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Re: [Freesurfer] Calling segmentThalamicNuclei.sh Issue
by fsbuild 07 Aug '23

07 Aug '23

External Email - Use Caution That error is usually from using the wrong shell being used to run a script..  Could you send along the command being used or maybe a screenshot of how it is being run from the terminal ? - R. On Aug 7, 2023, at 07:11, Rowan Lawrence <rowan.lawrence(a)postgrad.manchester.ac.uk> wrote:        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 CandidateSchool of Health SciencesZochonis G30, M13 9NT_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Talairach Transform: transforms/talairach.xfm ***FAILED***
by Ha Manh Luu 07 Aug '23

07 Aug '23

External Email - Use Caution Hi Hello FreeSurfer Developers, I Install FS V6.0.0 on Mac OS updated to 12.6.7 and I have the following error when I run recon -all. I also attach tailairach_avi.log and recon-all.log files. Could you help me to fix the bux? #@# Talairach Failure Detection Sat Jul 29 11:35:18 EDT 2023 /Users/hamanhluu/Ha_working/Freesurfer_edit/Test_case_FS/Recon_Pre_T1_source_Mac1/1387/1387_20181219_083728/FreeSurfer/mri \n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0018, pval=0.0000 < threshold=0.0050) \nManual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See:\n http://secure-web.cisco.com/14QnFk2g7tp3Mp1PtQq7sMpaNgFNBZjfVLGW1UVjBu699cT… \nERROR: Talairach failed!\n Darwin MAC198536 21.6.0 Darwin Kernel Version 21.6.0: Thu Jun 8 23:57:12 PDT 2023; root:xnu-8020.240.18.701.6~1/RELEASE_X86_64 x86_64 recon-all -s FreeSurfer exited with ERRORS at Sat Jul 29 11:35:18 EDT 2023 Thank you, Ha

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Bad skull strip
by DS 07 Aug '23

07 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, please see below. 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 more brain tissues. Looking forward to your reply. Thanks. Best, Cain

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mri_segstats --sbTIVin
by Woo-Suk Tae 07 Aug '23

07 Aug '23

External Email - Use Caution Dear Freesurfer developer. According to the explanation in the https://secure-web.cisco.com/1coHbpSG3RMsDJ9eWWcn4zb_ld9qaPCVetqOo5rL5vuLfQ…, it seems that the TIV volume of SAMSEG pipeline could be added to the aseg.stats with the option of mri_segstats --sbTIVin <sbtiv.stats> ... But, I can not find "--sbTIVin" option in the mri_segstats command of FreeSurfer 7.4.1 or the recent developer version. How can I add sbTIV to aseg.stats? Sincerely yours Woo-Suk, Tae -- ---------------------------------------------------------------------------------------- Woo-Suk, Tae Ph.D. Research Professor Brain Convergence Research Center, Medical Research Center Anam Hospital, Korea University Medical Center, Seoul, Korea mobile: 82-10-9120-4629 office: 82-2-920-6831 email: wstae(a)korea.ac.kr, woosuk.tae(a)gmail.com, wo <woostae(a)naver.com>ostae(a)gmail.com ----------------------------------------------------------------------------------------

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Question about group analysis
by inbal paran 07 Aug '23

07 Aug '23

External Email - Use Caution Hello FreeSurfer Developers, I have a question regarding group analysis: When I followed the instructions on how to build my FSGD file, it said that:"FSGD files are created automatically by qdec, but qdec is currently (12/9/08) limited to two continuous variables and two discrete variables with two levles. Is this still the case, or is it possible to include more than 2 continuous variables? 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/10EVZ2XzBNwOtEFs0cIPJQpknExlvtm8Aa2FqcVbk4fO2zM…>.* 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.

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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.

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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

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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

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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.

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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

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