Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

question about ventricular volume calculation
by Jiao Qing 11 Nov '20

11 Nov '20

External Email - Use Caution Dear FreeSurfer Developers: I want to calculate ventricular volume using the 'recon-all' procedure. I believe the method of calculation of ventricular volume is different from that of subcortal nuclei. In the 31 steps(Autorecon Processing Stages), which steps are related with ventricular volume? It seem that the steps after 16 are not for ventricular volume calculation,right? FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Platform:Ubuntu 14.04. Best wishes Qing Jiao, Ph.D Department of Radiology Shandong First Medical University, China

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please help me
by saman fouladi 11 Nov '20

11 Nov '20

External Email - Use Caution hi I want to process MRI images to extract Morphology features. I convert my dcm file to nii format by mri-convert command and then I used FSL software and BET(Best extraction Tool). Next I do not know what to do to extract morphological features? My other question is what is the difference between recon-all and use FEAT( in FSL software)? What are the uses of each? Thank you

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Fwd: using CAT12 segmentation for PVC
by Donatienne Van Weehaeghe 11 Nov '20

11 Nov '20

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

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Re: [Freesurfer] mri_glmfit_sim error (Douglas N. Greve)
by Basavaraju, Rakshathi 11 Nov '20

11 Nov '20

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: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> On Behalf Of freesurfer-request(a)nmr.mgh.harvard.edu Sent: 05 November 2020 11:29 To: freesurfer(a)nmr.mgh.harvard.edu Subject: [EXTERNAL] Freesurfer Digest, Vol 201, Issue 6 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://secure-web.cisco.com/1Bx-PtjccZ-WhuGdxndP-26xpcos_CUcEUhlPHPl_IGH5K… or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu 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" <eanelson(a)uab.edu> Subject: [Freesurfer] LGI quality control {Disarmed} To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <DM6PR07MB791577DA3BB61700D9F42BE5C7EF0(a)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_dq63kxl7l6… . I<https://secure-web.cisco.com/1Hod0xhqjDXliu4d6GvJjLlbNiHOsmMLOvn77883QuHzRr… >. 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

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strange error in lme_mass_RgGrow
by Knut J Bjuland 11 Nov '20

