Freesurfer

freesurfer@nmr.mgh.harvard.edu

11 participants
30080 discussions

Re: [Freesurfer] VM image passcode
by fsbuild 22 Jun '22

22 Jun '22

External Email - Use Caution Please check your email again. - R. On Jun 22, 2022, at 17:38, Sean Kelso <skelso(a)outlook.com> wrote:        External Email - Use Caution        I still have not received the passcode..Thanks,Sean On Jun 20, 2022, at 1:55 PM, Sean Kelso <skelso(a)outlook.com> wrote:Hi, what is the pass code needed to expand the Ubuntu archive? Thanks! Sean_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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VM image passcode
by Sean Kelso 22 Jun '22

22 Jun '22

External Email - Use Caution Hi, what is the pass code needed to expand the Ubuntu archive? Thanks! Sean

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Re: [Freesurfer] 7z virtualbox passcode request
by fsbuild 22 Jun '22

22 Jun '22

External Email - Use Caution How fast/efficient a VM runs on a host usually depends upon how much memory and how many processors you can allocate to the VM and what the host machine is running that competes for those resources.   We can't really predict what the performance will be on each users machine.  But if you can install and run directly onto linux or MacOS, then I suggest using the package installers (if you have sudo/admin privileges) instead of the tar archives. Please note all requests for the VM info are being replied to directly using the email address of the sender, and not being copied to the freesurfer list.  Dr. Gregori should have already received the VM info. - R. On Jun 22, 2022, at 13:33, Bouchra Guelib <bouchra.guelib(a)univ-constantine2.dz> wrote:        External Email - Use Caution        Hi,I already used VMware as virtual machine to install Freesurfer, I would advice you to change your OS to linux or Mac , it won't take the same time as you run Freesurfer on VM, also the installation is easy, just download the freesurfer and use tar commend line to install it.Please let me know if you face problem Le mer. 22 juin 2022 à 17:27, Gregori, Johannes, Prof. Dr. <johannes.gregori(a)h-da.de> a écrit :        External Email - Use Caution        HelloI would like to try out th 7z virtual machine image containing freesurfer. Could you send me the passcode? Thanks in advancemit freundlichen Grüßen / best regardsJohannes Prof. Dr. Johannes Gregorih_daHochschule DarmstadtUniversity of Applied SciencesFachbereich Mathematik und NaturwissenschaftenSchöfferstr. 3D-64295 DarmstadtMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1WNHPeRkbS3nRlAs5qToJ2vaGrrpV0d79z966n… mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1lyl_zun4PI5oJRR96Ww6c8fNpeqx9wSphcOiP… 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 Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1IzmRZBWywkssd8SbDBWXR_gcGm8v2UY8Gr_Mg… has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1dqzNt3akI2_u7BpZ7h6IkFGdoyvoBrDTX5e91…; .Please note that this e-mail is not secure (encrypted).  If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately.  Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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7z virtualbox passcode request
by Gregori, Johannes, Prof. Dr. 22 Jun '22

22 Jun '22

External Email - Use Caution Hello I would like to try out th 7z virtual machine image containing freesurfer. Could you send me the passcode? Thanks in advance mit freundlichen Grüßen / best regards Johannes Prof. Dr. Johannes Gregori h_da Hochschule Darmstadt University of Applied Sciences Fachbereich Mathematik und Naturwissenschaften Schöfferstr. 3 D-64295 Darmstadt https://secure-web.cisco.com/1_sKuRnSJKjVJJm47O1OBgQL0QQC_DUYx3VfrsIJoKJuO9…

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VM Password
by Jessica Ramamurthy 21 Jun '22

21 Jun '22

External Email - Use Caution Hi, Could you please provide me with the password to expand the archive for FreeSurfer 7.2.0 so I may import it into the virtual machine? Thank you!

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mri_aparc2aseg bad incorrect ROIs
by Benjamin Deck 21 Jun '22

21 Jun '22

External Email - Use Caution Hi Freesurfer experts, I am attempting to turn my surface-based parcellation into a segmentation file using the following command: mri_aparc2aseg --s sub-DAEK --annot yeo2011 --annot-table sub-DAEK_yeoLUT.txt --threads 6 --rip-unknown --volmask However, when I load the resulting volume using my custom LUT the ROIs get labeled to the white matter and subcortical structures leaving the grey matter unlabeled. When I examine the annotation files, they look appropriate and there isn't any overlap. Do I need to include the subcortical structures in my custom LUT to avoid this from happening or is there a better solution? Thank you! -- *Benjamin L. Deck* *Doctoral Student* *Applied Cognitive and Brain Sciences* *Department of Psychological and Brain Sciences* *Drexel University* <https://secure-web.cisco.com/1QkkGrc1M5CNJQjlaL6JN2C_Kh4FZGHEk5bXUEdRCEnkZG…> Virus-free. http://secure-web.cisco.com/12C_QfaDOwg3LKh_yiXvYrqC0D4zGBhxMG0vzRqgBwZzH5m… <https://secure-web.cisco.com/1tDhPrZdlS9NSF2Pe-eEm0Zojd9ScbaKYJdMT0872rwJGr…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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using brain mask from older FreeSurfer version on a newer
by Aaron Tanenbaum 21 Jun '22

21 Jun '22

External Email - Use Caution Our lab is moving from FreeSurfer 5.3 to 7.2. We have thousands of scans to do. I see that you can give freesurfer a brainmask. I was thinking of giving freesurfer a brainmask from the previous from 5.3 to 7.1. Is this a wise idea? Do you have any objections?

