Freesurfer August 2023

freesurfer@nmr.mgh.harvard.edu

89 participants
126 discussions

How to compute the merged volume of both hemispheres per each ROI
by inbal paran 07 Aug '23

07 Aug '23

External Email - Use Caution Hello FreeSurfer Developers, I need to compute the volume of specific bilateral cortical and subcortical ROIs. I already ran reacon-all on all of my subjects, and I extracted volumes of the ROIs per hemisphere of both the cortical and subcortical brain regions (aseg and aparc). How can I compute the merged volume of both hemispheres per each ROI? The freesurfer version I am using: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 Thank you Inbal -- *Inbal Paran, M.PT <http://secure-web.cisco.com/1dUL-xmv_VpHQT4s0hPfzZjFPufKHWvX3qxyzuwCCmLC-l-…>.* Schwartz Movement analysis & Rehabilitation Laboratory, Physical Therapy Department, Recanati School for Community Health Professions. Faculty of Health Sciences at Ben-Gurion University of the Negev.

2 1

Errors Running tkmedit
by Edwards, Vincent 07 Aug '23

07 Aug '23

External Email - Use Caution Hello, Our lab has been using Freesurfer 5.3 for it's ongoing longitudinal study. I attempted to quality check one of our brains using tkmedit - I usually don't have any issues following our pipeline or running the tool. This time I received this message: ERROR: A segfault has occurred. This is not your fault, : but is most likely an unrecoverable error and has : made the program unstable. : : Please send the contents of the file .xdebug_tkmedit : that should be in this directory to freesurfer(a)nmr.mgh.harvard.edu : : Now exiting... : I'm not sure where the xdebug file is located - it isn't anywhere in our Freesurfer directory in the server. Where can I find this file, and how can I fix this error? I've tried trouble shooting with some solutions I've seen in the archive. We have checked permissions, I use a PC - not a mac, and I have checked the main freesurfer directories as well as the directories associated with the brain I want to check. I have also tried to open other brains in the viewer resulting in the same error message. Is there a fix for this - ideally, one that doesn't require switching Freesurfer versions? Thanks for any help you can provide! Vincent Edwards

2 1

Issue with mri_vol2surf nearest interpolation
by Sun, Wendy 07 Aug '23

07 Aug '23

External Email - Use Caution Good afternoon, We are encountering an issue with getting non-integer values (input file has all integers) when using the “nearest” interpolation method in mri_vol2surf. Here is the command we ran: mri_vol2surf --mov ${anatIn} --regheader ${REG} --hemi lh --projfrac 0.5 --trgsubject fsaverage6 --o $Limg --reshape --interp nearest The input file ${anatIn} has values ranging from 0 to 255 and are all integers. The ${REG} folder is created during recon-All. We expected the output to be all integers, given the interpolation method, but we see non-integer values. Do you know why this is the case and how to fix it? Thank you, Wendy — Wendy Sun Graduate Student, Buckner Lab PD Soros Fellow, 2020 Cambridge Integrated Clerkship 18 MD/PhD Candidate, HMS