11 Nov '20

External Email - Use Caution When I run lme_mass_RgGrow on mgh using lme it wil fit 20 % before it quite. Is there a problem with my system? Region 4450: Convergence at iteration 3. Initial and final likelihoods: 473.1215, 473.7587. Aproximate percentage of fitted locations: 20% Region 4451: Convergence at iteration 3. Initial and final likelihoods: 395.2576, 395.4612. Region 3984: Convergence at iteration 10. Initial and final likelihoods: 6166.5159, 6308.9265. Region 3997: Convergence at iteration 7. Initial and final likelihoods: 6416.8295, 6486.6. Region 4004: Convergence at iteration 7. Initial and final likelihoods: 6502.0812, 6556.0947. Region 4017: Convergence at iteration 6. Initial and final likelihoods: 5238.416, 5260.2966. Region 4024: Convergence at iteration 9. Initial and final likelihoods: 5717.0694, 5869.6523. Region 4037: Convergence at iteration 8. Initial and final likelihoods: 5780.9679, 5869.0804. Region 4044: Convergence at iteration 7. Initial and final likelihoods: 5198.7665, 5280.596. Region 4057: Convergence at iteration 11. Initial and final likelihoods: 5363.591, 5546.6867. Region 4064: Convergence at iteration 8. Initial and final likelihoods: 5900.1618, 6026.5605. Region 4077: Convergence at iteration 12. Initial and final likelihoods: 4778.4173, 4981.1345. Region 4084: Convergence at iteration 14. Initial and final likelihoods: 3774.7994, 4066.6808. Region 4097: Convergence at iteration 8. Initial and final likelihoods: 4876.8165, 4906.7731. Region 4104: Convergence at iteration 15. Initial and final likelihoods: 3534.9077, 3902.7112. Region 4117: Convergence at iteration 12. Initial and final likelihoods: 3507.1867, 3737.6882. Region 3965: Convergence at iteration 9. Initial and final likelihoods: 5986.0723, 6083.7278. Region 3976: Convergence at iteration 11. Initial and final likelihoods: 6281.3707, 6563.964. Region 3985: Convergence at iteration 5. Initial and final likelihoods: 6301.9946, 6338.9599. Region 3996: Convergence at iteration 8. Initial and final likelihoods: 5856.8615, 6212.0574. Region 4005: Convergence at iteration 8. Initial and final likelihoods: 6873.475, 7446.4396. Region 4016: Convergence at iteration 7. Initial and final likelihoods: 6217.0534, 6244.5827. Region 4025: Convergence at iteration 9. Initial and final likelihoods: 5113.7322, 5330.6839. Region 4036: Convergence at iteration 7. Initial and final likelihoods: 5283.615, 5356.654. Region 4045: Convergence at iteration 7. Initial and final likelihoods: 5184.5815, 5220.6488. Region 4056: Convergence at iteration 21. Initial and final likelihoods: 5427.8908, 6068.4834. Region 4065: Convergence at iteration 7. Initial and final likelihoods: 5249.0298, 5402.8081. Region 4076: Convergence at iteration 19. Initial and final likelihoods: 4277.3846, 4531.6266. Region 4085: Convergence at iteration 5. Initial and final likelihoods: 4330.5351, 4358.1673. Region 4096: Convergence at iteration 24. Initial and final likelihoods: 4079.7519, 4868.4444. Region 4386: Convergence at iteration 3. Initial and final likelihoods: 323.3627, 323.5732. Region 4395: Convergence at iteration 3. Initial and final likelihoods: 305.988, 306.5865. Region 4406: Convergence at iteration 3. Initial and final likelihoods: 330.1895, 330.9518. Region 4415: Convergence at iteration 4. Initial and final likelihoods: 359.8304, 364.2057. Region 4426: Convergence at iteration 4. Initial and final likelihoods: 439.5375, 443.9663. Region 4435: Convergence at iteration 4. Initial and final likelihoods: 484.5466, 486.2776. Region 4446: Convergence at iteration 4. Initial and final likelihoods: 501.1848, 503.3314. Region 4455: Convergence at iteration 3. Initial and final likelihoods: 428.3561, 429.518. Region 4107: Convergence at iteration 9. Initial and final likelihoods: 4476.7465, 4566.4605. Region 4114: Convergence at iteration 21. Initial and final likelihoods: 3737.363, 4272.8042. Region 4127: Convergence at iteration 27. Initial and final likelihoods: 3192.7459, 3416.7. Region 4134: Convergence at iteration 8. Initial and final likelihoods: 4269.5658, 4566.6162. Region 4147: