External Email - Use Caution Hi Douglas,
This is for a lGI analysis. I used a fwhm of 10 and not 38: mri_surf2surf --hemi lh --s fsaverage --sval lh.lgi.mgh --fwhm 10 --cortex --tval lh.lgi.10B.mgh So why am I getting this error? cannot find > /usr/local/freesurfer/average/mult-comp-cor/fsaverage/rh/cortex/fwhm38/abs/th13/mc-z.csd When I run : mri_glmfit-sim --glmdir rh.project.glmdir --cache 2 abs --cwpvalthresh .05 --2spaces?? -----Original Message----- From: [email protected] <[email protected]> On Behalf Of [email protected] Sent: 05 November 2020 11:29 To: [email protected] Subject: [EXTERNAL] Freesurfer Digest, Vol 201, Issue 6 Send Freesurfer mailing list submissions to [email protected] To subscribe or unsubscribe via the World Wide Web, visit https://secure-web.cisco.com/1Bx-PtjccZ-WhuGdxndP-26xpcos_CUcEUhlPHPl_IGH5KTb1y-l3Al4TlDLM_5vQPd-zr6nLbRW5TH4QKszwqFDc3qHzH7kvqCGFf6s8bMCzyHe1-z9-2U-a6lL5Z0BB_eclfDjoLf8h9bac7i-rRAsmpPEu3KtaRM7d1p6XXp20UuVmzpxDBfXhmMAlETbtRYkSxao4UC4imoAajyxZxw/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer%26d%3DDwICAg%26c%3DG2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U%26r%3D4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo%26m%3DhNoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3D4D9hF7ZxOn9Vv33WCY8DWv9lfylIBHva4_0nqVRZqEg%26e%3D or, via email, send a message with subject or body 'help' to [email protected] You can reach the person managing the list at [email protected] When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. LGI quality control {Disarmed} (Nelson, Eric) 2. Re: Meta-analysing brain measure statistics across multiple cohorts using different versions of Freesurfer (Stephanie K) 3. Re: Meta-analysing brain measure statistics across multiple cohorts using different versions of Freesurfer (Ammon, William) 4. Re: aparcstats2table {Disarmed} (Kiyotaka Nemoto) 5. Fwd: Welcome to the "Freesurfer" mailing list {Disarmed} (Nicholas BH NG (NUHS)) 6. Fwd: using CAT12 segmentation for PVC (Donatienne Van Weehaeghe) 7. aparcstats2table (Saman Fouladi) 8. Join the Brainhack donostia (Vicente Ferrer) 9. repeated measures ANOVA 2x2 two groups two times {Disarmed} (Agurne Sampedro Calvete) 10. Re: .mgh file unknown, GLM paired analysis {Disarmed} (Agurne Sampedro Calvete) 11. Re: mri_glmfit_sim error (Douglas N. Greve) 12. Re: mri_convert error (Douglas N. Greve) 13. Re: Extract he value of area and volume in the fsaverage for every subject {Disarmed} {Disarmed} (Douglas N. Greve) 14. Re: Question about smoothing for extracting anatomical stats {Disarmed} (Douglas N. Greve) 15. Re: Troubleshooting -parallel flag for Freesurfer, error in the cortical ribbon mask stage during recon-all {Disarmed} (Douglas N. Greve) 16. Re: Fixing error with pial surface {Disarmed} (Douglas N. Greve) 17. Re: mris_anatomical_stats error: stating file (Douglas N. Greve) 18. Re: (no subject) (Douglas N. Greve) 19. Re: Fwd: using CAT12 segmentation for PVC (Douglas N. Greve) 20. Re: repeated measures ANOVA 2x2 two groups two times {Disarmed} (Douglas N. Greve) 21. Re: LGI quality control {Disarmed} (Douglas N. Greve) 22. Re: repeated measures ANOVA 2x2 two groups two times {Disarmed} (Agurne Sampedro Calvete) 23. Re: trac-preproc error (Hasimoglu, Yasemin) 24. Re: mris_anatomical_stats error: stating file (Chan, Shi Yu) ---------------------------------------------------------------------- Message: 1 Date: Wed, 4 Nov 2020 19:12:50 +0000 From: "Nelson, Eric" <[email protected]> Subject: [Freesurfer] LGI quality control {Disarmed} To: "[email protected]" <[email protected]> Message-ID: <dm6pr07mb791577da3bb61700d9f42be5c7...@dm6pr07mb7915.namprd07.prod.outlook.com> Content-Type: text/plain; charset="us-ascii" External Email - Use Caution Hello, I am using FreeSurfer 7.1.1 to run LGI and have done so successfully. I am now trying to quality check my data using tksurfer as described on the wiki tksurfer my_subject_id lh inflated -overlay lh.pial_lgi However the LGI overlay is not covering the entirety of the inflated brain. Specifically the medial frontal surface and some subcortical are not measured for LGI. Here is a link of the overlay images for a few subjects: https://secure-web.cisco.com/1y5I8DUvRNOHPY2e1TIaZl17tWS96xMg81U_dq63kxl7l6AzhIHGJ1n_RkWTtFi43C9TmLq9-9E8mMv1eTjrrQXrrali5ROGyECGx4rU9Qlue07HIQL4TtXy3NQQCd906OROLqKSRFGkChdZJBdHHPop8M85BIIesobKc3sqEJ1LJqxYxEcnzjuFoifk4VuXnO-s8GvYOarGu09awDRkZ4Q/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__secure-2Dweb.cisco.com_1FvGKanOWU0exqsmfZZWyCdCgTFgqf8kB2BXdsF-2D5A035k1rc5i2ECL9Bt-2Dsn8Wd9sg8LgyvKPIHD-5FK3n3d8aIlOYT7vHfQVCA6sCq1NlzFrs-5FVjn74CGIhg1nIjX-5FcsnDAnz8kzCUBLMiTd7c6DTZvaQ5aM3UeKBq-2DPVh8O5XAwOUvbQ3-5F05ie7fb0YGRsg8Q2DrGwEWtgQCqpUnhvIPdA_https-253A-252F-252Fwww.dropbox.com-252Fs-252F9pt8rti4yjudrza-252FLGI-5FQC.png-253Fdl-253D0%26d%3DDwICAg%26c%3DG2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U%26r%3D4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo%26m%3Dh NoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3D7wiCSt92CUigLhdzg8LhducfMTfDwOdJhAfgtnz4h3s%26e%3D . I<https://secure-web.cisco.com/1Hod0xhqjDXliu4d6GvJjLlbNiHOsmMLOvn77883QuHzRrGBa7GggFQo6_5SqqseXfoghnsaujQ9zGKYGuA_remL_CERWESaByKhLtz4bQUjvConfAiBbhgfVsbPU4TyPEQ9WZDRGlZBoXUooO0aX5qwuKlFAaxyowVT_e8FSOB5yozdytInE20U4V_mIq9_GemyQ9Lla0KEy85KubvhkCQ/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__secure-2Dweb.cisco.com_1yytrZan4Ml7C4NJTkc91uplhrETEPm4MAwDFEYaEAXtVlSnzGTjs5BjzZZSDOtTgizZpSDnl3ThVIFkaiXv-2D-2DDGYo5izF1yFMK4gbyOHaQIVo-5F20HarcOi-5FHT6zrv2m6X-5FpzP4BKEZbOmkD8UlglJjPZELhvw-2DkW4tNs-5Fq2K97iR-2DnN8xvGyh2mHAgjXm9saalzD0cAqzMFUXXNDhGfoyA_https-253A-252F-252Fwww.dropbox.com-252Fs-252F9pt8rti4yjudrza-252FLGI-5FQC.png-253Fdl-253D0.-252520I-252520%26d%3DDwICAg%26c%3DG2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U%26r%3D4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo%26m%3DhNoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3Dcq0aJlDd4oMVL7tadGmdJMaerCp6IYrshMg4oZ4r_y8%26e%3 D >. I haven't been able to find any images ! of what this overlay should look like so I don't know if this is expected or if som ething has gone wrong with the processing. Any feedback would be greatly appreciated Best, Eric -------------- next part -------------- An HTML attachment was scrubbed... URL: https://secure-web.cisco.com/1ZhNFc0btg5d1z3D6b7tU5TfFd1GLyeCvASljZaN5uRgxJo5V3UUSHtVXC27T3T6w3CWYOZZfsC4Sf7uXUy3KLIkXpBTgVokrsMZGGraWRGbl4t8jO9x6VETUEW6cSeVtRKYTqO4qTJ7RLFWnZKICdvJgw227KKCZSZN2x8rK-jTGo_ZLgimgBRdO2EsqIYfgFegRBHJCPcfuvhkrQPLCLQ/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__mail.nmr.mgh.harvard.edu_pipermail_freesurfer_attachments_20201104_ba800b58_attachment-2D0001.html%26d%3DDwICAg%26c%3DG2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U%26r%3D4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo%26m%3DhNoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3Dxl_xoA1AQGgOZUo_jk7xIPuTbiGCJ5BtIDseRCRAMSM%26e%3D ------------------------------ Message: 2 Date: Wed, 4 Nov 2020 19:59:46 +0000 From: Stephanie K <[email protected]> Subject: Re: [Freesurfer] Meta-analysing brain measure statistics across multiple cohorts using different versions of Freesurfer To: [email protected] Message-ID: <CABwOaTUw=h4bcjazxwjaktue8ck88+8satc84zf0oiozbhz...@mail.gmail.com> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Hi, I am planning on meta-analysing the effects of regional and global cortical thickness + surface area, as well as subcortical volumes of 3 cohorts. Two of them have been processed using Freesurfer 5.3 and one one of them has been Freesurfer 6.0. Is it wrong to meta-analyse them due to differences in the pipeline? I would really appreciate your advice. Thanks -------------- next part -------------- An HTML attachment was scrubbed... URL: https://secure-web.cisco.com/1ALhprSSFTPtr-yNTTtY7ueN6YmaF5G4UbTd1U1oIwvv1kurMr2TDSKD3Od_vJspmfyqpGdjmQsPA4mSvo0Qs0v6xQcD7WxtpcjOIvhPPlDj642IgKOTW_vP5q0OWTYfXwCIcT78hCtsAMBlnn_mO-E1JJ2qJGYlDiOX8xz2K5ZPPeOKkLi5lnsyT896YRJZjPgoCnMe3t0CaJ5OSxBMgHw/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__mail.nmr.mgh.harvard.edu_pipermail_freesurfer_attachments_20201104_63f39a15_attachment-2D0001.html%26d%3DDwICAg%26c%3DG2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U%26r%3D4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo%26m%3DhNoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3D0MfS6A1UTO0ofiEOLZIYIvRzqwhxRmLH4enOm0jqryc%26e%3D ------------------------------ Message: 3 Date: Wed, 4 Nov 2020 20:59:20 +0000 From: "Ammon, William" <[email protected]> Subject: Re: [Freesurfer] Meta-analysing brain measure statistics across multiple cohorts using different versions of Freesurfer To: Freesurfer support list <[email protected]> Message-ID: <[email protected]> Content-Type: text/plain; charset="utf-8" Hello, It is not advisable to mix versions of FreeSurfer as results across different versions of FreeSurfer are expected to differ, even if by a little. We recommend that the same version of FreeSurfer be used to process every case in your dataset. If you were to proceed with an analysis of, for example, a cohort processed with 5.3 versus 6.0, differences in stats could be partially due to difference in version. Cheers, Bill From: <[email protected]> on behalf of Stephanie K <[email protected]> Reply-To: Freesurfer support list <[email protected]> Date: Wednesday, November 4, 2020 at 3:00 PM To: "[email protected]" <[email protected]> Subject: Re: [Freesurfer] Meta-analysing brain measure statistics across multiple cohorts using different versions of Freesurfer External Email - Use Caution Hi, I am planning on meta-analysing the effects of regional and global cortical thickness + surface area, as well as subcortical volumes of 3 cohorts. Two of them have been processed using Freesurfer 5.3 and one one of them has been Freesurfer 6.0. Is it wrong to meta-analyse them due to differences in the pipeline? I would really appreciate your advice. Thanks -------------- next part -------------- An HTML attachment was scrubbed... URL: https://secure-web.cisco.com/1DaGbNUpP4Ep4cLuYcuxl8RNBfl6Y6V3YbDqwuxzylYH9yZ83e8F-O7uJFz9Uzc-Hnc-t5-e0iP5cFIfXik1UD2mxqE7eLODtGoXOtKdFWC2iDFQT0_W3pBPXFBA_TZOKSUPj_h2zi6c___vE6B9X5wFMBdvOyaR6ioVDpSW774yvVypSvGPiTtTCZ3aCci3cSyzFM4-M2CUXpNXIBwFR1w/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__mail.nmr.mgh.harvard.edu_pipermail_freesurfer_attachments_20201104_1c5c4880_attachment-2D0001.html%26d%3DDwICAg%26c%3DG2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U%26r%3D4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo%26m%3DhNoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3DCIPVqBtwPdbyMsvHusMkfcsFHcmlqElN3rurZe_ht1k%26e%3D ------------------------------ Message: 4 Date: Thu, 5 Nov 2020 09:27:46 +0900 From: Kiyotaka Nemoto <[email protected]> Subject: Re: [Freesurfer] aparcstats2table {Disarmed} To: Freesurfer support list <[email protected]> Message-ID: <CAHvOE4FY4jHCQPrA9pKfxZFQdT46JMPP=UUVh211Z_9ys9=r...