2 1

cortical boundary and center of gravity
by Alexandra.Korda＠uksh.de 07 Aug '23

07 Aug '23

External Email - Use Caution Hello FreeSurfer Developers, I need to compute the distance between the center of the mass in grey matter images and the cortical boundary. Then, I need this spatial-series to be saved in a csv. It is also possible to save the cortical boundary series and the center of gravity and then externally calculate the distances. I've searched for it in the archived question but I didn't find anything similar. Looking forward to your response. With kind regards, Dr. -Ing. Alexandra Korda Forschung & Lehre Zentrum für Integrative Psychiatrie ZIP gGmbH Campus Lübeck Ratzeburger Allee 160 I Haus B7 I 23538 Lübeck Tel.: +49 451 500-98715 alexandra.korda(a)uksh.de<mailto:mihai.avram@uksh.de> I http://secure-web.cisco.com/1kjPgsmVDmckwQECyP-u3VHis_G3UTBRfaGW5nBWnoOZ_A6…<https://secure-web.cisco.com/1YbIIElV63eryvTPycz1rwlHnTXCKH5QIVHqvKeuBQOTbv…> https://secure-web.cisco.com/1LBiUwtsltNc-BXRSlxA10cSmuxQKqQl4sLcRE1H3NCCq2… [https://secure-web.cisco.com/1AOOsqucbGmTeJdM-yAtUPIzv7tfFlnW2B7m613-b26KYy…]<https://secure-web.cisco.com/1sCPy2VI9VIeqBFD-78XnzcpPLre5X30Ap7YIpu2wGcBlc…> UKSH hilft Ukraine: Wir machen weiter. Helfen Sie uns, zu helfen! Unterstützung für die Menschen in und aus der Ukraine. UKSH-Gutes tun!-Spendenkonto zur Aktion Empfänger: UKSH WsG e.V. IBAN: DE75 2105 0170 1400 1352 22 | BIC: NOLADE21KIE Angabe bei Ihrer Überweisung im Verwendungszweck: FW14042: UKSH hilft Ukraine Spenden via PayPal: Spenden per PayPal<https://secure-web.cisco.com/19zuU7kAXVZctDul3KKV_Or91foAK2DNNZElMPDJPSvwoO…> Alle Infos: http://secure-web.cisco.com/1Yp2GziezQ--zorAWLWgh3JZPDvYVbGWcPyrW9Oj_shCvKt…<http://secure-web.cisco.com/1Yp2GziezQ--zorAWLWgh3JZPDvYVbGWcPyrW9Oj_shCvKt…> [UKSH logo] Universitätsklinikum Schleswig-Holstein Rechtsfähige Anstalt des öffentlichen Rechts der Christian-Albrechts-Universität zu Kiel und der Universität zu Lübeck Vorstandsmitglieder: Prof. Dr. Dr. h.c. mult. Jens Scholz (Vorsitzender/CEO), Peter Pansegrau (CFO), Corinna Jendges (COO), Prof. Dr. Thomas Münte, Prof. Dr. Joachim Thiery Vorsitzender des Aufsichtsrates: Guido Wendt Bankverbindungen: Förde Sparkasse IBAN: DE14 2105 0170 0000 1002 06 SWIFT/BIC: NOLA DE 21 KIE Commerzbank AG IBAN: DE17 2308 0040 0300 0412 00 SWIFT/BIC: DRES DE FF 230 Gemeinsam Gutes tun! Spenden: Alle UKSH-Spendenmöglichkeiten unter http://secure-web.cisco.com/1PM4Bl_XCW2TI9S7xBSfxsI0bNs2hyeV1XHLSi6-EhvbIpx…<http://secure-web.cisco.com/1PM4Bl_XCW2TI9S7xBSfxsI0bNs2hyeV1XHLSi6-EhvbIpx…> Spendenkonto: Förde Sparkasse IBAN: DE75 2105 0170 1400 1352 22 | BIC: NOLADE21KIE | Empfänger: UKSH WsG e.V. Diese E-Mail enthält vertrauliche Informationen und ist nur für die Personen bestimmt, an welche sie gerichtet ist. Sollten Sie nicht der bestimmungsgemäße Empfänger sein, bitten wir Sie, uns hiervon unverzüglich zu unterrichten und die E-Mail zu vernichten. Wir weisen darauf hin, dass der Gebrauch und die Weiterleitung einer nicht bestimmungsgemäß empfangenen E-Mail und ihres Inhalts gesetzlich verboten sind und ggf. Schadensersatzansprüche auslösen können.

2 9

Calling segmentThalamicNuclei.sh Issue
by Rowan Lawrence 07 Aug '23

07 Aug '23

External Email - Use Caution Hello FreeSurfers, I have a student who is trying to run the segmentThalamicNuclei module on some T1 images, using the segmentThalamicNuclei.sh script. All of the subjects have been run through the main recon-all pipeline and each participant has their own folder in the directory which is set to SUBJECTS_DIR containing this output. When calling segmentThalamicNuclei.sh with a subject ID, nothing happens except the following is printed in the terminal: If: Expression syntax. We are assuming that the SUBJECT_ID here corresponds to the name of a participant folder inside of SUBJECTS_DIR containing their recon-all output - is this correct? Is this a syntax error inside of segmentThalamicNuclei.sh, or is there an issue in the way that we are trying to run it? The student is using MacOS Ventura V13.4.1, FreeSurfer V7.4.1, and has the v2019b MATLAB runtime installed. Thank you for any advice! Best wishes, Rowan __________________________________________________________________________________________________ GTA/PhD Candidate School of Health Sciences Zochonis G30, M13 9NT