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postdoc at Martinos/LCN
by Douglas N. Greve 20 Jun '22

20 Jun '22

A postdoctoral fellow position in the Lab for Computational Neuroimaging (LCN) under Dr. Douglas Greve is available. We are seeking a highly motivated and talented researcher to pursue independent research. The role will be to develop new algorithms within FreeSurfer, including multi-modal, modality-independent surface placement and brain image segmentation (volume and surface) for both cross-sectional and longitudinal analysis. The projects will use conventional Bayesian and machine learning techniques. The work will mostly focus on structural MRI, but there will be applications to PET (PETsurfer) and fMRI (FSFAST). The candidate should be an accomplished computer programmer with experience in brain image analysis, strong analytical skills, and an ability and desire to do independent research. The ideal candidate would hold a Ph.D. degree in Neuroscience, MR Physics, Biomedical Engineering, or a related field; however, strong candidates with other scientific backgrounds will also be considered. The candidate must have an interest in understanding FreeSurfer at a deep level and welcome the opportunity to leverage this understanding into public visibility through helping to maintain and support FreeSurfer. Interested applicants are invited to send a cover letter describing research interests and experience, an up-to-date CV, and names and contact information of three references to: dgreve(a)mgh.harvard.edu This position is full-time with benefits and is available immediately. The Massachusetts General Hospital and Harvard Medical School are an equal opportunity employer, and all qualified applicants will receive consideration for employment without regard to race, color, religion, sex, national origin, disability status, protected veteran status, gender identity, sexual orientation, pregnancy and pregnancy-related conditions or any other characteristic protected by law. best doug

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FreeSurfer Password
by Mattia Pagano 20 Jun '22

20 Jun '22

External Email - Use Caution Good morning, I need the password to expand the archive for Freesurfer 7.2.0 release in Ubuntu. Thanks, Mattia

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mris_label2annot seed not set
by Benjamin Deck 19 Jun '22