Convergence at iteration 5. Initial and final likelihoods: 3606.8877, 3633.1639. Region 4154: Convergence at iteration 13. Initial and final likelihoods: 3816.0024, 4030.1052. Region 4167: Convergence at iteration 11. Initial and final likelihoods: 3156.972, 3198.5802. Region 4174: Convergence at iteration 8. Initial and final likelihoods: 2540.0254, 2687.2559. Region 4187: Convergence at iteration 8. Initial and final likelihoods: 2732.6083, 2766.4362. Region 4194: Convergence at iteration 11. Initial and final likelihoods: 2904.8543, 2948.6889. Region 4207: Convergence at iteration 9. Initial and final likelihoods: 3173.3919, 3220.6856. Region 4214: Convergence at iteration 17. Initial and final likelihoods: 2292.1555, 2371.4073. Region 4227: Convergence at iteration 6. Initial and final likelihoods: 1927.7947, 1935.1905. Region 4124: Convergence at iteration 10. Initial and final likelihoods: 3395.7905, 3456.0824. Region 4137: Convergence at iteration 13. Initial and final likelihoods: 3144.3683, 3252.4981. Region 4144: Convergence at iteration 7. Initial and final likelihoods: 3616.5298, 3638.9022. Region 4157: Convergence at iteration 7. Initial and final likelihoods: 3994.7191, 4081.6581. Region 4164: Convergence at iteration 8. Initial and final likelihoods: 3069.1727, 3083.2809. Region 4177: Convergence at iteration 12. Initial and final likelihoods: 2855.9023, 3111.4421. Region 4184: Convergence at iteration 10. Initial and final likelihoods: 2602.0641, 2736.3126. Region 4197: Convergence at iteration 10. Initial and final likelihoods: 2575.9477, 2652.5406. Region 4204: Convergence at iteration 8. Initial and final likelihoods: 2827.6445, 2858.7798. Region 4217: Convergence at iteration 8. Initial and final likelihoods: 2185.6552, 2201.4679. Region 4224: Convergence at iteration 13. Initial and final likelihoods: 1947.6529, 2019.9921. Region 4237: Convergence at iteration 10. Initial and final likelihoods: 1992.7653, 2109.8762. Region 4244: Convergence at iteration 5. Initial and final likelihoods: 2011.0102, 2012.3774. Region 4257: Convergence at iteration 9. Initial and final likelihoods: 2089.3226, 2116.5027. Region 4264: Convergence at iteration 4. Initial and final likelihoods: 2043.0603, 2047.3301. Region 4277: Convergence at iteration 9. Initial and final likelihoods: 1242.1654, 1298.8671. Region 4284: Convergence at iteration 15. Initial and final likelihoods: 931.6477, 1072.3483. Region 4297: Convergence at iteration 6. Initial and final likelihoods: 1117.948, 1119.9788. Region 4105: Convergence at iteration 9. Initial and final likelihoods: 4304.0258, 4562.3424. Region 4116: Convergence at iteration 14. Initial and final likelihoods: 3486.4583, 3692.2359. Region 4125: Convergence at iteration 9. Initial and final likelihoods: 4166.8753, 4363.0712. Region 4136: Convergence at iteration 7. Initial and final likelihoods: 3405.6061, 3467.4061. Region 4145: Convergence at iteration 11. Initial and final likelihoods: 3839.79, 3920.9005. Region 4156: Convergence at iteration 18. Initial and final likelihoods: 2761.0518, 3293.1863. Region 4165: Convergence at iteration 15. Initial and final likelihoods: 2800.9099, 2945.5367. Region 4176: Convergence at iteration 25. Initial and final likelihoods: 2850.6054, 3208.5289. Region 4185: Convergence at iteration 5. Initial and final likelihoods: 2814.0058, 2818.3573. Region 4196: Convergence at iteration 17. Initial and final likelihoods: 2045.844, 2618.2478. Region 4205: Convergence at iteration 12. Initial and final likelihoods: 2403.7824, 2567.9232. Region 4216: Convergence at iteration 11. Initial and final likelihoods: 2325.306, 2375.4947. Region 4225: Convergence at iteration 26. Initial and final likelihoods: 1576.2928, 1830.0616. Region 4234: Convergence at iteration 9. Initial and final likelihoods: 2458.1317, 2491.6322. Region 4247: Convergence at iteration 7. Initial and final likelihoods: 2260.9006, 2302.8498. Region 4254: Convergence at iteration 13. Initial and final likelihoods: 1838.9015, 2007.5048. Region 4267: Convergence at iteration 24. Initial and final likelihoods: 1832.4045, 1955.755. Region 