@mail.gmail.com> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Hi, Suppose the fsid of your subj10 is subj10 and you set SUBJECTS_DIR correctly to /home/team33/MRI4, the command should be aparcstats2table --hemi lh --subjects subj10 --parc aparc.a2009s --meas meancurv --tablefile /home/team33/aparcstats.txt I noticed that there is a space between team33/ and aparcstats.txt, which will cause another problem. Hope this helps, Kiyotaka 2020/11/5 0:24 saman fouladi <[email protected]>: > External Email - Use Caution > > hi > > I run in linux command: > """"""""""""""""""""""""""""""""""""""""""" > aparcstats2table --hemi lh --subjects /home/team33/MRI4/subj10/stats > --parc aparc.a2009s --meas meancurv --tablefile /home/team33/ aparcstats > .txt > """"""""""""""""""""""""""""""""""""""""""" > but show below error an i can not solve it nix: > > """"""""""""""""""""""""""""""""""""""""""" > File "/usr/local/freesurfer/bin/aparcstats2table", line 156 > print 'ERROR: atleast 1 subject must be provided' > """"""""""""""""""""""""""""""""""""""""""" > > I changed the code several times, but in all cases there is this error. > This error also happens to asegstats2table. > > please help me > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://secure-web.cisco.com/10PoLhzRVYTqQB_6ZGlT9VOAYqG5PXgdVqwCZlaPRQJf8mFa8pY46TZLSUkLTAqxdbeGSDQpLcDVfQ9QJ56mq_eK_GatHkkMPc4HHIh7GxMID9FRqEiw4X-9wu7CVMTeRMfni142Q_AiExSvEzOweKPsaXzqZVmxpQpKaOr7DNPupW8brV9QNkOgnEuNaxeeCWXrufE7F4aWrO_94aPoIpQ/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__secure-2Dweb.cisco.com_1cvwnliBEQF1AmGZlpH3pfTq05Ws5G3jBZGmy-5FRJuGbUUDic-5FwarS6Cj15iHHT4Rd8AuG4XHWICk9sA5AvxzSOXkRHs6-5FxFu-2DHxTxwpASsX95EWfwhebDAvNLaDVWcXX6afQVPdjvxXvn-2DTouU93nYJCVJu2-2Dt8vxOOb8K-5FwstaLC7by-5FF-5FbHpbW84AlqnRSd1rxNsvHb5WEpSk8are55vA_https-253A-252F-252Fmail.nmr.mgh.harvard.edu-252Fmailman-252Flistinfo-252Ffreesurfer%26d%3DDwICAg%26c%3DG2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U%26r%3D4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo%26m%3DhNoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3Dhj4FuFBfzMBmN3FKK3rJecz1odPh2wPi1BrckM_Hn8A%26e%3D > -- Kiyotaka Nemoto, M.D., Ph.D. Associate Professor Department of Psychiatry Division of Clinical Medicine, Faculty of Medicine University of Tsukuba 1-1-1Tennodai Tsukuba, Ibaraki 305-8575, Japan E-mail: [email protected] -------------- next part -------------- An HTML attachment was scrubbed... URL: https://secure-web.cisco.com/14whehLr7d8g8e-mcD957DO21xtvP59PE8UD2bU6J3GdnEWR2Bo5mWnV6BVbZ3Mcb2dmJzkvyXoiZEwlBtR-oia6cVrxR5L_P7ohILt52rcc_H5fPmJLH9bn5zJmWie3VnHQou5EjkGhHLp2ZXhDJ7ZboH_ZMlEMv5hPLk4Aw0Et2NCCsYFf_aisikI5K3GNT9sDYEiwjrp2kA4S3lBUljg/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__mail.nmr.mgh.harvard.edu_pipermail_freesurfer_attachments_20201105_fc677dd6_attachment-2D0001.html%26d%3DDwICAg%26c%3DG2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U%26r%3D4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo%26m%3DhNoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3DoS2bfVFy9pWJEsN43VbeNDKzLrZ8fuORvNjXEYK5Qs0%26e%3D ------------------------------ Message: 5 Date: Thu, 5 Nov 2020 03:58:19 +0000 From: "Nicholas BH NG (NUHS)" <[email protected]> Subject: [Freesurfer] Fwd: Welcome to the "Freesurfer" mailing list {Disarmed} To: "[email protected]" <[email protected]> Message-ID: <[email protected]> Content-Type: text/plain; charset="us-ascii" External Email - Use Caution Dear Free Surfer I followed the excellent video step by step instructions. At the last part of putting the code/ key into the terminal, I encountered the error message as below: no such file or directory. As such I think my set up was not complete. Kindly advice. Thank you Nicholas Nicholass-MacBook-Pro:~ Nic$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -bash: /Applications/freesurfer/7.1.0/SetUpFreeSurfer.sh: No such file or directory Nicholass-MacBook-Pro:~ Nic$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -bash: /Applications/freesurfer/7.1.0/SetUpFreeSurfer.sh: No such file or directory Nicholass-MacBook-Pro:~ Nic$ Begin forwarded message: From: <[email protected]<mailto:[email protected]>> Subject: Welcome to the "Freesurfer" mailing list Date: 5 November 2020 at 11:56:45 AM SGT To: <[email protected]<mailto:[email protected]>> Email is from external source. Do not click on links or open files if unsure of sender. Welcome to the [email protected]<mailto:[email protected]> mailing list! 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Name: image94f29b.PNG Type: image/png Size: 7481 bytes Desc: image94f29b.PNG Url : https://secure-web.cisco.com/1YR6dnJEOQJp79U4OkqsVnkwl5Zn53Rog70bDvZPvNrDs1bnpKVQtuek5_Mg2J05nVwTd1IHLrHRsSSgjupQPgBaPSl-joC_JH0Syh0ZQp6TNG2gGGYSD5P25XW9pOH-YHCxn7Rmu0vukZ7t1T8c63hqF7njs2MHuyLFN84pFVWvz2tp2ZrbnT9b3rG1IJ9ysqN9E1t2ROImA4EzjjIN6hA/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__mail.nmr.mgh.harvard.edu_pipermail_freesurfer_attachments_20201105_d24edce3_attachment-2D0001.png%26d%3DDwICAg%26c%3DG2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U%26r%3D4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo%26m%3DhNoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3DPBdDiEzuj5n3Hh2KXWZSTNqN39ntJXKzv9JwvqZhQ7U%26e%3D ------------------------------ Message: 6 Date: Thu, 5 Nov 2020 08:15:23 +0100 From: Donatienne Van Weehaeghe <[email protected]> Subject: [Freesurfer] Fwd: using CAT12 segmentation for PVC To: Freesurfer support list <[email protected]> Message-ID: <CA+W1dKxo=xpj9xfbfhy6xqxpedyb89f1+jwktea7w6gnf1x...@mail.gmail.com> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Dear, The segmentation using Freesurfer was incorrect, however we have a good segmentation from Cat 12. Can we use this segmentation for PVC in PETsurfer? Kind regards Donatienne -------------- next part -------------- An HTML attachment was scrubbed... URL: https://secure-web.cisco.com/1thOQo-KiSIRIEPW3_CEHa2Up0XHRzymme6zPuqjy8vGWoAxk6ZPp9_ZQM4qpnI7m85baTq9JG7sFj4ebscZFJKA32YqiHQiPG85UE3NMvwPqLEQlTBosTI-6nZNpPbAZNWbz4yGkso_afiDQP7wa2RXa9ePfdEkMy51gE4TfvyZP89Jfl-3JhTx8U-WdctNJinrbiDZtEenAi_kMeCG-hQ/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__mail.nmr.mgh.harvard.edu_pipermail_freesurfer_attachments_20201105_1eaedc7c_attachment-2D0001.html%26d%3DDwICAg%26c%3DG2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U%26r%3D4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo%26m%3DhNoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3DJ2tSGI_D8vacVZjrmD76oYgDKaJrqRfC3wW8yiAHxI8%26e%3D ------------------------------ Message: 7 Date: Thu, 5 Nov 2020 11:26:34 +0330 From: Saman Fouladi <[email protected]> Subject: [Freesurfer] aparcstats2table To: [email protected] Message-ID: <cabskvgqsdf-iszofk6jhmda-jqyucs27lgycb+vgkvm1-jz...@mail.gmail.com> Content-Type: text/plain; charset="utf-8" External Email - Use Caution hi I run in linux command: """"""""""""""""""""""""""""""""""""""""""" aparcstats2table --hemi lh --subjects /home/team33/MRI4/subj10/stats --parc aparc.a2009s --meas meancurv --tablefile /home/team33/ aparcstats .txt """"""""""""""""""""""""""""""""""""""""""" but show below error an i can not solve it nix: """"""""""""""""""""""""""""""""""""""""""" File "/usr/local/freesurfer/bin/aparcstats2table", line 156 print 'ERROR: atleast 1 subject must be provided' """"""""""""""""""""""""""""""""""""""""""" I changed the code several times, but in all cases there is this error. This error also happens to asegstats2table. please help me -------------- next part -------------- An HTML attachment was scrubbed... URL: https://secure-web.cisco.com/1kZWpF6XWhi6Heo7zC5TKjYPI5oY0fVs3OSd74u2neb_24crzgipJMDIYYMFprIVCmCrJSzBWN5T3_f49tbKyzRAZ7sDw4boiUlLTyg2RFBjDIm8I27VVSah8_yjC1sNYNphCY3GkQ_asCKyYQu1oS4IQQawVyr-PVHHuOU30mN0bmEZBK_NnEZsvZk-Fle3CjCnMlU2rUFo2F6bR4zhNLw/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__mail.nmr.mgh.harvard.edu_pipermail_freesurfer_attachments_20201105_6eb2c3c1_attachment-2D0001.html%26d%3DDwICAg%26c%3DG2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U%26r%3D4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo%26m%3DhNoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3D-BXQr2D12ODvBuzOA1r7nXA-tgBZm_KVYBLMIDd2LQM%26e%3D ------------------------------ Message: 8 Date: Thu, 5 Nov 2020 10:08:22 +0100 (CET) From: Vicente Ferrer <[email protected]> Subject: [Freesurfer] Join the Brainhack donostia To: freesurfer <[email protected]> Message-ID: <[email protected]> Content-Type: text/plain; charset="utf-8" External Email - Use Caution The Basque Center on Cognition, Brain and Language (BCBL) is holding a free online next week. We hope that it can be of interest to this community, and that you could forward others this information. At the BCBL, we are organizing the third edition of Brainhack Donostia (https://secure-web.cisco.com/11fhiIheP-EzF2ZKXeRyAj4E2y8B8ejC6oj_0-5fp_yTqCTfnTr-3bLQ6mlDbxB318G6cTwDZPIxgOApaWghpfwjjGjmTDeFEZ7VuR4OuEus7Ld257woXiuzSUXvty-tnyEEBpi314rekeZzUW_7swFBgFcAe10SjtNypgrUNvokhAQVo7wcJWs6csx6Zmq9uK336VqaH6kJLvaTsIQ1OSA/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__secure-2Dweb.cisco.com_1GC1hh4vsRCGfthBadagfSojiEis8P2rIcxlvHWMBmSe1mUpZN3XGoyqUkNT24qIKWA4N8W1cAJhN-5F7ft-2DaQLlYJIb0H8TlsJ9S54qyypnyL1ycUZHdN3oJG0eaekXVHXHFEXOi0PDEQBEuw2jFVaDaDUYvE-5F7MLqarw-5F3M7j-2DhxsrsF9Y7THetqI-2DQ1Ea-2DzdxXCdhCXqEkCdMwHY5Wtj2A_https-253A-252F-252Fbrainhack-2Ddonostia.github.io%26d%3DDwICAg%26c%3DG2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U%26r%3D4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo%26m%3DhNoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3D44pL1xRAokrr-NJVpMzjN-uODI9aMzp6xtWghCN8Uq0%26e%3D ), an event focused on neuroscience and the promotion of open-source resources in an acces sible way across disciplines and experience levels. This year's edition is taking place from November 9 through November 13: it will be held online and will be completely free. The focus of BHD2020 will be OpenScience, covered from a variety of pertinent perspectives (e.g., MEG, fMRI and fNIRS). We are going to have the cream of the crop as invited speakers, check the schedule here: https://secure-web.cisco.com/1wc0JWmWZ4kupvuyxKM5rx9423o60wcNe93NbGtEivo_jmepdUpLNzQgfmFHC6oh8zuNWwsDuZJecATPp6Zc7FN73utE1SvsxSPmsFG2VYq5ejm8d4RhJRIWoE5Cw6FciZX9WqJEhb1KluvHKmTRzGjz3f2kumbTg2ofyzH4NroTJbWAYq3Xj5A0KZGPhfMoYOP6bngJ48IOmHnDl9WDxzA/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__secure-2Dweb.cisco.com_1nN-5FlXzurOj1ntsI3lbjeAWTurwndamZGsnyiXQE9Xqhw7ivPBzYGFR4-2DRAqIVlVWDs96ck1xVRomqnOIgkrdtL0kUMVfuhPq-5F2aalh5CMTkP3S7VKCbuF0UbbhqJVXFJW-2DMFeH45x1Us-2DvPHABKO2RgJMyuWyV4cdUeEGJEWw7WiIrllUoN98LCI-2Dd4ormPXudSRhw-2DXF0TPSqL-2DjO8n9A_https-253A-252F-252Fbrainhack-2Ddonostia.github.io-252Fschedule-252F%26d%3DDwICAg%26c%3DG2MiLlal7 SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U%26r%3D4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo%26m%3DhNoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3DaAL_0YaPiIPWS4orNcd-0o0zcuZrw5IIvklF_L68zoA%26e%3D . Even though we will be physically distant, there will be the possibility to come together and socialize on the Brainhack Donostia GatherTown platform. We will be using the platform to host exciting social activities throughout the event. Stay tuned for the social activities program! We invite all neuroscience aficionados, students of neuroscience-related subjects, professors and professionals to participate. Registrations are now open at https://secure-web.cisco.com/1w6jq6p4e4pM4XkJzZ5IXUgxeELx0hNrDA0lm0tK8NsH0KcZl2992T2hW1xZKaqX0gbvDBEiKbuzanuzslUJuWSGR-Woqw6gx1VwL36QqWhiUhjFB2zilPVP4TEOQvKkhfquOnfbc7oVwEKIUdmLLTghPIVXRQsFlcGqPTrKnYa28steR4wAwTeZ3SiUhjl0y8i1QgVH9vzC6ybmqr_IaSw/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__secure-2Dweb.cisco.com_1d3VTvJ1ukmPmrYp15NgAyjM96L0VJDHuND2s9vyXzTZc5kij6rj-5F8FjmimUU-2DATDmbz31T5ZunN4ZMQuKhA2L9S-5FtJaf2RH-5F5JCuyO9GbyUeRTL0vUAJ5mfA-5FGF3aX8OcrtT2CYADu6DC5fDjAeKMTDIP59-5Fwf8oIQESZzt3nOUXJ3NQWOcCy0pKuYDq0-5Fio8yIr-5FizuOWbBI2TGCcIPyA_https-253A-252F-252Fbrainhack-2Ddonostia.github.io-252Fregistration-252F%26d%3DDwICAg%26c%3DG2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U%26r%3D4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo%26m%3DhNoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3D5zn_lQdQ-RDTigxVfbm6pqKVXb9cGh9 SMt0ssgqG0Ok%26e%3D . Best regards, Vicente Ferrer Predoctoral Researcher BCBL https://secure-web.cisco.com/1NzYf5XHplyKITiujVdc0-46MKvJ8GYh3cDFHcuw72y9LT4oES2DXx0wH4xymwgrjvPO1ZmSUXIrkQKd56KQC_88Hbk2HeHz992kLOopFHejCPaZMZQ53zy-HYYfPkhb4JNGX9XLBCp5xy7xi48uwkZf6t9df3zi3Cv6Tyhj63qaGskOgaHotzeZaD-SPph5qQJPLGR1XiB9H_FJP6ZtPyw/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__secure-2Dweb.cisco.com_12Abv6l6-5FPtwWS0hk38LzFrcDpN7GEtPA16QooQuy-5FXnRh0GP6GkjqGbuaF9k6hrtOi69W3U7Gt8aSCjj1a0Fh21L9w3pz3iNFEkY67rrKLurTsMS1LoDQmBHIYo73yygeu1xH5QXTdKVorwcucifZx3HuXjAN0PRiUy6wqsvRDpc9KVRjNFU9XCPbqZGA3ZvAqFBuDLyPPMU8MotUZG5Zw_http-253A-252F-252Fwww.bcbl.eu%26d%3DDwICAg%26c%3DG2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U%26r%3D4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo%26m%3DhNoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3DPGm0RybvVUNyPOhxPb0NLabB92u68H36N0vRQotP7VE%26e%3D Legal disclaimer/Aviso legal/Lege-oharra: https://secure-web.cisco.com/1_jb0JUgD5pAEO8meOIU3OUG7m-8BwsZbldSCBimNuGZBszKv_xCKAEjPFqAIdNetAt2Rcxz2uQ-CjIVgFhXlZOlK7DsXEMimfvh_rwyLqjoKzcmKhMqgjV27UaCJ0jrV3pzfOsBg99ZLabmOTPOHkfbDXrqaMmuxgN8wXo1kl9gzotVC0SWIvSEQEHacKkYdjhZWDgR8iO0WPMquGKw2og/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__secure-2Dweb.cisco.com_15zTX7kAQnbTPpg6u-5FChbnA89bSxwOzqP4KMe91gP9IM05TpxoibRNWORl7qZBMDZIEqjxXnezRb0K5zavCxmGCb7-5FrgeJI9Mp-5FgWPf-5F6IthVlitaKE8eIbIJf5XVDD4oBaWAWHtFzxn2gSV70bWsN2cidaq0yWM-5FAs0FIdzkBMQdW94X0dCfrctp-2DUaYuXkW-2DrnnNV7m4cDO9qXsuY4GRQ_http-253A-252F-252Fwww.bcbl.eu-252Flegal-2Ddisclaimer%26d%3DDwICAg%26c%3DG2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U%26r%3D4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo%26m%3DhNoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3DKmwioPA2jcr8Ph736O5YjlsDdh8ObYO_LCxZaQgTLDI%26e%3D ------------------------------ Message: 9 Date: Thu, 5 Nov 2020 10:32:54 +0100 From: Agurne Sampedro Calvete <[email protected]> Subject: [Freesurfer] repeated measures ANOVA 2x2 two groups two times {Disarmed} To: [email protected] Message-ID: <cajsj2xjpdh++s2ktrd7vscy3rhjdihvzyoxeuqr7ixherwo...