Freesurfer August 2022

freesurfer@nmr.mgh.harvard.edu

85 participants
120 discussions

accumbens nucleus volumes
by Alexopoulos, Dimitrios 08 Aug '22

08 Aug '22

External Email - Use Caution The accumbens nucleus is very difficult to delineate in some younger (3yo) subjects and in infants run through the infant pipeline. The pipelines segment the region but I'm not sure how reliable the volume measures are. Can the accumbens volume be included with another structure (i.e caudate)? Jim ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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segmentation of thalamic nuclei: possibility of generating connectome
by Lauren Taylor 08 Aug '22

08 Aug '22

External Email - Use Caution Hello FreeSurfer Developers, I am trying to generate a connectome in MRtrix3 using FreeSurfer parcellations and segmentations. I am specifically interested in the subregions of the thalamus and noticed that the newest version of FreeSurfer (7.3.1) has added segment_subregions. This command runs on my M1 mac without error and successfully outputs ThalamicNuclei.FSvoxelSpace.mgz, ThalamicNuclei.mgz, and ThalamicNuclei.volumes.txt. I am wondering if it is possible to generate a file similar to aparc+aseg.mgz that is generated in recon-all, but with thalamic subregion segmentations included. I was thinking that the following steps could possibly work: * Run recon-all * Run segment_subregions thalamus * mri_surf2volseg: * mri_surf2volseg --i ThalamicNuclei.FSvoxelSpace.mgz --fix-presurf-with-ribbon ribbon.mgz --o aseg_new.mgz \ --lh-cortex-mask ../label/lh.cortex.label \ --rh-cortex-mask ../label/rh.cortex.label \ --lh-white ../surf/lh.white --lh-pial ../surf/lh.pial \ --rh-white ../surf/rh.white --rh-pial ../surf/rh.pial * merge seg --src aseg.mgz --merge aseg_new.mgz --o aseg_all.mgz * mri_surf2volseg --i aseg_all.mgz --label-cortex --o aparc+aseg_thalamus.mgz --lh-annot ../label/lh.aparc.annot 1000 --rh-annot ../label/rh.aparc.annot 2000 --lh-cortex-mask ../label/lh.cortex.label --rh-cortex-mask ../label/rh.cortex.label --lh-white ../surf/lh.white --lh-pial ../surf/lh.pial --rh-white ../surf/rh.white --rh-pial ../surf/rh.pial I appreciate your time, and I look forward to hearing from you. Thanks, Lauren Taylor

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Tracula Config file.
by Alan Francis 08 Aug '22

08 Aug '22

External Email - Use Caution Hi Anastasia - Hope you are well. I am running tracula on FS 7.2. I created the RC file based on your recommendations. However it is giving me an error message when I run it. The error is : Unmatched ' " " I have attached the RC file. Could you please see where I have made an error. Thanks so much, Best regards, Alan -- *|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|* *Alan N. Francis PhDAssistant Professor of NeuroscienceInstitute of Neuroscience* *University of Texas, School of Medicine* *Rio Grande Valley* *Texas.*

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Analysing pediatric data & ROI analysis
by Rio Yamaguchi 08 Aug '22

08 Aug '22

External Email - Use Caution Dear Freesurfer experts, I am a complete novice analysing brain images and would like to double check if what I have been doing is correct. 1) I ran the recon-all script for the T1 images of all the subjects 2) I ran the aparcstats2table (meas volume) script and the asegstats2table (meas thickness for both hemispheres) to extract the volumes and the thickness information of various regions. 3) Exported the resulting tables to excel (and subsequently to SPSS) for statistical analysis. Our subjects are children 8-12 years old. According to this information, https://secure-web.cisco.com/1DjimnZeU0HWYyktwcKlLOM5c2t98vyC804Lh_aGhlh_Q1… perhaps I need to manually edit some of the data that is automatically generated from recon-all? If so, if you could guide me to the relevant guidelines (with details) that will be most greatly appreciated. Also, as I would like to obtain the volume of anterior cingulate cortex, I included --segno --segno 1002 1026 2002 2026 3002 3023 3026 4002 4026 3201 3203 4201 4203 in the asegstats2table command as I thought the corresponding regions and their ID can be found on this list https://secure-web.cisco.com/1yGAjLK_b5XwLg1HBgql1vPDqiO5rhoboItkqiQ2I-zOhp… <https://secure-web.cisco.com/1yGAjLK_b5XwLg1HBgql1vPDqiO5rhoboItkqiQ2I-zOhp…> However, I have an error message saying " cannot find the corresponding segmentation for the id:1002 you provided in any of the .stats files parsed" Do I first need to label these specific regions of interest? If you could point me to the right direction, it will be most greatly appreciated. Thank you in advance. Kind regards, Rio ============================================== Rio Yamaguchi [PhD Candidate] yamaguchi-rio(a)g.ecc.u-tokyo.ac.jp University of Tokyo Department of Child Neuropsychiatry, ==============================================

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Fwd: eTIV
by Bouchra Guelib 07 Aug '22

07 Aug '22

External Email - Use Caution ---------- Forwarded message --------- De : Bouchra Guelib <bouchra.guelib(a)univ-constantine2.dz> Date: mer. 27 juil. 2022 à 19:28 Subject: eTIV To: <freesurfer-owner(a)nmr.mgh.harvard.edu> I hope you can help me with this point I extracted the measures in 'aseg.stats', 'lh.aparc.stats',and 'rh.aparc.stats'. Now I want to use these measures as input data for my model. However, I read that we need to normalize this data using eTIV. Can you tell me how? -- *GUELIB Bouchra: *Ph.D. student *Lire *Laboratory University: Constantine 2-Abdelhamid Mehri- *Algeria * Alternative email: Guelibbouchra(a)gmail.com

