures. I found significant differences in some regions but they were not significant after FDR correction. The majority of p-values are really high and only some of them are small, I would like to know is that can affect the result. Additionally, I read that it is interesting to do a power analysis to know the amount of difference that can be detected based on the sample size and I would like to know if it is a good approach to follow trying to explain why some results were not significant after multiple comparison correction. Thank you, Laura

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Pial edition and Intensity Normalization / Control points
by Rosalia Dacosta Aguayo 19 Nov '18

19 Nov '18

External Email - Use Caution Dear Free Surfer team, I have edited the pial surface and I am running: -autorecon-pial. This process is taking its time. Then I will look for intensity normalization and control points. Then I will have to run recon-all -autorecon2-cp -autorecon3. I wonder if: 1. Is there any way to do pial and normalization/control points at the same time, so I only have to run the process one time (speed in it up). 2. Is there any other change I should consider when editing? Best regards, Rosalia

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Error tkmedit
by Rosalia Dacosta Aguayo 19 Nov '18

19 Nov '18

External Email - Use Caution Dear Free Surfer experts, I am trying to load my brainmask and the T1 to make editions but I have a problem I do not know how to solve. I would much appreciate your helping here. Best regards, Rosalia *Problem: * ms_naroa@neuroimagen1:~/Escritorio/subjects_controls$ ls 001 006 013 021 027 031 035 039 047 fsaverage 002 008 014 023 028 032 036 040 betn_controls NN 004 009 015 024 029 033 037 043 correct_errors 005 010 017 026 030 034 038 046 Errors_list.ods ms_naroa@neuroimagen1:~/Escritorio/subjects_controls$ tkmedit 002 brainmask.mgz -aux T1.mgz *ERROR: cannot find subject 002 in /home/ms_naroa/subjects or it is not readable by you*

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Re: [Freesurfer] Segmentation fault
by fsbuild 19 Nov '18

19 Nov '18

External Email - Use Caution Hello Jon, Can you get any stack or backtrace information after the segfault occurs ?, e.g., Mac OS has the option to display the crash report with a trace.  On Linux you could run thru gdb and get a back trace.   This would help us to see where the code is exiting..

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Research Associate Position: Molecular Imaging in Neurodegenerative Disease, Johns Hopkins University
by Gwenn Smith 19 Nov '18

19 Nov '18

External Email - Use Caution Research Associate Molecular Brain Imaging in Neurodegenerative Disease A full-time opening is available for a Research Associate in the Department of Psychiatry and Behavioral Sciences and Radiology and Radiological Sciences at Johns Hopkins University School of Medicine. The research program focuses on applying multi-modality PET and MR imaging to investigate the neurobiology of late life depression, mild cognitive impairment and Parkinson's disease. Responsibilities include design and implementation of human neuroimaging research studies and image processing, in collaboration with the interdisciplinary team. The position is a great opportunity for self-motivated individuals to take the lead on scientific publications and presentations and to develop independent projects and grant submissions. Position Requirements: Candidates should have a doctorate (Ph.D. or M.D) in Experimental Psychology, Neuropsychology, Neuroscience, Neurology or a comparable discipline. Experience in the conduct of clinical research studies is required. Experience in PET or MRI image analysis is preferred. Review of applications will begin immediately and will continue until the position is filled. Applicants should send their Curriculum Vitae and a statement of academic interests to: Gwenn S. Smith, PhD (gsmith95(a)jhmi.edu<mailto:gsmith95@jhmi.edu>), Division of Geriatric Psychiatry and Neuropsychiatry, Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine 5300 Alpha Commons Drive, Baltimore, MD 21224

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loading and rendering the Amygdala nuclei only in Freeview
by Erik O'Hanlon 19 Nov '18

19 Nov '18

External Email - Use Caution Hi FS Experts, I'm trying to make some images of my amygdala nuclei in freeview and selected my T1 as background and then loaded up lh.hippoAmygLabels-T1-HippoAMYT1andT2FLAIR.v20.FS60.FSvoxelSpace.mgz image which loads up perfectly. I selected the "show existing labels " and the freesurfer colour LUT but when I select the range for 7001-7015 for amygdala only, the hippocampal subfields are still there. Is there a way to only load the amygdala nuclei. I'm sure it's something simple I'm just not doing, but I can't seem to get it to work. Any pointers gladly accepted Thanks Erik Erik O'Hanlon Postdoctoral researcher [cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png] RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont D9 Ireland T: 8093740 E: erikohanlon(a)rcsi.ie W: www.rcsi.com<http://www.rcsi.com/> Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022<http://www.rcsi.ie/strategy2018> [cid:AS_BRONZE_IIDD_65c26b0a-ea45-42c8-956e-5d84e884e4e6.png]