@mail.gmail.com> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Dear Freesurfer experts, I am trying to do a longitudinal repeated measures ANOVA 2x2, with two groups (experimental vs control) and two time points (pre and post treatment). Although I have run a paired t-test, now I would like to do a repeated measures anova 2x2, since I am doing the same analyses with other data in other softwares. I am trying to follow the tutorial https://secure-web.cisco.com/1qvWd6p4YcYUfWhhXgCvLaWK3sRlm_x4JFjCwRFq_A0U3O1ylyWXlTak1xwVyRXwPC6abxekS922joGCSv89ocjkhP6qnahRIogNux9Tt3eSxzzg5yYq-o5AIbNRcqq2vvvuwNy5iQQVHRgJJH8sNHvfWdmob0BOIKBiQUwE1YaIKrcjX_uYxtNBbsMQyKaiLbmFA0EK2I4cTFYwRJNeyww/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__secure-2Dweb.cisco.com_1xcEvqAuPN3MsqK1JjC6qoZbooZS3kpB4WEU1Lx8hK28grFkOWFgj7ja5TXppcZRh8Vr2s3TJyQKT-2Dsr-2Dc0qt4XJSU7f74cElgVAI4K1nOBI5i5L0YQBzYutTVn-2DMwCGM-5FOotAt9VM1mzmm1MUuXbYtZC4-2DQfIujBH30LAwD5RtwZ6vGRv4JC7ocISixV0s52BsCadrLE2J-2D3CdqLLZnJRA_https-253A-252F-252Fsurfer.nmr.mgh.harvard.edu-252Ffswiki-252FRepeatedMeasuresAnova%26d%3DDwICAg%26c%3DG2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U%26r%3D4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo%26m%3DhNoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3DKEHkIFsrntENbUL-ZK8Ski3x38Z_n8QnmvAGTSMhjs8%26e%3D , but I have several doubts when designing the FSGD file as well as the contrasts. How should it be the FSGD file? I have seen in a previous post the following design for the same number fo groups and time points: GroupDescriptorFile 1 Class Subject1 Class Subject2 Variables Tp1vsTp2.GrExp Tp1vsTp2.GrControl Input Subject1_time1 Subject1 1 0 Input Subject1_time2 Subject1 -1 0 Input Subject2_time1 Subject2 0 1 Input Subject2_time2 Subject02 0 -1 Design matrix: 1 0 1 0 1 0 -1 0 0 1 0 1 0 1 0 -1 Contrasts (.mtx files): Tp1vsTp2.GrExp 0 0 1 0 Tp1vsTp2.GrControl 0 0 0 -1 Interaction 0 0 1 -1 Would this design be the correct one to use in this case? Alternatively, could it be this the correct one? GroupDescriptorFile 1 Class Subject1 Class Subject2 Variables Tp1vsTp2 Groupxtime Input Subject1_time1 Subject1 1 1 Input Subject1_time2 Subject1 -1 *-1* Input Subject2_time1 Subject2 1 *-1* Input Subject2_time2 Subject02 -1 1 Design matrix: 1 0 1 1 1 0 -1 -1 0 1 1 -1 0 1 -1 1 Contrasts (.mtx files): Tp1vsTp2 0 0 1 0 Groupxtime Interaction 0 0 0 1 Thank you very much in advance. Kind regards, Agurne Neuropsychology of Severe Medical Conditions Research Team Dpt of Methods and Experimental Psychology Faculty of Psychology and Education University of Deusto neurolab.deusto.es Avda. de las Universidades 24, 48007, Bilbao (Spain) Phone: +34 944139000 (ext. 3015) -------------- next part -------------- An HTML attachment was scrubbed... URL: https://secure-web.cisco.com/1U1Dzf28vpnPFg2BtzFhdygs3ovrFXnWojUwxe6aNA4xB-RbBlX88moctKPSxHmz-uipNnOpcMW6Mnm0-DNMtm-5bT3vejfiNisZ-klXxOGt5siaTaDn_pysU8bvjtE4ZGCNwDjoPJcgdLlIezwzLznwW3BirBsd5l0c1K2zmySjLNYmix54A-005QUfronHr4d_JvuGeZW7JD-5hpCbR-Q/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__mail.nmr.mgh.harvard.edu_pipermail_freesurfer_attachments_20201105_d9f516ed_attachment-2D0001.html%26d%3DDwICAg%26c%3DG2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U%26r%3D4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo%26m%3DhNoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3D0rR1Ixie17V_a2NI4noXcjDBJvM3gzKRH3dFjc5-2iU%26e%3D ------------------------------ Message: 10 Date: Thu, 5 Nov 2020 11:57:20 +0100 From: Agurne Sampedro Calvete <[email protected]> Subject: Re: [Freesurfer] .mgh file unknown, GLM paired analysis {Disarmed} To: [email protected] Message-ID: <CAJsj2xgy8cG=6xn3yujolrdlzv1tzzc2qam6p+jy4rjcyvg...@mail.gmail.com> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Dear FS experts, I have removed the backslashes "\" and now it works, so problem solved. Thank you very much. Regards, Agurne Neuropsychology of Severe Medical Conditions Research Team Dpt of Methods and Experimental Psychology Faculty of Psychology and Education University of Deusto neurolab.deusto.es Avda. de las Universidades 24, 48007, Bilbao (Spain) Phone: +34 944139000 (ext. 3015) El lun., 2 nov. 2020 a las 18:27, Agurne Sampedro Calvete (< [email protected]>) escribi?: > Dear Freesurfer Experts, > > I am trying to perform a paired analysis in FreeSurfer following this > tutorial > https://secure-web.cisco.com/1NNzdH2MfyBVhO_al0KZMOfbMxMQvFOuKmeE95mrXN_duBKJuOP8tc0Pxq8fKqeMtcFqdYFH6fpy_cWwIVzRa-eqjc-VrDyrRyOY-inoqPPUXZqW_Pp6ILfdxZp-q8NC2kq1xFQaswZdMUwDYcWY3BCXD9zdwwCAeRUDV-lA-_xbmOWFoPavz601b977uWiM_DC0MaIZ5ld5zDWwY_JXZ4g/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__secure-2Dweb.cisco.com_1GGOE7lAk9DEhVom372ksbhQpoUEm3yIVLX4YqDE8HfMpeOEgVTUnDNdXv-5FpENZI-5FZj8E1pQJo1vbndz8QuwfXZeLFZrg8uFaXPMF0SqFXPUHmLNodW7Jl-2DSXS-2DePsn2uN1wrgmWAb4tMFpdB1JokGuLZFVIqK-5FlmBvM7eufXwSmiMuSvGQ2NREwZt2mxapAyIqfuj9JwrJS-2DMUE9Nm4DNw_https-253A-252F-252Fsurfer.nmr.mgh.harvard.edu-252Ffswiki-252FPairedAnalysis%26d%3DDwICAg%26c%3DG2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U%26r%3D4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo%26m%3DhNoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3D_kDbQLjFGDb_IfSuKGeqRh-mRHk_Rbl6WSEpmPyxuAo%26e%3D > and I > have some problems when running the spatially smooth. > > I ran the following command: mri_surf2surf --s fsaverage --hemi lh --fwhm > 5\ --sval lh.paired-diff.thickness.mgh \ --tval > lh.paired-diff.thickness.sm05.mgh > > And I found this error: > ERROR: lh.paired-diff.thickness.mgh unknown freesurfer > > This file is in my subject directory, but when I see the file properties, > in the "file type" box it says: unknown. I have read that other users have > experienced the same error. > > What can I do to solve this problem? > > Thanks in advance. > > Kind regards, > > Agurne Sampedro > > > > Neuropsychology of Severe Medical Conditions Research Team > > Dpt of Methods and Experimental Psychology > Faculty of Psychology and Education > > University of Deusto > > neurolab.deusto.es > > > > Avda. de las Universidades 24, > > 48007, Bilbao (Spain) > > Phone: +34 944139000 (ext. 3015) > -------------- next part -------------- An HTML attachment was scrubbed... URL: https://secure-web.cisco.com/1wxpwnYM3HJxMmBdFKMt5CNFQQQDeIGggF0YNeUJPg8WMiS78CgIkaCYr9UWUU79MH8ROH9yz3-rarxExsIRWBlJz7KYiDUORfmOe5rV7gNGFzM4iq1W2ed1IWJmXfkCa34BQVARHT34lCa2dwrYF_VAAcQGhW6UCuuT4hIfm2ypYDvu60BSwOP_vhXMS4019QXhPljCX5oLWIjgtwiBcMw/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__mail.nmr.mgh.harvard.edu_pipermail_freesurfer_attachments_20201105_75e186c0_attachment-2D0001.html%26d%3DDwICAg%26c%3DG2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U%26r%3D4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo%26m%3DhNoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3DwQQtYOrYlkBTSTQNG1lHmRgeyJ9ATBPxIFwW-YR3oiQ%26e%3D ------------------------------ Message: 11 Date: Thu, 5 Nov 2020 09:34:03 -0500 From: "Douglas N. Greve" <[email protected]> Subject: Re: [Freesurfer] mri_glmfit_sim error To: <[email protected]> Message-ID: <[email protected]> Content-Type: text/plain; charset="windows-1252" Information about multiple comparisons correction has been pre-computed for various parameters, including the FWHM. In this case, the measured FWHM (38) is outside of the precomputed range. 38 is extremely high. Is this a thickness study? What smoothing level did you apply (--fwhm in mri_glmfit)? On 11/2/2020 2:22 PM, Basavaraju, Rakshathi wrote: > > ????????External Email - Use Caution > > Hi all, > > I ran a multiple comparison correction for a surface based analysis > with this command: > > mri_glmfit-sim --glmdir rh.project.glmdir --cache 2 abs --cwpvalthresh > .05 --2spaces > > But I am getting the following error: > > cannot find > /usr/local/freesurfer/average/mult-comp-cor/fsaverage/rh/cortex/fwhm38/abs/th13/mc-z.csd > > What might this error mean? I searched in the mail archives but could > not get any proper answer. Kindly help me. > > Thanks > > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://secure-web.cisco.com/1Bx-PtjccZ-WhuGdxndP-26xpcos_CUcEUhlPHPl_IGH5KTb1y-l3Al4TlDLM_5vQPd-zr6nLbRW5TH4QKszwqFDc3qHzH7kvqCGFf6s8bMCzyHe1-z9-2U-a6lL5Z0BB_eclfDjoLf8h9bac7i-rRAsmpPEu3KtaRM7d1p6XXp20UuVmzpxDBfXhmMAlETbtRYkSxao4UC4imoAajyxZxw/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer%26d%3DDwICAg%26c%3DG2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U%26r%3D4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo%26m%3DhNoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3D4D9hF7ZxOn9Vv33WCY8DWv9lfylIBHva4_0nqVRZqEg%26e%3D > -------------- next part -------------- An HTML attachment was scrubbed... URL: https://secure-web.cisco.com/1O-f6hBFwDTbkcbkI4DoU6tpXcJ1EDcxPFxcPljYKRV5jgxIDRZZQCIiOet-KH9aYeNUyCHE5Nx-6gnyGNnNxubNKFRaFpDUgavFSE5qd6beEn2KBKbrsnvfghUBH2xCxNRnRpdTVpXxMGZ2wyViNKUhp05dUZ9Wn6qDrRtQnv6yEdYE-v7jAjezY-xfo8msk4DksC3SDQvxdwQjaxF8kpQ/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__mail.nmr.mgh.harvard.edu_pipermail_freesurfer_attachments_20201105_0a89b527_attachment-2D0001.html%26d%3DDwICAg%26c%3DG2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U%26r%3D4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo%26m%3DhNoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3DhaH5xHiWmEo4VJ4zoF4P0mJ36JzY5WeA6aCSLjubvOs%26e%3D ------------------------------ Message: 12 Date: Thu, 5 Nov 2020 09:35:57 -0500 From: "Douglas N. Greve" <[email protected]> Subject: Re: [Freesurfer] mri_convert error To: <[email protected]> Message-ID: <[email protected]> Content-Type: text/plain; charset="utf-8" It looks like it is trying to extract diffusion info. Try running it with --no-dwi On 11/2/2020 5:11 PM, Georgina Angelopoulou wrote: > > ????????External Email - Use Caution > > Dear Freesurfer Developers, > > I am sorry I did not include the error message. > I am attempting to convert some dicom files to mgz via mri_convert > command. However, for only 5 participants from my cohort I get the > following error. > Could you please help me to resolve the problem? > > (base) Georgias-MBP:HC21 georgina$ mri_convert > 1.3.46.670589.11.38127.5.0.4944.2019102316491068177.dcm 001.mgz > mri_convert.bin > 1.3.46.670589.11.38127.5.0.4944.2019102316491068177.dcm 001.mgz > $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ > reading from 1.3.46.670589.11.38127.5.0.4944.2019102316491068177.dcm... > Starting DICOMRead2() > dcmfile = > /Users/georgina/Downloads/HD/HC21/1.3.46.670589.11.38127.5.0.4944.2019102316491068177.dcm > dcmdir = /Users/georgina/Downloads/HD/HC21 > ERROR: GetDICOMInfo(): dcmGetDWIParams() 9 > DICOM File: > /Users/georgina/Downloads/HD/HC21/1.3.46.670589.11.38127.5.0.4944.2019102316491068177.dcm > break DICOMRead.c:5228 > Ref Series No = 201 > Found 172 files, checking for dicoms > ERROR: GetDICOMInfo(): dcmGetDWIParams() 9 > ERROR: GetDICOMInfo(): dcmGetDWIParams() 9 > DICOM File: > /Users/georgina/Downloads/HD/HC21/1.3.46.670589.11.38127.5.0.4944.2019102316491025102.dcm > break DICOMRead.c:5228 > First Sorting > Computing Slice Direction > Vs: -0.99478 0.102 0.0033 > Vs: -0.994779 0.102 0.0033 > Second Sorting > IsDWI = 0, IsPhilipsDWI = 0 > Counting frames > nframes = 1 > nslices = 82 > ndcmfiles = 82 > PE Dir =? (dicom read) > CTABreadASCII(/Applications/freesurfer/FreeSurferColorLUT.txt): could > not open file > Too many open files > ERROR: reading /Applications/freesurfer/FreeSurferColorLUT.txt > Loading pixel data > ERROR: > /Users/georgina/Downloads/HD/HC21/1.3.46.670589.11.38127.5.0.4944.2019102316490992042.dcm > > is not a dicom file > 70092 Requested element (18 9089) not found in DCM_GetElementVM > > > Thank you in advance, > Georgina > > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://secure-web.cisco.com/1Bx-PtjccZ-WhuGdxndP-26xpcos_CUcEUhlPHPl_IGH5KTb1y-l3Al4TlDLM_5vQPd-zr6nLbRW5TH4QKszwqFDc3qHzH7kvqCGFf6s8bMCzyHe1-z9-2U-a6lL5Z0BB_eclfDjoLf8h9bac7i-rRAsmpPEu3KtaRM7d1p6XXp20UuVmzpxDBfXhmMAlETbtRYkSxao4UC4imoAajyxZxw/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer%26d%3DDwICAg%26c%3DG2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U%26r%3D4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo%26m%3DhNoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3D4D9hF7ZxOn9Vv33WCY8DWv9lfylIBHva4_0nqVRZqEg%26e%3D > -------------- next part -------------- An HTML attachment was scrubbed... URL: https://secure-web.cisco.com/1aPx5KYxp1stcWrebOqO7PQFNq3p5j6J9EFZBosqUTA4EsFjV3CFtqZu3vGbVflUpvks2TguxbJQSes7I5mBanBkv2BkGGIbnffRuG_I3iyoffCA0WnK9VrifnFqMueitPbD9P_MK2ztzbSoMA36iPo_B4rPT35tT6LCyhV0xcsOQkp-atAsV9f5zAA25TqL7fPGFND_ic5z-Ke_0n26X7A/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__mail.nmr.mgh.harvard.edu_pipermail_freesurfer_attachments_20201105_81da59c7_attachment-2D0001.html%26d%3DDwICAg%26c%3DG2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U%26r%3D4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo%26m%3DhNoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3DzlONjdUzI1oCbWfXrpo6pBU8bRwslTW566cCFlPEDNY%26e%3D ------------------------------ Message: 13 Date: Thu, 5 Nov 2020 09:37:07 -0500 From: "Douglas N. Greve" <[email protected]> Subject: Re: [Freesurfer] Extract he value of area and volume in the fsaverage for every subject {Disarmed} {Disarmed} To: <[email protected]> Message-ID: <[email protected]> Content-Type: text/plain; charset="utf-8" Try --slabel fsaverage lh /path/to/lh.areapial.label On 11/2/2020 10:24 PM, ??? wrote: > > ????????External Email - Use Caution > > Thank you very much! I tried to extract the areas with the following > codes: > mri_segstats > --seg qdec/Areapial_15_L/y.mgh (y.mgh was created after Qdec) > --slabel lh.areapial.label (This was the label extracted from the > fsaverage after multi-correction) > --avgwf lh_areapial.avgwf.dat (output file) > --accumulate > --sum lh_areapial.sum (output file) > I did not get a text file including the areas of all subjects. Is this > code correct? > > -----????----- > *???:*"Douglas N. Greve" <[email protected]> > *????:*2020-11-02 23:36:14 (???) > *???:* [email protected] > *??:* > *??:* Re: [Freesurfer] Extract he value of area and volume in the > fsaverage for every subject {Disarmed} > > I think the reason for this may be that the data in fsaverage > space (after mris_preproc) will have had a jacobian correction > which will not be in data on the native surface. For this reason, > I would not use #1. #2 is fine.You can apply your label in > fsaverage space to the y.mgh used as input to mri_segstats > specifying the label using --slabel and using --avgwf output and > also use --accumulate; run it with --help for more info. This will > create a text file of the areas or volumes (depending upon which > y.mgh you input) all your subjects for that label. > > > On 10/30/2020 10:37 PM, ??? wrote: >> >> ????????External Email - Use Caution >> >> Dear Professors: >> ? I compared the thickness, area, volume in the mild traumatic >> brain injury patients with health control by FreeSurFer, and >> found statistic difference region in the cortex area, >> volume?respectively. I defined the?statistic difference regions >> as a label on the fsaverage and mapped this label to subjects by >> Qdec/mri_label2label. The label defined on the fsaverage was >> mapped onto all subjects successfully, and the label in subjects >> matched well with the inflated cortex of subjects in?Freeview? >> Then the value of the label in every single subjects was >> extracted, and I found that there is no statistic difference in >> the value regarding to the area and volume?between the mild >> traumatic brain injury patients and health control subjects. >> Following are my questions: >> >> (1)Can I carry out correlation analysis between the?cortex area >> and volume with the behavior scores through these non-statistical >> extracted values? >> (2)Can I?extract the value of?cortex area and volume in the >> standard space for every TBI and health control subjects, and >> carry out correlation analysis between the?cortex area and volume >> with the behavior scores. How can I extract the value of?cortex >> area and volume in the standard space for every TBI and health >> control subjects >> >> Best wishes >> Mengjun Li >> >> >> -----????----- >> *???:*"Douglas N. Greve" <[email protected]> >> *????:*2020-10-30 23:40:30 (???) >> *???:* [email protected] >> *??:* >> *??:* Re: [Freesurfer] Extract he value of area and volume in >> the fsaverage for every subject >> >> Do you mean you compared your TBI subjects against fsaverage? >> That is not proper methodology. >> >> On 10/29/2020 9:51 PM, ??? wrote: >>> >>> ????????External Email - Use Caution >>> >>>> Dear FreeSurfer Developers: >>>> >>>> ?I compared the cortical thickness, area, volume in the >>>> mild traumatic brain injury patients with health control by >>>> FreeSurFer, and found a?statistic difference region in the >>>> cortex area and volume after correction. How can I extract >>>> the value of cortex area and volume for every subject in >>>> the fsaverage with the?code of?mri_segstats >>>> >>>> FreeSurfer >>>> version:?freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c >>>> Platform: macOS High Sierra. >>>> >>>> Best wishes >>>> Mengjun Li >>>> Second Xiangya Hospital >>>> Central South University >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> [email protected] >>> *MailScanner has detected a possible fraud attempt from >>> "secure-web.cisco.com" claiming to be* >>> >>> https://secure-web.cisco.com/1Bx-PtjccZ-WhuGdxndP-26xpcos_CUcEUhlPHPl_IGH5KTb1y-l3Al4TlDLM_5vQPd-zr6nLbRW5TH4QKszwqFDc3qHzH7kvqCGFf6s8bMCzyHe1-z9-2U-a6lL5Z0BB_eclfDjoLf8h9bac7i-rRAsmpPEu3KtaRM7d1p6XXp20UuVmzpxDBfXhmMAlETbtRYkSxao4UC4imoAajyxZxw/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer%26d%3DDwICAg%26c%3DG2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U%26r%3D4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo%26m%3DhNoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3D4D9hF7ZxOn9Vv33WCY8DWv9lfylIBHva4_0nqVRZqEg%26e%3D >>> >> >> >> _______________________________________________ >> Freesurfer mailing list >> [email protected] >> *MailScanner has detected a possible fraud attempt from >> "secure-web.cisco.com" claiming to be* >> >> https://secure-web.cisco.com/1Bx-PtjccZ-WhuGdxndP-26xpcos_CUcEUhlPHPl_IGH5KTb1y-l3Al4TlDLM_5vQPd-zr6nLbRW5TH4QKszwqFDc3qHzH7kvqCGFf6s8bMCzyHe1-z9-2U-a6lL5Z0BB_eclfDjoLf8h9bac7i-rRAsmpPEu3KtaRM7d1p6XXp20UuVmzpxDBfXhmMAlETbtRYkSxao4UC4imoAajyxZxw/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer%26d%3DDwICAg%26c%3DG2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U%26r%3D4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo%26m%3DhNoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3D4D9hF7ZxOn9Vv33WCY8DWv9lfylIBHva4_0nqVRZqEg%26e%3D >> > > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://secure-web.cisco.com/1Bx-PtjccZ-WhuGdxndP-26xpcos_CUcEUhlPHPl_IGH5KTb1y-l3Al4TlDLM_5vQPd-zr6nLbRW5TH4QKszwqFDc3qHzH7kvqCGFf6s8bMCzyHe1-z9-2U-a6lL5Z0BB_eclfDjoLf8h9bac7i-rRAsmpPEu3KtaRM7d1p6XXp20UuVmzpxDBfXhmMAlETbtRYkSxao4UC4imoAajyxZxw/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer%26d%3DDwICAg%26c%3DG2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U%26r%3D4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo%26m%3DhNoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3D4D9hF7ZxOn9Vv33WCY8DWv9lfylIBHva4_0nqVRZqEg%26e%3D > -------------- next part -------------- An HTML attachment was scrubbed... URL: https://secure-web.cisco.com/1C6mBRXSdINjcW5bXtrnDe7HeFTQ7fXTeYwXo0vNU7m-e3DZR8tthyTZ9-NRKjWHaXQzycLkYj1YF1EgzucCdd3rdBlFimpbaOTlwugf2jWpHhWdwtyvTSi896MO0eNNRBiQcGW9-4PL44uFYHnGF1Zxl0qhiLW2s_l7l7UBFpoEufMsJla91VLUnAPvXI-p-Nt1aTWeGoO2S2zObFwMlDA/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__mail.nmr.mgh.harvard.edu_pipermail_freesurfer_attachments_20201105_3f23da94_attachment-2D0001.html%26d%3DDwICAg%26c%3DG2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U%26r%3D4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo%26m%3DhNoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3DOLbAZCkYO4xaL6mcM2vz7-isqLK8WYpZe37j05D8bH4%26e%3D ------------------------------ Message: 14 Date: Thu, 5 Nov 2020 09:38:29 -0500 From: "Douglas N. Greve" <[email protected]> Subject: Re: [Freesurfer] Question about smoothing for extracting anatomical stats {Disarmed} To: <[email protected]> Message-ID: <[email protected]> Content-Type: text/plain; charset="utf-8" This is not needed or recommended. Not needed because you are already averaging over space and not recommended because it would cause one region to bleed over into another. On 11/3/2020 7:00 AM, Hye Min Shin wrote: > > ????????External Email - Use Caution > > Hello experts, > > So I understand that when doing mri_glmfit you want to use smoothed > surface maps to comply with random field theory while controlling for > multiple comparisons (as discussed here: *MailScanner has detected a > possible fraud attempt from "secure-web.cisco.com" claiming to be* > https://secure-web.cisco.com/1dC38RyzLsVkHIRlARvXa9dw1Vk-3AsgXiv_lmyS3He2i2o2azEiLdKyoT2NjuvhQMvXgjuk_1tn96Mar23T1hSsJxKBGinlqlR97sCxuRsI7HGNLLi6UHIDnK3P5pjlkO4UOwQh5DLnTAtP5lRfSp7YOCOxWNj5G1rmkJeyrgiYvUhRUXBgeFSuWEWwUgbg1O7qTMpkALcUoBl6DOz4eWw/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__www.mail-2Darchive.com_freesurfer-40nmr.mgh.harvard.edu_msg67902.html%26d%3DDwICAg%26c%3DG2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U%26r%3D4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo%26m%3DhNoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3DtHvwmc9guiPLoOHiF_pKW8u_hLKXHYPhDQCVrf0yw9U%26e%3D > > <https://secure-web.cisco.com/1bK3a_jRC6tg-zpJ6mH0iUt_StpfKc9p5BPM0h1d-VT4Nx_vmus_s-66KtVcvsKC62nJ0poPQaKqWr7rLN69rc1aXU6tKlbd86bk5vR7xrv3sC96TnzOzvAQd20-5GjKUgJmh0lGpGENYya5a0MXW1s9UxE2D-sggK74nyZ0eF8ICA81jLE5G6--CEevEYoJIO7mY4cHRqUekBpRX9tiJsw/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__secure-2Dweb.cisco.com_1pNAU-2DNVIkRxQvX9B5btXENpnudT80URPA00UsXPU064w3aUW-5FOaoZyIsU5NouMPdeCqme-5F69nHwP4qY41-5FWBNPcHd8oC2GMFd1DoY894Y9xS-5F8eLF44pu50UoeiVxYWALBXvirnf1pwSIZJsIL3BAu2-5FRp94HyBmMmFnKl7zmtONnvA8zyW5grRM-5FWBQqpGpdMgxR9TJh5-2Dm4dkUtEnfYw_https-253A-252F-252Fwww.mail-2Darchive.com-252Ffreesurfer-2540nmr.mgh.harvard.edu-252Fmsg67902.html%26d%3DDwICAg%26c%3DG2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U%26r%3D4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo%26m%3DhNoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3DNxHNWtAM9j4rZBMGEzcEKdd8L0E5XeyAWtqaXsElGgg%26e%3D > >). > > > But I was also wondering whether we have to smooth surface maps when > using mri_anatomical_stats to extract anatomical measurements? I see > that mri_anatomical_stats has the option to smooth by # of iterations > but is there a way to know how many # of iterations would equal let's > say 15 FWHM? > > Best, > Julia Shin > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://secure-web.cisco.com/1Bx-PtjccZ-WhuGdxndP-26xpcos_CUcEUhlPHPl_IGH5KTb1y-l3Al4TlDLM_5vQPd-zr6nLbRW5TH4QKszwqFDc3qHzH7kvqCGFf6s8bMCzyHe1-z9-2U-a6lL5Z0BB_eclfDjoLf8h9bac7i-rRAsmpPEu3KtaRM7d1p6XXp20UuVmzpxDBfXhmMAlETbtRYkSxao4UC4imoAajyxZxw/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer%26d%3DDwICAg%26c%3DG2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U%26r%3D4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo%26m%3DhNoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3D4D9hF7ZxOn9Vv33WCY8DWv9lfylIBHva4_0nqVRZqEg%26e%3D > -------------- next part -------------- An HTML attachment was scrubbed... URL: https://secure-web.cisco.com/1r-0e7J8kRfyna9yzG9tRwyZGhGlUK4zVbD8aRaKTpQdSZOaed6__6N1aaedKZzuRl97NV27jqB-J8cHO7DwVjVtBsZFJiIoGdtl8hMH7gv_1sA3-PXbc-2nLlXcjAq81daHhwueOBRP-xK6lYlRAZLvjyn9Z92bBEJtMkSlvjX2epcIepb41CU3fxPkQepybIpsAiz2YcARhc2kraKXHaw/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__mail.nmr.mgh.harvard.edu_pipermail_freesurfer_attachments_20201105_6a90d28e_attachment-2D0001.html%26d%3DDwICAg%26c%3DG2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U%26r%3D4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo%26m%3DhNoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3DKziGFnxaFpSP4k3HBAU_gGmMJKLaSzR_eYm_Qvc54ZE%26e%3D ------------------------------ Message: 15 Date: Thu, 5 Nov 2020 09:40:37 -0500 From: "Douglas N. Greve" <[email protected]> Subject: Re: [Freesurfer] Troubleshooting -parallel flag for Freesurfer, error in the cortical ribbon mask stage during recon-all {Disarmed} To: <[email protected]> Message-ID: <[email protected]> Content-Type: text/plain; charset="utf-8" Hi Andy, this is a bug introduced in 7.1.1, some kind of race condition. You can fix it by commenting out this line in recon-all ? if($OMP_NUM_THREADS > 1 && ! $LHonly && ! $RHonly) set cmd = ($cmd --parallel) # just hemis doug On 11/3/2020 12:06 PM, Andy Worth wrote: > > ????????External Email - Use Caution > > Hello, > > We've experienced random crashes when using the -parallel flag with > the?official FS docker container at *MailScanner has detected a > possible fraud attempt from "secure-web.cisco.com" claiming to be* > https://secure-web.cisco.com/1V5KGPyijcFAIlsUOQdLk4Gs014KSZyRjuhxULqKl9x6aHwfQAysmvCul3NCr_4rRDhEpy-DLh9E49kzrmvncSpTX1MAUK0J_zTHUsheF0-T3yQpGF52iPKZpuP12iMkew1DTdkF1Xv37qrlR6NX-9ewc5WZGJ8K-a7fvnOoZnDeQyY4PLSaLwAupBm4JH6fjaNGjx0G0M1ACpApE7UqMhQ/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__hub.docker.com_r_freesurfer_freesurfer_%26d%3DDwICAg%26c%3DG2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U%26r%3D4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo%26m%3DhNoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3DSfzgFZNF6AABxB2xadrPvlNQqZFV1RQwJ8aa1vPvqL8%26e%3D > > <https://secure-web.cisco.com/1t_MXJ0LgeNw67tM1GzqcI42-H1DHjy26ZJvQScxqM5_uUMC1y3E7OFJB6mll24xVCT-U9N3iXICrY8E3jqgzaQkOdIHBfaUSJTom12PmqxrIu5fnWwVPit-FUYVvL9Ib-iuVSlVC916vhf9LDYDeVp9s7MdG73e7XgtzJYaZEp4kfpT8tZbDHjGsH0PR08vCj3pidB3h4BN_AbOdyjXgDA/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__secure-2Dweb.cisco.com_1Db9ik7eIvMj7kgkeTafe0s-5FPlT0VyO4BIvoM6Chj4jvyesjHAuR-2DkZyjg4ueyTkvPI2tO3aWk76nJniaideisxRFreGgC6FYkFflnw3OJSb2vizDEGe9I7-5F5KxymQSiL-5F4xv8wD673W6RdSI1m9IsESb2d-2DXzAu607hYqEI8dlEnHdiHr5ZAJMdz0-2DaiK0PYe-5FTawyFsTVoTaka9SYiXIQ_https-253A-252F-252Fhub.docker.com-252Fr-252Ffreesurfer-252Ffreesurfer-252F%26d%3DDwICAg%26c%3DG2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U%26r%3D4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo%26m%3DhNoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3DcrGw-XfBvCw4TTBhGfhXBVarHoIJvB1qidAaugeWgxE%26e%3D > >.? > It looks like this issue: *MailScanner has detected a possible fraud > attempt from "secure-web.cisco.com" claiming to be* > https://secure-web.cisco.com/1xf7Mjd9OxQUvzZe-UImvhCbq0nGceof95kBHFiCo5uvCMELU_r5QO8Hwx6S3MPcaJjtnC4gyf0UqT-EZO21rQ1wwc43Ckt1zWryb9HK0LOVgof_AZOUZ0KuNt2dSnLomQomL0OGtI-8xMcMzX_xyM6xH3fft81oTRP_163dhmeQ3gV7yxlE5xfQ0EZ8Aj2d2QJHL3Dj-gb11CECFVjdYyA/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__www.mail-2Darchive.com_freesurfer-40nmr.mgh.harvard.edu_msg67588.html%26d%3DDwICAg%26c%3DG2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U%26r%3D4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo%26m%3DhNoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3DdfmEyxKKiLZayyo0fAvVnKmYUsEYDG63eT5WvcaxgHU%26e%3D > > <https://secure-web.cisco.com/1ekQ2fRRPQAjG2G3lJaSiVPqLo-DN7hc5qAJhS5yDfir2bQnCp102v0r4uiRzplIUaX-SfJRE0rIUWyX0WG9X0j89hTm58VxFJJo9Ru134iDLX1_-PWn5mQ_t2f-NMPCTGBehdVa3LSHKg3FNMhonexgezY4D1WFuFnM420V5-FONvjgDhaHodcjG-YbOzzokfy40d93L04i8LsRirhII0g/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__secure-2Dweb.cisco.com_1RTUH2ziWrAzuafGfyVCoxnmVd6xWSC1pjYKx0ENFxB4V7TrwK2DIeOzM-5F0SxoK0wCKIy4l-5Fc2CnAyb-5FS4Jjk04MEmATnQrr7iSlt-2DSRGu38Kf53mx7-5Fbr6eN1MS-5FT55qftLf-5FtXHqrUIHOO6Yi1JDx5z3Bm4P6KAIQ5NwYf48lOKx7RV-2DJh0d4yWKrTZLUVX9JSnwKDOkBN6WpqbBgd9Ew_https-253A-252F-252Fwww.mail-2Darchive.com-252Ffreesurfer-2540nmr.mgh.harvard.edu-252Fmsg67588.html%26d%3DDwICAg%26c%3DG2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U%26r%3D4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo%26m%3DhNoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3D8ZGFEBoIv707GDBQaSdJm0yt7uNQHbD8cuUzhrSIN9E%26e%3D > >. > > Is there a fixed recon-all that I can use with that image (or maybe a > new image coming soon)? > > Thanks, > Andy Worth > Scientific Solutions Engineer > he, him, his > <https://secure-web.cisco.com/1nc-Av2fXyGpAaz4FbSwZolnD1-EAsy17RxpKr15KtnHh8j_PbVRVxvGdiIvbkcSts8LmOVsMMRqTCR9LL4ZYoV0CkKHMmiX7N5pUopTHsUhlFVWuw-vdX5vITr3r8UTe8Lg8CH2h-Aq_747l35LHEfPwv4n4XAg_8T18PNR5sRCvzyC-3EDbmpAYPcLBibmRizwkDF8HvK6YOv2QZR3tcQ/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__secure-2Dweb.cisco.com_1vnPdwWhDIRo0dgACPHUy8Cs0L0bRI0jZF0TyQMe6r95oCZi5ZZJrHwieBuwTyFHuXGfSk-2DEFFswgKI0y4TShj-2DugXmlLhN4ZMce8CQGrkghGM-5F5NKI-5FGBnrhl7xI1ESkPP351SklVdFREt2FF3H-2DLGVYQ81FNvEo5KGxT45BBlfYIaW2kbjipETH3zboahRGW81CHHztSz-2DxDdpqsCRX2g_http-253A-252F-252Fwww.flywheel.io-252F%26d%3DDwICAg%26c%3DG2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U%26r%3D4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo%26m%3DhNoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3DncTs5GtnMd8DguTVLGmZS-C8Qwrgjyn774cmuuZ444c%26e%3D > > > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://secure-web.cisco.com/1Bx-PtjccZ-WhuGdxndP-26xpcos_CUcEUhlPHPl_IGH5KTb1y-l3Al4TlDLM_5vQPd-zr6nLbRW5TH4QKszwqFDc3qHzH7kvqCGFf6s8bMCzyHe1-z9-2U-a6lL5Z0BB_eclfDjoLf8h9bac7i-rRAsmpPEu3KtaRM7d1p6XXp20UuVmzpxDBfXhmMAlETbtRYkSxao4UC4imoAajyxZxw/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer%26d%3DDwICAg%26c%3DG2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U%26r%3D4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo%26m%3DhNoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3D4D9hF7ZxOn9Vv33WCY8DWv9lfylIBHva4_0nqVRZqEg%26e%3D > -------------- next part -------------- An HTML attachment was scrubbed... URL: https://secure-web.cisco.com/1wDVm9s1BExC6SLOj24U9v6h4ugrmWfffOWQKghPvCjVUSACasKPF9joxplE9RRANg6-pv-aO73uiX6pjKJY9IYrDffuWlkrSp8W0p_7nquOx6pNu20HXHr1KeZ5w0gHr4exmEn3JBSnDNiYpiy2Y_t9iOaTg5BwdTVe0xdpOcvlJVycv5F5CdvyCVSyvoXL6nbUH5N46LPkbeMM1Wmdelg/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__mail.nmr.mgh.harvard.edu_pipermail_freesurfer_attachments_20201105_8e4013a3_attachment-2D0001.html%26d%3DDwICAg%26c%3DG2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U%26r%3D4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo%26m%3DhNoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3DjVnuQJEas0ojXhZQmi9K5_3hZochYNwLri2sHYRkUhQ%26e%3D ------------------------------ Message: 16 Date: Thu, 5 Nov 2020 09:41:52 -0500 From: "Douglas N. Greve" <[email protected]> Subject: Re: [Freesurfer] Fixing error with pial surface {Disarmed} To: <[email protected]> Message-ID: <[email protected]> Content-Type: text/plain; charset="utf-8" Try these instructions From the linux command line, Create the file you want to upload, eg, cd $SUBJECTS_DIR tar cvfz subject.tar.gz ./subject Now log? into our anonymous FTP site: ftp surfer.nmr.mgh.harvard.edu It will ask you for a user name: use "anonymous" (no quotes) It will ask you for a password: use "anonymous" (no quotes) cd transfer/incoming binary put subject.tar.gz Send an email that the file has been and the name of the file. On 11/3/2020 12:38 PM, Julie Ottoy wrote: > > ????????External Email - Use Caution > > Hi Bruce, > > Thanks for your answer and cc'ing Rob. > I did use anonymous as the username. > > Thanks, > Julie > > On Tue, 3 Nov 2020 at 11:44, Fischl, Bruce <[email protected] > <mailto:[email protected]>> wrote: > > Hmmm, did you log in as anonymous? I?ll cc Rob who should be able > to help > > Cheers > > Bruce > > *From:* [email protected] > <mailto:[email protected]> > <[email protected] > <mailto:[email protected]>> *On Behalf Of > *Julie Ottoy > *Sent:* Tuesday, November 3, 2020 11:12 AM > *To:* Freesurfer support list <[email protected] > <mailto:[email protected]>> > *Subject:* Re: [Freesurfer] Fixing error with pial surface {Disarmed} > > *????????External Email - Use Caution * > > Hi Bruce > > Thank you! > > Meanwhile, I tried to upload the subject on the server but I > always get the following error: > > 230 Login successful. > Remote system type is UNIX. > Using binary mode to transfer files. > ftp> cd transfer/incoming > 250 Directory successfully changed. > ftp> put subject_FS_upload.zip > local: subject_FS_upload.zip remote: subject_FS_upload.zip > 421 Service not available, remote server has closed connection > > Could you help me out with this? > > Thanks > > Julie > > On Mon, 12 Oct 2020 at 15:48, Fischl, Bruce > <[email protected] <mailto:[email protected]>> wrote: > > Hi Julie > > It?s really hard to diagnose this way. Are you able to upload > the subject? If so, please send us the coordinates of the > region where you think things are going wrong > > Cheers > > Bruce > > *From:* [email protected] > <mailto:[email protected]> > <[email protected] > <mailto:[email protected]>> *On Behalf Of > *Julie Ottoy > *Sent:* Monday, October 12, 2020 3:42 PM > *To:* Freesurfer support list <[email protected] > <mailto:[email protected]>> > *Subject:* Re: [Freesurfer] Fixing error with pial surface > > *????????External Email - Use Caution * > > Hi Bruce, > > Thanks for your answer. I have checked the wm.mgz but it does > not seem to be a topological error I think. > > I have added coronal, axial, and sag views in attachment (see > the red cursor). Also I have added the first (coronal) slice > that starts to show white matter (couple slices later). > > Let me know if you still would like me to upload the data. > > Best > > Julie > > On Mon, 12 Oct 2020 at 14:23, Fischl, Bruce > <[email protected] <mailto:[email protected]>> wrote: > > Hi Julie > > It?s hard to tell from the single slice. Is there white > matter in the wm.mgz that doesn?t have surface (?h.white) > covering it? That would indicate a topological defect. > > > If you upload the entire gzipped and tarred subject?s > directory we will take a look > > Cheers > > Bruce > > *From:* [email protected] > <mailto:[email protected]> > <[email protected] > <mailto:[email protected]>> *On > Behalf Of *Julie Ottoy > *Sent:* Sunday, October 11, 2020 3:51 PM > *To:* Freesurfer support list > <[email protected] > <mailto:[email protected]>> > *Subject:* [Freesurfer] Fixing error with pial surface > > *????????External Email - Use Caution * > > Dear Freesurfer team, > > I have a question related to fixing the pial surface when > a part was missed (see attachment). On the freesurfer > website, I only found how to erase the pial when there was > too much (see *MailScanner has detected a possible fraud > attempt from "secure-web.cisco.com" claiming to be* > > https://secure-web.cisco.com/1Ko09hmUESCLYPbIkWyuKI1XNYkN-focaY4kmKV2m9CTQv_IPLWQ2HOl9hHsdCR9Ku_ONmw-qO8V-aQYTC2XTEhSe1ccGQDSNKHBejXC0iEFp7suoVL1oI-vJ9x8_u1iYW0M0PfxzLkyEXXg0tfd9itcvsmPlr4bwkx89HA7wdrEdubPd1kqFUQzBRSVpg9sjXySyVr7PCGtj_V0XTfLoPQ/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__surfer.nmr.mgh.harvard.edu_fswiki_FsTutorial_PialEditsV6.0%26d%3DDwICAg%26c%3DG2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U%26r%3D4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo%26m%3DhNoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3DFpEjqo_j51JDIUrhmkN5WPeI5q8TQXy7nh35HXTTjsI%26e%3D > > > <https://secure-web.cisco.com/1a57tGn-DXTTCjV1loFA2-aeS0LtBvJ-YanB3VbOi3rCnWck7G2CGYMP4d-oCFgqRsDG0KpEkig7AUHVzrXSZGwFs4uIol4bRMiYjPyrcLbkXYaw9IquURThj5tGY9N_cUebFjub4l1jfsfv4pgqn9R01f3w8AqaoUw5AuntIeyLzC6A0upv6ixNIbpy63JBRg2_azD7l5NrzTacTzsuIkA/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__secure-2Dweb.cisco.com_1gpx46tpa8CTIUNay0UrrJ-2DgxsIj8Mag4YGO8J8nyhFBk-5FvUGzoIRj4Mcbd6QhCbXxxACP5NekTgpkwy1i-5F7hReP5AFQqNeKWbPlOKFgTdD71o6FOQEC25-2D2mLI9VIZ3DCCUILUIjSEHeA8PQm-2DjSQuf2Q35SRlvA0gE74LLqJnkql0Rs2lM9RWexhSh3jGixx7QPZFpX0y4nDvIsDFmhtQ_https-253A-252F-252Fsurfer.nmr.mgh.harvard.edu-252Ffswiki-252FFsTutorial-252FPialEditsV6.0%26d%3DDwICAg%26c%3DG2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U%26r%3D4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo%26m%3DhNoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3DyUqnsYzMLs8odlMtIvGZ0wbIWSQskNVZCdDk_uv8yDo%26e%3D > > > ), but I could not find what to do when there was too little. > > As there is no white matter in this particular area, it is > also not an option to place control points. Also the skull > stripping did not change anything: I tried both the > freesurfer skull stripping and an in-house skull stripping > algorithm. > > Thank you for your help. > > Best regards > > Julie > > _______________________________________________ > Freesurfer mailing list > [email protected] > <mailto:[email protected]> > *MailScanner has detected a possible fraud attempt from > "secure-web.cisco.com" claiming to