19 Jun '22

External Email - Use Caution Hi Freesurfer experts, While trying to create a custom annotation file I get the following warning: mris_label2annot --s sub-DAEK --a yeo2011 --no-unknown --ctab sub-DAEK_yeoLUT.txt --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels/ --hemi rh Reading ctab sub-DAEK_yeoLUT.txt Number of ctab entries 105 INFO: no labels specified, generating from ctab mris_label2anno supposed to be reproducible but seed not set 51 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_10_ROIs_1_rh_native.label 52 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_11_ROIs_1_rh_native.label 53 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_12_ROIs_1_rh_native.label 54 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_12_ROIs_2_rh_native.label 55 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_13_ROIs_1_rh_native.label 56 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_13_ROIs_2_rh_native.label 57 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_13_ROIs_3_rh_native.label 58 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_13_ROIs_4_rh_native.label 59 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_14_ROIs_1_rh_native.label 60 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_14_ROIs_2_rh_native.label 61 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_14_ROIs_3_rh_native.label 62 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_14_ROIs_4_rh_native.label 63 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_14_ROIs_5_rh_native.label 64 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_15_ROIs_1_rh_native.label 65 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_16_ROIs_1_rh_native.label 66 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_16_ROIs_2_rh_native.label 67 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_16_ROIs_3_rh_native.label 68 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_17_ROIs_1_rh_native.label 69 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_17_ROIs_2_rh_native.label 70 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_17_ROIs_3_rh_native.label 71 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_17_ROIs_4_rh_native.label 72 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_18_ROIs_1_rh_native.label 73 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_18_ROIs_2_rh_native.label 74 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_18_ROIs_3_rh_native.label 75 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_18_ROIs_4_rh_native.label 76 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_19_ROIs_1_rh_native.label 77 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_2_ROIs_1_rh_native.label 78 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_2_ROIs_2_rh_native.label 79 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_3_ROIs_1_rh_native.label 80 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_3_ROIs_2_rh_native.label 81 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_3_ROIs_3_rh_native.label 82 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_4_ROIs_1_rh_native.label 83 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_5_ROIs_1_rh_native.label 84 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_5_ROIs_2_rh_native.label 85 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_5_ROIs_3_rh_native.label 86 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_5_ROIs_4_rh_native.label 87 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_6_ROIs_1_rh_native.label 88 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_6_ROIs_2_rh_native.label 89 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_6_ROIs_3_rh_native.label 90 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_7_ROIs_1_rh_native.label 91 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_7_ROIs_2_rh_native.label 92 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_7_ROIs_3_rh_native.label 93 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_8_ROIs_1_rh_native.label 94 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_8_ROIs_2_rh_native.label 95 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_8_ROIs_3_rh_native.label 96 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_8_ROIs_4_rh_native.label 97 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_8_ROIs_5_rh_native.label 98 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_8_ROIs_6_rh_native.label 99 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_9_ROIs_1_rh_native.label 100 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_9_ROIs_2_rh_native.label 101 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_9_ROIs_3_rh_native.label 102 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_9_ROIs_4_rh_native.label 103 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_9_ROIs_5_rh_native.label 104 /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_9_ROIs_6_rh_native.label 7.2.0 cwd /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels cmdline mris_label2annot --s sub-DAEK --a yeo2011 --no-unknown --ctab sub-DAEK_yeoLUT.txt --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels/ --hemi rh sysname Linux hostname LAPTOP-LPS9CH5E machine x86_64 user bdeck8317 subject sub-DAEK hemi rh SUBJECTS_DIR /mnt/c/Users/Ben/freesurfer/subjects ColorTable sub-DAEK_yeoLUT.txt AnnotName yeo2011 nlables 54 LabelThresh 0 0.000000 Loading /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/surf/rh.orig 0 1316060 Net_10_ROIs_1_rh_native 1 14464220 Net_11_ROIs_1_rh_native 2 14423100 Net_12_ROIs_1_rh_native 3 11832480 Net_12_ROIs_2_rh_native 4 9180240 Net_13_ROIs_1_rh_native 5 8204875 Net_13_ROIs_2_rh_native 6 10542100 Net_13_ROIs_3_rh_native 7 9231380 Net_13_ROIs_4_rh_native 8 9221140 Net_14_ROIs_1_rh_native 9 14474380 Net_14_ROIs_2_rh_native 10 2763429 Net_14_ROIs_3_rh_native 11 1351760 Net_14_ROIs_4_rh_native 12 15736992 Net_14_ROIs_5_rh_native 13 6553700 Net_15_ROIs_1_rh_native 14 11146310 Net_16_ROIs_1_rh_native 15 13145750 Net_16_ROIs_2_rh_native 16 3311482 Net_16_ROIs_3_rh_native 17 2146304 Net_17_ROIs_1_rh_native 18 5935475 Net_17_ROIs_2_rh_native 19 681085 Net_17_ROIs_3_rh_native 20 23060 Net_17_ROIs_4_rh_native 21 3957760 Net_18_ROIs_1_rh_native 22 3311482 Net_18_ROIs_2_rh_native 23 1321040 Net_18_ROIs_3_rh_native 24 3276922 Net_18_ROIs_4_rh_native 25 6588260 Net_19_ROIs_1_rh_native 26 3957760 Net_2_ROIs_1_rh_native 27 50372 Net_2_ROIs_2_rh_native 28 2671812 Net_3_ROIs_1_rh_native 29 3957956 Net_3_ROIs_2_rh_native 30 6564036 Net_3_ROIs_3_rh_native 31 3945156 Net_4_ROIs_1_rh_native 32 13127690 Net_5_ROIs_1_rh_native 33 6604880 Net_5_ROIs_2_rh_native 34 2647140 Net_5_ROIs_3_rh_native 35 3937480 Net_5_ROIs_4_rh_native 36 665610 Net_6_ROIs_1_rh_native 37 50372 Net_6_ROIs_2_rh_native 38 706590 Net_6_ROIs_3_rh_native 39 5923840 Net_7_ROIs_1_rh_native 40 6579200 Net_7_ROIs_2_rh_native 41 32768 Net_7_ROIs_3_rh_native 42 25600 Net_8_ROIs_1_rh_native 43 13117500 Net_8_ROIs_2_rh_native 44 6574090 Net_8_ROIs_3_rh_native 45 51200 Net_8_ROIs_4_rh_native 46 8320 Net_8_ROIs_5_rh_native 47 25750 Net_8_ROIs_6_rh_native 48 1336330 Net_9_ROIs_1_rh_native 49 25740 Net_9_ROIs_2_rh_native 50 3983360 Net_9_ROIs_3_rh_native 51 7895160 Net_9_ROIs_4_rh_native 52 6553720 Net_9_ROIs_5_rh_native 53 25700 Net_9_ROIs_6_rh_native Writing annot to /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/rh.yeo2011.annot The annotation file looks fine, however, I am worried that this warning may be pointing at a larger issue. Can you advise? Thanks! FS: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b OS: WSL2 Ubuntu -- *Benjamin L. Deck* *Doctoral Student* *Applied Cognitive and Brain Sciences* *Department of Psychological and Brain Sciences* *Drexel University* <https://secure-web.cisco.com/1JUYvI6qR2KHny5pu-f9lEzMAikHDQnJEQzEy2bQcsPQ6R…> Virus-free. http://secure-web.cisco.com/1vXe16WpLwEeffCQQEIzrJynVkOZTnYNK4zHjcPCpq_MyoN… <https://secure-web.cisco.com/1VFMgx5tZC9GQwomPBkbGypdqGMLfiP59efwXDTUjsVj-S…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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