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回复： ?????? Recon-all run error
by 1013364183 18 Nov '18

18 Nov '18

External Email - Use Caution Dear Bruce, I am very sorry to bother you. We are currently experimenting with freesurfer, but I have encountered a lot of problems during the experiment. We have three resolutions of data, the skull of medium-resolution data can't be removed (neck can't be removed), and with high-resolution data, it will report memory transfer errors. You said before that we can submit data sets to you, how should we provide you with data sets? Thanks in advance yours yujunjie ------------------ 原始邮件 ------------------ 发件人: "Bruce Fischl"<fischl(a)nmr.mgh.harvard.edu>; 发送时间: 2018年11月7日(星期三) 凌晨2:42 收件人: "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu>; 主题: Re: [Freesurfer] ?????? Recon-all run error does it occur if you run it outside of recon-all? Do you have enough free ram? If so, you can filedrop us the dataset and we can try to replicate and fit ix. On Tue, 6 Nov 2018, 1013364183 wrote: > > External Email - Use Caution > > Dear Bruce, > I found the error location in the recon-all.log folder. Here is the place where it went wrong??I > don't think it's the reason for insufficient memory.. > ''mri_convert.bin: putget.c:322: fill_NC_var: Assertion `chunksz % 4 == 0' failed.'' > This data is ok when we run with versions prior to freesurfer 6.0. But after we run the 6.0 > version and set the expert file, this error will occur.Do I need to step through the instructions to > see the problem? How should this error be solved? > > Thanks in advance > > yours yujunjie > > ------------------ ???????? ------------------ > ??????: "Bruce Fischl"<fischl(a)nmr.mgh.harvard.edu>; > ????????: 2018??11??6??(??????) ????9:40 > ??????: "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu>; > ????: Re: [Freesurfer] Recon-all run error > > that certainly looks like something is running out of ram. Can you run > the command that failed directly on the command line and see if it works? > Was anything else running on the machine at the time? We do report total > and free memory at the start of the recon in the recon-all.log file > > cheers > Bruce > On Tue, > 6 Nov 2018, 1013364183 wrote: > > > > > External Email - Use Caution > > > > Dear FS, > > When we run ??recon-all?? with a 5GB high-resolution image, core dumped appears when the > mri_convert > > command is executed. The specific errors are as follows: > > /opt/el7/pkgs/freesurfer/freesurfer_6.0/bin/mri_convert: line 3: 29235 Aborted (core dumped) > > mri_convert.bin "$@" > > ERROR: converting to minc > > We want to know if our high resolution image is too large for freesurfer to handle, or our > computer > > memory (64GB running memory) is limited. > > > > Thanks a lot in advance! > > yours sincerely, > > yu junjie > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Installing Two Versions of FreeSurfer on One System at the Same Time
by Maedeh Khalilian 18 Nov '18

18 Nov '18

External Email - Use Caution Dear FreeSurfer experts, I wonder if I can install two versions of FreeSurfer (the latest one and an older one) on one system at the same time. Thanks more. Best Maedeh,

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Re: [Freesurfer] Modify defect failed
by 1013364183 18 Nov '18

18 Nov '18

External Email - Use Caution Dear Bruce Fischl, Thank you very much for your reply. I checked the effect of going down the skull and found that a large part of the skull has not been removed. The appendix contains images of skull removal. I want to know how we should handle it. yours yujunjie ------------------ Original ------------------ From: "Bruce Fischl"<fischl(a)nmr.mgh.harvard.edu>; Date: Sun, Nov 18, 2018 00:10 AM To: "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu>; Subject: Re: [Freesurfer] Modify defect failed Hi yujunjie the last entry in the log file is: CORRECTING DEFECT 5 (vertices=53772, convex hull=1434, v0=15308) XL defect detected... this is a giant defect - about 1/4 of your total surface. It means that something major went wrong - skull attached, or hemis connected or something. You should look at the rh.orig.nofix and the rh.inflated.nofix surfaces to see what it is. cheers Bruce On Sat, 17 Nov 2018, 1013364183 wrote: > > External Email - Use Caution > > Dear FS, > I ran the recon-all command and it failed to fix it for many days when I fixed the defect. I have > modified the threshold of the split algorithm. I want to know if there are other ways to fix the Its > log file is in the attachment. > > Thank you in advance > > yours yujunjie > > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer November 2018