be* > > https://secure-web.cisco.com/1Bx-PtjccZ-WhuGdxndP-26xpcos_CUcEUhlPHPl_IGH5KTb1y-l3Al4TlDLM_5vQPd-zr6nLbRW5TH4QKszwqFDc3qHzH7kvqCGFf6s8bMCzyHe1-z9-2U-a6lL5Z0BB_eclfDjoLf8h9bac7i-rRAsmpPEu3KtaRM7d1p6XXp20UuVmzpxDBfXhmMAlETbtRYkSxao4UC4imoAajyxZxw/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer%26d%3DDwICAg%26c%3DG2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U%26r%3D4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo%26m%3DhNoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3D4D9hF7ZxOn9Vv33WCY8DWv9lfylIBHva4_0nqVRZqEg%26e%3D > > > 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<https://secure-web.cisco.com/1yf-BZPW8ZhXGR04O5o4QctY8YHhHkZU7nqvYi-uFggbJXO85NIUD4d07029d3jpOVQYx9AmH6E1Bg_YE3Auyzu9WD7U65onwKPrGjCN6HEPrtqcTTAPqVuwSLOoGKAxgObeMy-B6bTYJASuc0UdrNKMkI-5d2NKb-GjtGoNZDTwfhTMydhy3DX2HZH5XjenJDY4zUbnHRErTkfzVC-8TVA/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__secure-2Dweb.cisco.com_1aSysztaOg72LTSrHZ8IMlAHyx36lqzh-5FmhacRbfU85DOTLuITwz3kWnasOayZnNZpzHZSWb5yin6dOCPVg41bA3XaEhUSmu2qLzGmwvcmvNrteWu-2D9Bq02pR9SPHPFq5coAaCcaqLAJPYFbqOglbTzBLSd3Jj0DTqAj7WlndHsL0y2Oth1Io1uSTzIyh1lgScLGMaZlhF10kZeZegItM5w_https-253A-252F-252Fmail.nmr.mgh.harvard.edu-252Fmailman-252Flistinfo-252Ffreesurfer%26d%3DDwICAg%26c%3DG2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U%26r%3D4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo%26m%3DhNoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3DwETPubXsvCK5u1e-QI0J0CkFKWIEDjojJcfAUFFBZkk%26e%3D > > > > _______________________________________________ > Freesurfer mailing list > [email protected] <mailto:[email protected]> > 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<https://secure-web.cisco.com/1UB9da3XgbC1uBtNCgToy-cFi-gCWeXjwRygYRhe6HoERqZwI08BPC8FmOUu9cJLOM8Ostuq3QZW23NfStLXGpkjFTMqMpihP_7GWipVzxKH0ERxaQPkCtcEYVoeCqLWxoLQuqa9WvhnZn8JdZXVaPUwr3UsqOamvTpWkLKVBzcirlvbxvo46l5UAiYHTTVBUHfNmcVVONRo75-SyNkEp9w/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__secure-2Dweb.cisco.com_1EifvyV6KDi8xRojSTCOF-5F0h85ZTUKALs1YwF9ySx1YcICWTSXQLB3CUPQ2EgK5a0Og5d6R5uyCNU1uMo4PX7DRktWoMD-2D0a-5FQ-2Dkbu2-2DiuUwS4USDs4M9BbJHzl1PKOMRwjtUhYn40kTVoyL-5FsxFlFpjxMqKkTbc8lqCqqrLcHYhBAruJJv6GeVVbwP3Jjr-5FTXKX3fY8KeDSR8noon91OUw_https-253A-252F-252Fmail.nmr.mgh.harvard.edu-252Fmailman-252Flistinfo-252Ffreesurfer%26d%3DDwICAg%26c%3DG2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U%26r%3D4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo%26m%3DhNoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3DrrQ0Q0KJAXH3xd-ftB-_Gk7NCzyqiFl_fG_TG-wX-Lo%26e%3D > > > > > _______________________________________________ > Freesurfer mailing list > [email protected] > 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URL: https://secure-web.cisco.com/16wMFNFjJITMLkfPSZLHxMGwrQ3C_HHDtvxpp7m6pG-UshJvr49qVyEWA29-IYgHJnil4_B3z3sGkMasUvUMmwHfgmprodw_ImM-oYcJps3kTvAb89_3n6p3poidraUW1M2Jqc9gqqI5dN3UnGKC4G23PMYQuzfGTTCY-8iIBy6q7m31PHDX5MUxO8F_SLBsEmaXs2MyEhzIUrLTdKgLVzg/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__mail.nmr.mgh.harvard.edu_pipermail_freesurfer_attachments_20201105_f1722248_attachment-2D0001.html%26d%3DDwICAg%26c%3DG2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U%26r%3D4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo%26m%3DhNoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3DKqJVhqug5QGZOXUr2_iWqjOGwdWVw10S1H33RmbhMAU%26e%3D ------------------------------ Message: 17 Date: Thu, 5 Nov 2020 09:44:37 -0500 From: "Douglas N. Greve" <[email protected]> Subject: Re: [Freesurfer] mris_anatomical_stats error: stating file To: <[email protected]> Message-ID: <[email protected]> Content-Type: text/plain; charset="windows-1252" Is that the right error msg? It says it can't find the RH, but you are running it with LH. Can you post the entire terminal output? On 11/3/2020 2:00 PM, Chan, Shi Yu wrote: > > Hi FreeSurferDevelopers, > > > I'm trying to calculate cortical thickness statistics from the Yeo 17 > Network cortical parcellation and have used mri_surf2surf to get the > .annot files for each subject. > > > However, when I run mris_anatomical_stats, I get an error: > > > ERROR: stating file > subjects_dir/sub-001/label/sub-001/label/rh.Yeo2011_17Networks_N1000.annot > > > It seems like the "sub-001/label" portion is repeated. > > > The command I use for mris_anatomical_stats is: > > > mris_anatomical_stats -th3 -mgz -cortex sub-001/label/lh.cortex.label > -f sub-001/stats/lh.Yeo_17Networks.stats -b -a > sub-001/label/lh.Yeo2011_17Networks_N1000.annot sub-001 lh white > > > The command still runs despite the error, and outputs the stats files > accordingly, so I'm not sure how important this error is, but I can't > figure out how to fix it. > > > This is a similar issue to: > https://secure-web.cisco.com/10waLEz44qxXcmkseCz51_sUNS8Az150VCaqX7nV29-uMwDA6gpEcb06L95n2zCySASssMszX6xOQKl8h08e2e5vA_h_tvkFhM3outYuxJBtfgC9Mk1bfV376TlGPYi6EzmWYzEmLnhr5NXtAyDG1Nl5HmDDV1JlIlQFedI_7djBtVrFKd9CQLgrvjCDBgeFJoeoe1rYg2c1d8Yn4C9CBfQ/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__www.mail-2Darchive.com_freesurfer-40nmr.mgh.harvard.edu_msg67595.html%26d%3DDwICAg%26c%3DG2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U%26r%3D4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo%26m%3DhNoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3Dan3ONmgofEz6yp4K21D5jYihFWgcM0MCpml8JYGc9f4%26e%3D > > <https://secure-web.cisco.com/10waLEz44qxXcmkseCz51_sUNS8Az150VCaqX7nV29-uMwDA6gpEcb06L95n2zCySASssMszX6xOQKl8h08e2e5vA_h_tvkFhM3outYuxJBtfgC9Mk1bfV376TlGPYi6EzmWYzEmLnhr5NXtAyDG1Nl5HmDDV1JlIlQFedI_7djBtVrFKd9CQLgrvjCDBgeFJoeoe1rYg2c1d8Yn4C9CBfQ/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__www.mail-2Darchive.com_freesurfer-40nmr.mgh.harvard.edu_msg67595.html%26d%3DDwICAg%26c%3DG2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U%26r%3D4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo%26m%3DhNoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3Dan3ONmgofEz6yp4K21D5jYihFWgcM0MCpml8JYGc9f4%26e%3D > >?but > I've checked $SUBJECTS_DIR, and it is correct. If I run ls > $SUBJECTS_DIR/sub-001 I'll see all the different sub-folders in > sub-001 (mri stats labels etc) > > Any help would be much appreciated! Thank you! > > > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://secure-web.cisco.com/1Bx-PtjccZ-WhuGdxndP-26xpcos_CUcEUhlPHPl_IGH5KTb1y-l3Al4TlDLM_5vQPd-zr6nLbRW5TH4QKszwqFDc3qHzH7kvqCGFf6s8bMCzyHe1-z9-2U-a6lL5Z0BB_eclfDjoLf8h9bac7i-rRAsmpPEu3KtaRM7d1p6XXp20UuVmzpxDBfXhmMAlETbtRYkSxao4UC4imoAajyxZxw/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer%26d%3DDwICAg%26c%3DG2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U%26r%3D4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo%26m%3DhNoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3D4D9hF7ZxOn9Vv33WCY8DWv9lfylIBHva4_0nqVRZqEg%26e%3D > -------------- next part -------------- An HTML attachment was scrubbed... URL: https://secure-web.cisco.com/1Zwi8rn_kH0KJz0siH60sBL7HQFMm-BrRTt6WgRhvShIXvrkE6SmZWYVu4qsVnJvlHqtO3XE9I_I7PJ0vCezy1e9bwCyhIQqZnSm80SArU0bQlkzDTUdQ5EcSd_KWJdro7z26x0Own6Fh3FkS9gH5Aeahg2-ncueauBUwT8ZQEpxYkwSxY3B--Ax2thdmdokrJvMro5PK9oNM55aQB48sgg/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__mail.nmr.mgh.harvard.edu_pipermail_freesurfer_attachments_20201105_baaf0dbd_attachment-2D0001.html%26d%3DDwICAg%26c%3DG2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U%26r%3D4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo%26m%3DhNoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3DNsf6yW4Y8sofUzm0TrkH6T5AFFa6oZu-QVqJyp9CoME%26e%3D ------------------------------ Message: 18 Date: Thu, 5 Nov 2020 09:45:36 -0500 From: "Douglas N. Greve" <[email protected]> Subject: Re: [Freesurfer] (no subject) To: <[email protected]> Message-ID: <[email protected]> Content-Type: text/plain; charset="utf-8" Try this instead aparcstats2table --hemi lh? --subjects subj10 --parc aparc.a2009s? --meas meancurv --tablefile /home/team33/ aparcstats.txt On 11/3/2020 12:20 PM, saman fouladi wrote: > > ????????External Email - Use Caution > > hi > > I run in linux command: > """"""""""""""""""""""""""""""""""""""""""" > aparcstats2table --hemi lh? --subjects /home/team33/MRI4/subj10/stats > --parc aparc.a2009s? --meas meancurv --tablefile /home/team33/ > aparcstats.txt > """"""""""""""""""""""""""""""""""""""""""" > but show below error an i can not solve it nix: > > """"""""""""""""""""""""""""""""""""""""""" > ?File "/usr/local/freesurfer/bin/aparcstats2table", line 156 > ??? print 'ERROR: atleast 1 subject must be provided' > """"""""""""""""""""""""""""""""""""""""""" > > I changed the code several times, but in all cases there is this error. > This error also happens to asegstats2table. > > please help me > > > > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://secure-web.cisco.com/1W0eA_gfCAmT910h7azDjMdE7YN_Mk1vXirLYm_pLfbFRGj-vl4KDWZogNQWfFOCH44gZeu6avSJNmhxGj-gBThc1MBzULPFtZWm6B-gEH1nAyZ0W9ELn76CbHIJwPHHXb1yWH8sr0AU9zmPLY34LgrTEtMWSkWJ1l6Ttsu4av7X3eod5Pv5ajziuzM-wPCEZwu6NytZIAUlZj34tQ1aE5Q/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer%26d%3DDwICAg%26c%3DG2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U%26r%3D4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo%26m%3DhNoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3D4D9hF7ZxOn9Vv33WCY8DWv9lfylIBHva4_0nqVRZqEg%26e%3D > -------------- next part -------------- An HTML attachment was scrubbed... URL: https://secure-web.cisco.com/10f4ftXYNCBBCY8t7xl573GNDSf9lz09BWzhBEh0zuXJrZGuFosyC_HA2lME798hy4U7ZxWU7iUSZaDKn_cyzFbLbzQvcQ6T6N4RFaUmvEBuUtlFYExMfUTgFT3HqtM8aPU5iT03GwE02X29W8TpsbQBCUyIqlwytDvRDwNaoFLcfuQuSn_teELwUq6iqWIdasZhVjZo00Tx-3jysujnpYQ/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__mail.nmr.mgh.harvard.edu_pipermail_freesurfer_attachments_20201105_88740fc9_attachment-2D0001.html%26d%3DDwICAg%26c%3DG2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U%26r%3D4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo%26m%3DhNoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3DTYCibp--wbwlT_ZpA7X1wH2XLkDk5TlkbQVdpCEraPU%26e%3D ------------------------------ Message: 19 Date: Thu, 5 Nov 2020 09:49:57 -0500 From: "Douglas N. Greve" <[email protected]> Subject: Re: [Freesurfer] Fwd: using CAT12 segmentation for PVC To: <[email protected]> Message-ID: <[email protected]> Content-Type: text/plain; charset="utf-8" I don't think CAT creates white or pial surfaces, so no. What is wrong with your FS analysis? On 11/5/2020 2:15 AM, Donatienne Van Weehaeghe wrote: > > ????????External Email - Use Caution > > Dear, > > The segmentation using Freesurfer was incorrect, however we have a > good segmentation from Cat 12. Can we use this segmentation for PVC in > PETsurfer? > > Kind regards > Donatienne > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://secure-web.cisco.com/1W0eA_gfCAmT910h7azDjMdE7YN_Mk1vXirLYm_pLfbFRGj-vl4KDWZogNQWfFOCH44gZeu6avSJNmhxGj-gBThc1MBzULPFtZWm6B-gEH1nAyZ0W9ELn76CbHIJwPHHXb1yWH8sr0AU9zmPLY34LgrTEtMWSkWJ1l6Ttsu4av7X3eod5Pv5ajziuzM-wPCEZwu6NytZIAUlZj34tQ1aE5Q/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer%26d%3DDwICAg%26c%3DG2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U%26r%3D4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo%26m%3DhNoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3D4D9hF7ZxOn9Vv33WCY8DWv9lfylIBHva4_0nqVRZqEg%26e%3D > -------------- next part -------------- An HTML attachment was scrubbed... URL: https://secure-web.cisco.com/16FWQ0ue7qtb5UN8BWBtH-UHx72v4LUoBPTys7_EmWQsPwbOfAkmVERheswYuZwtULKUodVdrcfEGHVXk_8wUSLKS27DeqlLgEQPCjz0xLMhaAXFckCDT_WNcYe8nPSahVo5uk0EnctSohN0qiQmww2mK_bc_5atG_uCxEmAPygGZL-9uDYuJlW_4AolfBjQ4rAzO4z-GolAN_ZpMH2fXuQ/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__mail.nmr.mgh.harvard.edu_pipermail_freesurfer_attachments_20201105_a6cce58b_attachment-2D0001.html%26d%3DDwICAg%26c%3DG2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U%26r%3D4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo%26m%3DhNoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3Da0lGqITJoYF-BcXpiwWxSEv9UOcgPmkBntpjN1SlBao%26e%3D ------------------------------ Message: 20 Date: Thu, 5 Nov 2020 09:57:23 -0500 From: "Douglas N. Greve" <[email protected]> Subject: Re: [Freesurfer] repeated measures ANOVA 2x2 two groups two times {Disarmed} To: <[email protected]> Message-ID: <[email protected]> Content-Type: text/plain; charset="utf-8" In this case, the paired-t is identical to RM 2x2 ANOVA. But to answer your question, the first example you give is the right way to handle it. On 11/5/2020 4:32 AM, Agurne Sampedro Calvete wrote: > > ????????External Email - Use Caution > > Dear Freesurfer experts, > > I am trying?to do a longitudinal repeated measures ANOVA 2x2, with?two > groups?