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Processed AHBA data
by William Snyder 06 Aug '22

06 Aug '22

External Email - Use Caution Dear FreeSurfer experts, Where can I find the FS v5.3 surfaces/segmentations of the Allen Human Brain Atlas donor brains? I noticed it here (https://secure-web.cisco.com/19CpgIyzbr0Z6CSkmfWcrKXLQR_u1AXjX0kOsx6WWuiqfU…) but the data seems to be removed from the ftp server. I am hoping to create custom parcellations in subject native space using the geometries from previously manually corrected surfaces, as I am having difficulty automatically generating good donor brain surfaces. Thank you! Will Snyder Get Outlook for iOS<https://secure-web.cisco.com/1QE1GcwWaldiDhJ801m9Y7J8RKBl1MiL64elFp_7a1bqMj…>

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Brain Hole
by Ben Pluger 06 Aug '22

06 Aug '22

External Email - Use Caution Hi, I've been getting these emails for about 2 years in the hope I would be able to understand Freesurfer better. Five years ago I underwent a craniotomy for a tumor found during an MRI and was diagnosed with a Stage 2 Astrocytoma soon after. I've used your software to extract my brain in an attempt to 3D print it. I did print what was output from the program but was unsatisfied with the results (cerebellum was missing ect). I was hoping you could put me in touch with someone who could assist me. I recently lost access to the computer I was running Linux on with my Freesurfer files and only have the STL / raw DICOM files left. As such we will most likely be starting over on this project. Thank you for your time, -Ben Pluger (Brain hole Ben)

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Re: [Freesurfer] Freeview Closes Unexpectedly
by fsbuild 04 Aug '22

04 Aug '22

External Email - Use Caution You need to use the sudo command to modify something under /Applications, so you could do$ sudo cp ~/Downloads/license.txt /Applications/freesurfer You could also just set FS_LICENSE to point to license.txt% setenv FS_LICENSE  ~/Downloads/license.txt You could also add that setenv in your shell initializaztion file so it will be set the next time you open a terminal window. - R. On Aug 4, 2022, at 17:48, user2038178(a)gmail.com wrote:        External Email - Use Caution        Thank you!When I try to copy the license.txt file I receive this:% cp ~/Downloads/license.txt /Applications/freesurfercp: /Applications/freesurfer/license.txt: Permission deniedHow can this be resolved?On Fri, Jul 22, 2022 at 6:37 AM Wang, Ruopeng <RWANG4(a)mgh.harvard.edu> wrote:Here is the instruction:MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1OShD5Wc9pbKTVxIZ4IEWEKwdg0ubHAEIAp6ka… Jul 22, 2022, at 12:52 AM, user2038178@gmail.com wrote:        External Email - Use Caution        Hi,To make sure, can you send me the instructions on how to download the FS license file?On Fri, Jul 22, 2022 at 1:31 AM Wang, Ruopeng <RWANG4(a)mgh.harvard.edu> wrote:Have you install the FS license file properly? Another thing to check is to make sure you have granted freeview permission to access your disk files. You can check it in the system preferences.RuopengOn Jul 21, 2022, at 12:31 PM, user2038178@gmail.com wrote:        External Email - Use Caution        Hi,When I try to open any files in Freeview on a MacBook, the application closes unexpectedly. I only receive a message from Apple that says "Freeview quit unexpectedly" but gives no reason. This happens after I open the application and try to load a volume. After Freeview closes, I can open it again but the file does not open. How can this be resolved?_______________________________________________Freesurfer 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/1dv8o7rEH_IGxjNFFEfw-XePreZ1nr2vzA4y3a… 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/10KIxVnVqqQqYY1a73np9ukKIyMG2-uiEsKJiw… 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/1ZKO5bwanjF6pvAP5ME4qDcD5Jw_t-srRyhVIQ… has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1Hw0LUsW27WyqQzAl2HBqUGg42pngLQlyG5vVa…; .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(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/14xMA4MSJzu8dcQPDV6N9iWLv_28gskAk7e3J-… 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/10KIxVnVqqQqYY1a73np9ukKIyMG2-uiEsKJiw… 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/1ZKO5bwanjF6pvAP5ME4qDcD5Jw_t-srRyhVIQ… has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1Hw0LUsW27WyqQzAl2HBqUGg42pngLQlyG5vVa…; .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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Freeview Closes Unexpectedly
by _ _ 04 Aug '22

04 Aug '22

External Email - Use Caution Hi, When I try to open any files in Freeview on a MacBook, the application closes unexpectedly. I only receive a message from Apple that says "Freeview quit unexpectedly" but gives no reason. This happens after I open the application and try to load a volume. After Freeview closes, I can open it again but the file does not open. How can this be resolved?

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Postdoc position available at FS team (NIH BRAIN Initiative project)
by Iglesias Gonzalez, Juan E. 04 Aug '22

04 Aug '22

Dear all, Prof. Fischl and I are looking for a postdoc to work on a multi-site, international project (18 institutions, 3 continents) sponsored by the NIH BRAIN Initiative. Details on the project, position, and application here: https://scholar.harvard.edu/iglesias/jobs Cheers, Juan Eugenio Iglesias www.jeiglesias.com<http://www.jeiglesias.com>

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Freesurfer August 2022