1 0

Bad skull stripping
by DS 06 Aug '23

06 Aug '23

External Email - Use Caution Hi expert, I found an issue when I do skull stripping. I used the following command line. recon-all \ -skullstrip \ -s fs_output \ -clean-bm \ -wsthresh 100 But, I found too much brain tissue has been removed, particularly for the visual and motor cortex (almost the entire visual cortex has been removed). Do you have any thoughts about this issue? Even though I tried wsthresh=100, it's still not working. I am not sure how I can include all of the brain tissues. Thanks. PS. I am trying to attach a screenshot to show the skull stripping results, however, I found the message with figure has been filtered. So, I have to post this question without any figures. I am not sure whether I clarify my question. Can I post any questions by showing screenshots? Best, Cain

2 3

How is cache.th40.pos.sig.voxel.mgh computed, exactly?
by Mark Ebden 04 Aug '23

04 Aug '23

External Email - Use Caution Hi, I was wondering if anyone knows how the numbers in cache.th40.pos.sig.voxel.mgh are computed, or where I'd look to learn this. There is a one-liner in the documentation<https://secure-web.cisco.com/1R2vQZUhHj-zAreoIH8kMlOuUPh5jYx8TyPmfmDzbM1Dl-…> but I'd like the mathematical details of the correction etc. so I can determine what the final numbers (from 0 to 1) represent. I've noticed from browsing the plot in FreeView that significant areas have values close to 1, which is puzzling. Thanks if you could point me in the right direction. Kind regards, Mark Mar [cid:b7c6e65e-f85e-4206-aaa0-1ec00aa2fde2] Mark Ebden, D.Phil (Pronouns: He/Him) Research Analyst The Hospital for Sick Children 555 University Ave, Toronto ON M5G 1X8 P 416.888.0841 [cid:3b077a75-32bb-46ed-b1d2-b74379e6a8d1]<https://secure-web.cisco.com/17-WtJwO2uIWyZ7umzDRCiH0I5Q1NZ-tfYcx_zx9tznEDb…> ________________________________ This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies.

2 6

freeview (visualize pial and white surface)
by DS 04 Aug '23

04 Aug '23

External Email - Use Caution Hi experts, I have a question about freeview. Recently, when I loaded lh.pial and lh.white at the same time, the freeview was suddenly aborted and reported the following error. ../mesa-22.0.3/src/mesa/vbo/vbo_attrib_tmp.h:234:_save_Vertex3fv: Assertion `used_next <= save->vertex_store->buffer_in_ram_size' failed. But, if I only load lh.pial or lh.white separately, I found it’s working. I guess there might be inconsistent parameters between the two files, because when I check another subject, both files can be visualized. Do you have any thoughts about this issue? Thank you so much for any suggestions.

2 3

Re: [Freesurfer] error in my software
by fsbuild 04 Aug '23

04 Aug '23

External Email - Use Caution  Hello Mikel, Can you send us more details like terminal output or perhaps screenshot from the terminal that shows the error ? - R. On Aug 4, 2023, at 15:54, MIKEL GARCÍA AGUIRRE <Mikel.Garcia(a)alu.uclm.es> wrote:        External Email - Use Caution        Hello,I am working with a MacBook M1 from 2020 and I downloaded two versions of Freesurfer. The first one was the 7.4.1 version, but I have also tried the 7.2.0 version. The problem that I have is that whenever I tried to upload one file, the program directly produces a force quit and I can not work with it. Do you have any recommendations for fixing this problem?Looking forward to hearing from you,Best regards,Mikel_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

error in my software
by MIKEL GARCÍA AGUIRRE 04 Aug '23

04 Aug '23

External Email - Use Caution Hello, I am working with a MacBook M1 from 2020 and I downloaded two versions of Freesurfer. The first one was the 7.4.1 version, but I have also tried the 7.2.0 version. The problem that I have is that whenever I tried to upload one file, the program directly produces a force quit and I can not work with it. Do you have any recommendations for fixing this problem? Looking forward to hearing from you, Best regards, Mikel

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Freesurfer August 2023