(experimental vs control) and two time points (pre and post > treatment). > > Although I have run?a paired t-test, now I would like to do a repeated > measures anova 2x2, since I am doing the same analyses with other data > in other softwares. > > I am trying to follow the tutorial *MailScanner has detected a > possible fraud attempt from "secure-web.cisco.com" claiming to be* > https://secure-web.cisco.com/19Jx3wc9Dxd2PyydkSrtbrg3-AnA3zC1dNgiT2dHhZjLMfZvqHnJzn6EqZvEraGsKXWWwgzPTuF1ldAa53xSQJ92zYggVOlIA1QI6kDqohJBIXsvqSNcVVqj9uwocNJVEOAHiboYu9ZntkH0811CJzgYe1MgsqpSpoNcFByNY3DNUAumweRqa_8MscB3fVA3VrdtnaoJ33p92rIfb7ugULg/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__surfer.nmr.mgh.harvard.edu_fswiki_RepeatedMeasuresAnova%26d%3DDwICAg%26c%3DG2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U%26r%3D4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo%26m%3DhNoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3D725LzAbcQFHqkaMXOREvI2uk9vG9ctDpeMfVn5Cn-cE%26e%3D > > <https://secure-web.cisco.com/1i_5jthFSKWYKZM_ANkjGuBqUL7hhHTahjS54p1lPzUvk_jUC_sQkEAFAEN1Bhs6ftlzz2rxIZP6LSjt3CGqf6XPI2ucsCrqFNKFu4QdcpIKZrKsm4b9MLTVSI9HYak91H54-at8FIW3cU35qd-EidijiaDWk2wS8CxdPQ8O_G2pbPewjulxGfYygSYSbkS6KV5loJ_2f9k7tSqA-SfHyBw/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__secure-2Dweb.cisco.com_1xcEvqAuPN3MsqK1JjC6qoZbooZS3kpB4WEU1Lx8hK28grFkOWFgj7ja5TXppcZRh8Vr2s3TJyQKT-2Dsr-2Dc0qt4XJSU7f74cElgVAI4K1nOBI5i5L0YQBzYutTVn-2DMwCGM-5FOotAt9VM1mzmm1MUuXbYtZC4-2DQfIujBH30LAwD5RtwZ6vGRv4JC7ocISixV0s52BsCadrLE2J-2D3CdqLLZnJRA_https-253A-252F-252Fsurfer.nmr.mgh.harvard.edu-252Ffswiki-252FRepeatedMeasuresAnova%26d%3DDwICAg%26c%3DG2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U%26r%3D4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo%26m%3DhNoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3DKEHkIFsrntENbUL-ZK8Ski3x38Z_n8QnmvAGTSMhjs8%26e%3D > >, > but I have several doubts when designing the FSGD file as well as the > contrasts. > > How should it be the FSGD file? > > I have seen in a previous post the following design for the same > number fo groups and time points: > > GroupDescriptorFile 1 > > Class Subject1 > > Class Subject2 > > Variables ????????????????????????????????????????????Tp1vsTp2.GrExp > ???Tp1vsTp2.GrControl > > Input? ?Subject1_time1 ?Subject1???? > ????1???????????????????????????????? 0 > > Input? ?Subject1_time2 ?Subject1??????? > -1??????????????????????????????? 0 > > Input ??Subject2_time1 ?Subject2 0???????????????????????????????? 1 > > Input? ?Subject2_time2 ?Subject02????? > ?0???????????????????????????????? -1 > > Design matrix: > > 1 0 1 0 > > 1 0 -1 0 > > 0 1 0 1 > > 0 1 0 -1 > > > Contrasts (.mtx files): > Tp1vsTp2.GrExp? ? ? ? 0 0 1 0 > Tp1vsTp2.GrControl? 0 0 0 -1 > Interaction 0 0 1 -1 > > Would this design be the correct one to use in this case? > > Alternatively, could it be this the correct one? > > GroupDescriptorFile 1 > > Class Subject1 > > Class Subject2 > > Variables ????????????????????????????????????????????Tp1vsTp2 > ?????????Groupxtime > > Input ?Subject1_time1 ?Subject1 ????1??????????????????????????????? 1 > > Input ?Subject1_time2 ?Subject1 -1 *-1* > > Input ??Subject2_time1 ?Subject2 ??1 *-1* > > Input ?Subject2_time2 ?Subject02 ?-1????????????????????????????? 1 > > Design matrix: > > 1 0 ?1 1 > > 1 0 -1 -1 > > 0 1 ?1 -1 > > 0 1 ?-1 1 > > Contrasts (.mtx files): > > Tp1vsTp2 0 0 1 0 > > Groupxtime Interaction ? 0 0 0 1 > > > Thank you very much in advance. > > Kind regards, > > Agurne > > Neuropsychology of Severe Medical Conditions Research Team > > Dpt of Methods and Experimental Psychology > Faculty of Psychology and Education > > University of Deusto > > neurolab.deusto.es > <https://secure-web.cisco.com/11FgXO8TgE5q6-H0i2cNKsR-Uu_5pVQZLqR0kR5sCNW6xA7OnOR9WVWazHlwIm5skvIPeuCdwyaR5fmnw4r7SxzWkp2on1aV3COktePMAPSyvT_eq34z-4pg6JhWtnv56XvaEOpTe7EvwtZlibvWb9IjYgVA9k9X-DDZR7EwOiY5xq8n6BtRWb1xwcl52-tWoSGgiXfZLlHjChbAQH_yThQ/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__secure-2Dweb.cisco.com_1J2XHqATjb-2Ds81WNLHHOzFHoMov247ukeyY9r-5F63MCuIYY3b3cgBooSYVXAHcxmruuUhAJRQeOK-5FM6GhmpQ2HLsoPViHsaOnuQmnS-5FhX44VhcAXEpVQmkpDhtamFGdp-5FY3WSVnP0Hb0VMfltJoov6c0TVAyZfGD7j4wcdLUcORgyyH2uu-5FWSTkVwMZ87NUx0paSiYbguuSG9LFBN-5FNCd9ZQ_http-253A-252F-252Fneurolab.deusto.es-252F%26d%3DDwICAg%26c%3DG2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U%26r%3D4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo%26m%3DhNoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3D2J0ixxb0QpbpFysiBVZ4bTG3vIaiOm1IqrIgOBxU2mI%26e%3D > > > > Avda. de las Universidades 24, > > 48007, Bilbao (Spain) > > Phone:?+34 944139000 (ext. 3015) > > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://secure-web.cisco.com/1W0eA_gfCAmT910h7azDjMdE7YN_Mk1vXirLYm_pLfbFRGj-vl4KDWZogNQWfFOCH44gZeu6avSJNmhxGj-gBThc1MBzULPFtZWm6B-gEH1nAyZ0W9ELn76CbHIJwPHHXb1yWH8sr0AU9zmPLY34LgrTEtMWSkWJ1l6Ttsu4av7X3eod5Pv5ajziuzM-wPCEZwu6NytZIAUlZj34tQ1aE5Q/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer%26d%3DDwICAg%26c%3DG2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U%26r%3D4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo%26m%3DhNoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3D4D9hF7ZxOn9Vv33WCY8DWv9lfylIBHva4_0nqVRZqEg%26e%3D > -------------- next part -------------- An HTML attachment was scrubbed... URL: https://secure-web.cisco.com/146-BJ1astkMG2t8Gn-5upsgMl1FrLW6FdbS1iOydmy0h0tSwoyN2sBfEK76CeZkxVfT8-1Ar4JrOjnwN6dBx-sPXorCBPRJgCQtW2I0MaTf5kvLDoKr2UeR_H0kgN_ceB1hQ4Me1XaM_UfxBuo9L56LAi46wGfglcKYxJ718qX2GINiAXXE7RFyd_NagmGr0D5Mr3GKe6FXWvxavL2zksA/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__mail.nmr.mgh.harvard.edu_pipermail_freesurfer_attachments_20201105_32ae2575_attachment-2D0001.html%26d%3DDwICAg%26c%3DG2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U%26r%3D4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo%26m%3DhNoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3DBT4OF4-v21_oqHFSvJ3-lnCKLx6yhDjUf8CJSK3A8pw%26e%3D ------------------------------ Message: 21 Date: Thu, 5 Nov 2020 10:00:57 -0500 From: "Douglas N. Greve" <[email protected]> Subject: Re: [Freesurfer] LGI quality control {Disarmed} To: <[email protected]> Message-ID: <[email protected]> Content-Type: text/plain; charset="windows-1252" When you click on the gray areas, is the value 0 or just something very close to 0? You may need to set the lower threshold (default is 2). Also, I would recommend using freeview via tksurferfv (same command line as tksurfer) On 11/4/2020 2:12 PM, Nelson, Eric wrote: > > ????????External Email - Use Caution > > Hello, > > I am using FreeSurfer 7.1.1 to run LGI and have done so successfully. > I am now trying to quality check my data using tksurfer as described > on the wiki > > /tksurfer my_subject_id lh inflated -overlay lh.pial_lgi/ > > However the LGI overlay is not covering the entirety of the inflated > brain. Specifically the medial frontal surface and some subcortical > are not measured for LGI. ?Here is a link of the overlay images for a > few subjects: *MailScanner has detected a possible fraud attempt from > "secure-web.cisco.com" claiming to be* > https://secure-web.cisco.com/1TGuydF5Zu-G23BakiE5uOXTfyWdJujfOVmJR-e2dmS8lxVxML-4CnlvxGOTZLuOtQLiHUdhcAZGYMHEiXaZVzco2H5Hxeyf-aZ1LZODDoABy367CP0jJkhhjUlTmc2pJupmYQzRwM6TIwPbWIfI5Pij-WjggvNDg5xACWGHLmn2dPkPhBAENakR9bTfqTG4YnyyqxUrFB32oPiIDAh4qHw/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__www.dropbox.com_s_9pt8rti4yjudrza_LGI-5FQC.png-3Fdl-3D0%26d%3DDwICAg%26c%3DG2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U%26r%3D4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo%26m%3DhNoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3DWgL62N0ezzPmlm1HzUkcSSxGCXdZBj_V38chbh-I1hM%26e%3D > . I > <https://secure-web.cisco.com/1eE5oOZejFrXmm2X8F1tKRbSfpB8qH17Tmo8Fw28DaYCJLgRARre_JAl4DMYct_XeQi09sk0mXcpSJyZSDegBsCOfnjZ3oyLz9_V9UyTO9jsC3bbOBOFFlXyXpq3ZdE4PasaUIok9N0ZZv1vzT_7QAPClXVxJT8IjWDrk9jaznmZlE5FmozRQ2P174n1Qguuxym-R25AOIwairNWJ5vXSJg/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__secure-2Dweb.cisco.com_1yytrZan4Ml7C4NJTkc91uplhrETEPm4MAwDFEYaEAXtVlSnzGTjs5BjzZZSDOtTgizZpSDnl3ThVIFkaiXv-2D-2DDGYo5izF1yFMK4gbyOHaQIVo-5F20HarcOi-5FHT6zrv2m6X-5FpzP4BKEZbOmkD8UlglJjPZELhvw-2DkW4tNs-5Fq2K97iR-2DnN8xvGyh2mHAgjXm9saalzD0cAqzMFUXXNDhGfoyA_https-253A-252F-252Fwww.dropbox.com-252Fs-252F9pt8rti4yjudrza-252FLGI-5FQC.png-253Fdl-253D0.-252520I-252520%26d%3DDwICAg%26c%3DG2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U%26r%3D4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo%26m%3DhNoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3Dcq0aJlDd4oMVL7tadGmdJMaerCp6IYrshMg4oZ4r_y8%26e%3D > >. > I haven?t been able to find any images of what this overlay should > look like so I don?t know if this is expected or if something has gone > wrong with the processing. Any feedback would be greatly appreciated > > Best, > > Eric > > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://secure-web.cisco.com/1W0eA_gfCAmT910h7azDjMdE7YN_Mk1vXirLYm_pLfbFRGj-vl4KDWZogNQWfFOCH44gZeu6avSJNmhxGj-gBThc1MBzULPFtZWm6B-gEH1nAyZ0W9ELn76CbHIJwPHHXb1yWH8sr0AU9zmPLY34LgrTEtMWSkWJ1l6Ttsu4av7X3eod5Pv5ajziuzM-wPCEZwu6NytZIAUlZj34tQ1aE5Q/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer%26d%3DDwICAg%26c%3DG2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U%26r%3D4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo%26m%3DhNoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3D4D9hF7ZxOn9Vv33WCY8DWv9lfylIBHva4_0nqVRZqEg%26e%3D > -------------- next part -------------- An HTML attachment was scrubbed... URL: https://secure-web.cisco.com/1pH3toMlO0PInIzqumzXYRmZuPqrcl7lepJIO71iKeeHGmjzJ3q7VApbVduDEyZioaD60peyko4c1OisPIdwv5QTJbW91eSgzhPygJ0XTlU5YOWWH8iIrawHVrlCsam_2KduIz8-Q6gAunEeSnBfMJgLYFrEVObK1atEyOyiFcXpyrtwrCsSzrKAiNXrcDAuy89-jbE71nK3f3m5uRmbdkw/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__mail.nmr.mgh.harvard.edu_pipermail_freesurfer_attachments_20201105_363bfcc9_attachment-2D0001.html%26d%3DDwICAg%26c%3DG2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U%26r%3D4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo%26m%3DhNoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3DnuRod9AZ8X1F1npebVvDSc9Lh9kONGG8X7sUp_pCSGI%26e%3D ------------------------------ Message: 22 Date: Thu, 5 Nov 2020 16:32:59 +0100 From: Agurne Sampedro Calvete <[email protected]> Subject: Re: [Freesurfer] repeated measures ANOVA 2x2 two groups two times {Disarmed} To: Freesurfer support list <[email protected]> Message-ID: <CAJsj2xjDD=yx+jspdvyfb3q_rpydhgzptxuatoenpcwkguw...@mail.gmail.com> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Dear Douglas, Thank you very much for your rapid response. I have another question. I am following the FS Repeated Measures tutorial and therefore, I ran this: mris_preproc --target fsaverage --hemi lh --meas thickness --out lh.thickness.mgh --fsgd rmanova.fsgd. However, in the FS Group Analysis tutorial, it says that you must include "--cache-in thickness.fwhm10.fsaverage" if the data was preprocessed with recon-all with the -qcache option, which was my case. As I am doing longitudinal analyses, do I have to skip this option and just follow the Repeated Measures tutorial or do I have to include the --cache option? Thank you very much. Best regards, Agurne Neuropsychology of Severe Medical Conditions Research Team Dpt of Methods and Experimental Psychology Faculty of Psychology and Education University of Deusto neurolab.deusto.es Avda. de las Universidades 24, 48007, Bilbao (Spain) Phone: +34 944139000 (ext. 3015) El jue., 5 nov. 2020 a las 15:58, Douglas N. Greve (<[email protected]>) escribi?: > In this case, the paired-t is identical to RM 2x2 ANOVA. But to answer > your question, the first example you give is the right way to handle it. > > > On 11/5/2020 4:32 AM, Agurne Sampedro Calvete wrote: > > External Email - Use Caution > Dear Freesurfer experts, > > I am trying to do a longitudinal repeated measures ANOVA 2x2, with two > groups (experimental vs control) and two time points (pre and post > treatment). > > Although I have run a paired t-test, now I would like to do a repeated > measures anova 2x2, since I am doing the same analyses with other data in > other softwares. > > I am trying to follow the tutorial *MailScanner has detected a possible > fraud attempt from "secure-web.cisco.com" claiming to be* > https://secure-web.cisco.com/1BONkNj8u6Td2ShXTk0I7LNsyxeaW5vpitLWaVbRw0t0UdnBWOw8A6x9FhDrvNvByZ54yAq_8sipZ-f63__askkGnrquSK2xBEFsYy0d62KCeLdoFcj6Fzl1LPb6RPbPWIk9Tni3oVI-1kqoDdjW-nnr8CoPzbjKiBrvHgaNpgZ0Of8xzIdPwXrdKotYOCiK4hoVT8OHy0RNeLJc6Yoxtzg/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__secure-2Dweb.cisco.com_11u6-2DIyY2-2DP7w7M4zmGiLCyaG6g2vViEpx4ag8H474t-5FvAcKQofRlrgzoecVmHS-2DzCmukHiQ4nYncdNoWgv3qseGeeJ5V9DyPr8qfYwFtrgu7s9OZWm-2DZxMwuQ5ZFRq0n-2DrmVcPAZ0Hk-2DkzFtomVz5K6pII7oYat7YlIYPSB5e0Ig4auXkKYY9vdGnvAE3T5jbnApRosUxoICfXaCSW4-2DFw_https-253A-252F-252Fsurfer.nmr.mgh.harvard.edu-252Ffswiki-252FRepeatedMeasuresAnova%26d%3DDwICAg%26c%3DG2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U%26r%3D4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo%26m%3DhNoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3DxCGBDn8l0YMcKZyRaJe9MtM9NPkyg5nAidmsPM5dWJo%26e%3D > > <https://secure-web.cisco.com/1i_5jthFSKWYKZM_ANkjGuBqUL7hhHTahjS54p1lPzUvk_jUC_sQkEAFAEN1Bhs6ftlzz2rxIZP6LSjt3CGqf6XPI2ucsCrqFNKFu4QdcpIKZrKsm4b9MLTVSI9HYak91H54-at8FIW3cU35qd-EidijiaDWk2wS8CxdPQ8O_G2pbPewjulxGfYygSYSbkS6KV5loJ_2f9k7tSqA-SfHyBw/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__secure-2Dweb.cisco.com_1xcEvqAuPN3MsqK1JjC6qoZbooZS3kpB4WEU1Lx8hK28grFkOWFgj7ja5TXppcZRh8Vr2s3TJyQKT-2Dsr-2Dc0qt4XJSU7f74cElgVAI4K1nOBI5i5L0YQBzYutTVn-2DMwCGM-5FOotAt9VM1mzmm1MUuXbYtZC4-2DQfIujBH30LAwD5RtwZ6vGRv4JC7ocISixV0s52BsCadrLE2J-2D3CdqLLZnJRA_https-253A-252F-252Fsurfer.nmr.mgh.harvard.edu-252Ffswiki-252FRepeatedMeasuresAnova%26d%3DDwICAg%26c%3DG2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U%26r%3D4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo%26m%3DhNoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3DKEHkIFsrntENbUL-ZK8Ski3x38Z_n8QnmvAGTSMhjs8%26e%3D > >, > but I have several doubts when designing the FSGD file as well as the > contrasts. > > How should it be the FSGD file? > > I have seen in a previous post the following design for the same number fo > groups and time points: > > GroupDescriptorFile 1 > > Class Subject1 > > Class Subject2 > > Variables Tp1vsTp2.GrExp > Tp1vsTp2.GrControl > > Input Subject1_time1 Subject1 1 > 0 > > Input Subject1_time2 Subject1 -1 0 > > Input Subject2_time1 Subject2 0 > 1 > > Input Subject2_time2 Subject02 0 > -1 > > > > Design matrix: > > 1 0 1 0 > > 1 0 -1 0 > > 0 1 0 1 > > 0 1 0 -1 > > Contrasts (.mtx files): > Tp1vsTp2.GrExp 0 0 1 0 > Tp1vsTp2.GrControl 0 0 0 -1 > Interaction 0 0 1 -1 > > Would this design be the correct one to use in this case? > > Alternatively, could it be this the correct one? > > GroupDescriptorFile 1 > > Class Subject1 > > Class Subject2 > > Variables Tp1vsTp2 > Groupxtime > > Input Subject1_time1 Subject1 1 1 > > Input Subject1_time2 Subject1 -1 > *-1* > > Input Subject2_time1 Subject2 1 > *-1* > > Input Subject2_time2 Subject02 -1 1 > > Design matrix: > > 1 0 1 1 > > 1 0 -1 -1 > > 0 1 1 -1 > > 0 1 -1 1 > > > > Contrasts (.mtx files): > > Tp1vsTp2 0 0 1 0 > > Groupxtime Interaction 0 0 0 1 > > Thank you very much in advance. > > Kind regards, > > Agurne > > > > Neuropsychology of Severe Medical Conditions Research Team > > Dpt of Methods and Experimental Psychology > Faculty of Psychology and Education > > University of Deusto > > neurolab.deusto.es > <https://secure-web.cisco.com/11FgXO8TgE5q6-H0i2cNKsR-Uu_5pVQZLqR0kR5sCNW6xA7OnOR9WVWazHlwIm5skvIPeuCdwyaR5fmnw4r7SxzWkp2on1aV3COktePMAPSyvT_eq34z-4pg6JhWtnv56XvaEOpTe7EvwtZlibvWb9IjYgVA9k9X-DDZR7EwOiY5xq8n6BtRWb1xwcl52-tWoSGgiXfZLlHjChbAQH_yThQ/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__secure-2Dweb.cisco.com_1J2XHqATjb-2Ds81WNLHHOzFHoMov247ukeyY9r-5F63MCuIYY3b3cgBooSYVXAHcxmruuUhAJRQeOK-5FM6GhmpQ2HLsoPViHsaOnuQmnS-5FhX44VhcAXEpVQmkpDhtamFGdp-5FY3WSVnP0Hb0VMfltJoov6c0TVAyZfGD7j4wcdLUcORgyyH2uu-5FWSTkVwMZ87NUx0paSiYbguuSG9LFBN-5FNCd9ZQ_http-253A-252F-252Fneurolab.deusto.es-252F%26d%3DDwICAg%26c%3DG2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U%26r%3D4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo%26m%3DhNoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3D2J0ixxb0QpbpFysiBVZ4bTG3vIaiOm1IqrIgOBxU2mI%26e%3D > > > > > > Avda. de las Universidades 24, > > 48007, Bilbao (Spain) > > Phone: +34 944139000 (ext. 3015) > > _______________________________________________ > Freesurfer mailing > [email protected]https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://secure-web.cisco.com/16_BzqBsEA_TerxQm4Cr6KLbWuaAys8LwQkTla3Ka04j0acffUYZTzdVokbLlYvOHGJ4qZkfdC8PugkrJuFx2cM3LMh3T6tc6DqDb4weAPZA3zlNoQn1dJJbXqGY0qlkBrCCklLF6_bLGv9TpvnRRN3mFCQctSRTXYBMfzWE_U5MLjplfCbtdYPQtkZIOYy_K6tq2wnCMDL7T-W9ZE9tizw/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__secure-2Dweb.cisco.com_1Jem34chpPCHsjtBsJuqJZVyROTvpLIYYdJJC55-2DICnVW3ESEKCmsC6eW9LB5d5ifNKvbDn5kjCTLUgekR-5FiPR1nUUewDdNSAar-5F-5FUZ9NH2kcFsqXd4ArR4JKSJL6XT6lbPeqIve9m1qOwslfkpsChNtyAeWFsRGhX-2DoH5GTyh0j92WiaYNTiqROCWdLU6aRLwzbA0WJf6RWmMJFXv5cB4Q_https-253A-252F-252Fmail.nmr.mgh.harvard.edu-252Fmailman-252Flistinfo-252Ffreesurfer%26d%3DDwICAg%26c%3DG2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U%26r%3D4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo%26m%3DhNoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3DXb1QAiHwN59prK3JxNcJ_6KlQo9Upp-rbM6BpZZzvKM%26e%3D > -------------- next part -------------- An HTML attachment was scrubbed... URL: https://secure-web.cisco.com/1AWJbXipVpalEa83c-bsKRB1z6TdPaNzj8EshI_T_deCdbHXaL3FB2_Yz5PhIAcE0UN3c-xNQvchbnLsV-kdy8wbZQYW8iChzS_E8kdsDJnBbjW0lX0tdVnmUOYkadoxnkVfbXyKubToFpCevPYzzRVw7Qf5uk7BuzZHrFOLa5KqQhbhwgAhSpxp4OZEE_TyRqdMN6PmWaNuOWHvm4-lJ3w/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__mail.nmr.mgh.harvard.edu_pipermail_freesurfer_attachments_20201105_4318d94f_attachment-2D0001.html%26d%3DDwICAg%26c%3DG2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U%26r%3D4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo%26m%3DhNoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3DUATJ_rJBO9X4wWKyo7NsrRpTm2izRtX-U9EFgx5fLwY%26e%3D ------------------------------ Message: 23 Date: Thu, 5 Nov 2020 15:35:30 +0000 From: "Hasimoglu, Yasemin" <[email protected]> Subject: Re: [Freesurfer] trac-preproc error To: Freesurfer support list <[email protected]> Message-ID: <mn2pr04mb698988b00a4dd919351d5cd680...@mn2pr04mb6989.namprd04.prod.outlook.com> Content-Type: text/plain; charset="us-ascii" Hi Anastasia, I uploaded the files. Let me know if you have trouble viewing them! Best, Yasemin ________________________________ From: [email protected] <[email protected]> on behalf of Yendiki, Anastasia <[email protected]> Sent: Monday, November 2, 2020 10:57 PM To: Freesurfer support list <[email protected]> Subject: Re: [Freesurfer] trac-preproc error Hi Yasemin - If you upload all the tracula output files for me here, I'll take a look: https://secure-web.cisco.com/1Cat7QH7PrnWYpgLRCZqKDTlVt4cCsn03QocRZhF5IxkQzuMEUEXWCNh3e7q7GHhUgIlwuxV3irSZKcGUmdSUgd7BEb6ZeFzqA-fO0HMVtkkk9pSZ21AbJtuzx4p-LWkMsgDexRTAheapOA1PZXqi3vb49GMs_uixovOxovN0DCdeLbLBtzFMwKwP8SB-GPAv4fgnitH-YyXuVwit1c25bQ/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__gate.nmr.mgh.harvard.edu_filedrop2_%26d%3DDwICAg%26c%3DG2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U%26r%3D4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo%26m%3DhNoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3DLGqq3yYgmcDSj7sqKLlbd0hsHbxrrmJxg4F5Lfvky-0%26e%3D Please include all the output directories for this one subject in one zip file. Thanks! Anastasia. ________________________________ From: [email protected] <[email protected]> on behalf of Hasimoglu, Yasemin <[email protected]> Sent: Thursday, October 29, 2020 11:47 AM To: Freesurfer support list <[email protected]> Subject: [Freesurfer] trac-preproc error Hi, I'm running Tracula on a longitudinal dataset and it's failing at the preproc stage for one subject with the following message: INFO: Distances between consecutive points in test subject's space are 16 13 12 14 WARN: Could not find satisfactory control point fit - try 4967 Finding center streamline INFO: Step is 3 voxels WARN: Turning off deviation check for center streamline INFO: Step is 3 voxels WARN: Turning off FA check for center streamline INFO: Step is 3 voxels WARN: Turning off overlap check for center streamline INFO: Step is 3 voxels WARN: All checks already off. Exiting. Selecting 5 points on center streamline ERROR: Selected streamline has fewer than 5 points Linux zorii.nmr.mgh.harvard.edu 3.10.0-1062.4.3.el7.x86_64 #1 SMP Wed Nov 13 23:58:53 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Wed Oct 28 04:11:51 EDT 2020 It looks like the problem is with one specific pathway. I checked the brainmask and the inter and intra-subject registrations and they all look fine to me, so I'm not sure what else to check. The trac-all.log file is quite large, I attempted to attach it in this email several times, but it always gets rejected, so I'm not attaching it for now. I would greatly appreciate any advice! Best, Yasemin -------------- next part -------------- An HTML attachment was scrubbed... URL: https://secure-web.cisco.com/1IyxTmqR5PzVgI7BZMJ3wlY4fm3mGOs_0YMVG4_RdWIbGbRE3kwtKcc1EaZG2JP4FOMp06an19Ll8toNeTKfdO5UzC6fSN0dEC_XwzhWPy-Dq4lcKlW1BSe70B8JIq_ARHOQ2xBi6DEXZnd6wddpC1xk_FBy3HDpFYP7b2xgX0rQZGNqcp6g_jIntMCwmrCffBVUluersXG2Dve-Pwa-mFA/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__mail.nmr.mgh.harvard.edu_pipermail_freesurfer_attachments_20201105_78c255b8_attachment-2D0001.html%26d%3DDwICAg%26c%3DG2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U%26r%3D4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo%26m%3DhNoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3DlOJRVsC7g7nVFidkATem3HZF3sk8wVvDXCLTzBVgkrY%26e%3D ------------------------------ Message: 24 Date: Thu, 5 Nov 2020 16:29:06 +0000 From: "Chan, Shi Yu" <[email protected]> Subject: Re: [Freesurfer] mris_anatomical_stats error: stating file To: Freesurfer support list <[email protected]> Message-ID: <mn2pr04mb61608bb5e3217ae23ac8e4e58b...@mn2pr04mb6160.namprd04.prod.outlook.com> Content-Type: text/plain; charset="iso-8859-1" Hi, Yes, sorry! I copied the error message from terminal, but copied the command from my script so I copied the error message for the wrong hemisphere. I apologise for the confusion. I've attached the terminal output (I've put ##### at the lines above the error message) and the script I use in this email. Thank you for all your help! ________________________________ From: [email protected] <[email protected]> on behalf of Douglas N. Greve <[email protected]> Sent: Thursday, November 5, 2020 9:44 AM To: [email protected] <[email protected]> Subject: Re: [Freesurfer] mris_anatomical_stats error: stating file Is that the right error msg? It says it can't find the RH, but you are running it with LH. Can you post the entire terminal output? On 11/3/2020 2:00 PM, Chan, Shi Yu wrote: Hi FreeSurfer Developers, I'm trying to calculate cortical thickness statistics from the Yeo 17 Network cortical parcellation and have used mri_surf2surf to get the .annot files for each subject. However, when I run mris_anatomical_stats, I get an error: ERROR: stating file subjects_dir/sub-001/label/sub-001/label/rh.Yeo2011_17Networks_N1000.annot It seems like the "sub-001/label" portion is repeated. The command I use for mris_anatomical_stats is: mris_anatomical_stats -th3 -mgz -cortex sub-001/label/lh.cortex.label -f sub-001/stats/lh.Yeo_17Networks.stats -b -a sub-001/label/lh.Yeo2011_17Networks_N1000.annot sub-001 lh white The command still runs despite the error, and outputs the stats files accordingly, so I'm not sure how important this error is, but I can't figure out how to fix it. This is a similar issue to: https://secure-web.cisco.com/1Y8DxxcoYlFMOeHjcANm01y3JLYZX6yibj4F6yRaP5-GdorTtgHAn1b7g5NREkhS6peUTPr6u6HtDpF8DWfKRUVa5O3ILYUP0w2INRGJLo8ePccNfWa6arlseNF3qSBPCwx2WXXoh7DK54B6cL3vg-ffbCgZjh_q_Ij80nZQACnYl7fIBD4FqIonjMA0G85GSuXULXVXC4VqMnwTLQ-GdRw/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__www.mail-2Darchive.com_freesurfer-40nmr.mgh.harvard.edu_msg67595.html%26d%3DDwICAg%26c%3DG2MiLlal7SXE3PeSnG8W6_JBU6FcdVjSsBSbw6gcR0U%26r%3D4-qVbJceK55Szax7QMQk4nn905RtanIPcs1eFgJeMWo%26m%3DhNoiYxULpFqk_PF0Kgd0qg50gVyED256QE6pbof-VDY%26s%3Dan3ONmgofEz6yp4K21D5jYihFWgcM0MCpml8JYGc9f4%26e%3D but I've checked $SUBJECTS_DIR, and it is correct. If I run ls $SUBJECTS_DIR/sub-001 I'll see all the different sub-folders in sub-001 (mri stats labels etc) Any help would be much appreciated! 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