4274: Convergence at iteration 14. Initial and final likelihoods: 1601.9728, 2027.699. Region 4287: Convergence at iteration 3. Initial and final likelihoods: 1142.6921, 1143.1295. Region 4294: Convergence at iteration 21. Initial and final likelihoods: 1040.4745, 1190.8409. Region 4307: Convergence at iteration 20. Initial and final likelihoods: 939.726, 1492.1753. Region 4314: Convergence at iteration 23. Initial and final likelihoods: 1333.3944, 1467.1591. Region 4327: Convergence at iteration 7. Initial and final likelihoods: 1360.1691, 1363.6335. Region 4334: Convergence at iteration 4. Initial and final likelihoods: 1111.9455, 1113.9392. Region 4347: Convergence at iteration 10. Initial and final likelihoods: 1187.5667, 1219.3373. Region 4354: Convergence at iteration 10. Initial and final likelihoods: 1296.0977, 1303.1828. Region 4367: Convergence at iteration 6. Initial and final likelihoods: 1320.5446, 1330.7699. Region 4304: Convergence at iteration 8. Initial and final likelihoods: 1241.1904, 1261.0619. Region 4317: Convergence at iteration 8. Initial and final likelihoods: 1162.0756, 1187.6331. Region 4324: Convergence at iteration 16. Initial and final likelihoods: 973.2621, 1237.8304. Region 4337: Convergence at iteration 17. Initial and final likelihoods: 1210.8871, 1381.7809. Region 4344: Convergence at iteration 15. Initial and final likelihoods: 1007.8125, 1164.5606. Region 4357: Convergence at iteration 11. Initial and final likelihoods: 1121.5019, 1210.5144. Region 4364: Convergence at iteration 9. Initial and final likelihoods: 1316.26, 1329.9583. Region 4377: Convergence at iteration 11. Initial and final likelihoods: 1083.3015, 1117.8056. Region 4384: Convergence at iteration 8. Initial and final likelihoods: 1202.4067, 1206.9108. Region 4397: Convergence at iteration 3. Initial and final likelihoods: 455.7886, 456. Region 4404: Convergence at iteration 4. Initial and final likelihoods: 421.0432, 422.3794. Region 4417: Convergence at iteration 4. Initial and final likelihoods: 535.8643, 537.1298. Region 4424: Convergence at iteration 3. Initial and final likelihoods: 440.3669, 440.5871. Region 4437: Convergence at iteration 3. Initial and final likelihoods: 433.7267, 433.9047. Region 4444: Convergence at iteration 3. Initial and final likelihoods: 366.1862, 366.5702. Region 4236: Convergence at iteration 11. Initial and final likelihoods: 1940.7068, 1988.848. Region 4245: Convergence at iteration 7. Initial and final likelihoods: 2276.4873, 2343.7557. Region 4256: Convergence at iteration 10. Initial and final likelihoods: 1890.9237, 1984.0524. Region 4265: Convergence at iteration 9. Initial and final likelihoods: 2167.6349, 2204.2796. Region 4276: Convergence at iteration 22. Initial and final likelihoods: 1081.6507, 1174.5174. Region 4285: Convergence at iteration 15. Initial and final likelihoods: 1094.8024, 1172.0724. Region 4296: Convergence at iteration 10. Initial and final likelihoods: 1165.8842, 1204.7504. Region 4305: Convergence at iteration 16. Initial and final likelihoods: 1236.4803, 1317.1137. Region 4316: Convergence at iteration 22. Initial and final likelihoods: 1182.1206, 1289.8913. Region 4325: Convergence at iteration 17. Initial and final likelihoods: 1233.9583, 1298.6294. Region 4336: Convergence at iteration 5. Initial and final likelihoods: 1363.2995, 1363.9365. Region 4345: Convergence at iteration 5. Initial and final likelihoods: 1031.9699, 1034.9684. Region 4356: Convergence at iteration 17. Initial and final likelihoods: 807.4396, 1048.7552. Region 4365: Convergence at iteration 11. Initial and final likelihoods: 1174.4335, 1206.0356. Region 4376: Convergence at iteration 9. Initial and final likelihoods: 1221.4789, 1281.2862. Region 4385: Convergence at iteration 3. Initial and final likelihoods: 338.7425, 339.3615. Region 4396: Convergence at iteration 4. Initial and final likelihoods: 413.5567, 415.3263. Region 4405: Convergence at iteration 3. Initial and final likelihoods: 358.3976, 358.7214. Region 4416: Convergence at iteration 4. Initial and final likelihoods: 503.3176, 504.4978. Region 4425: Convergence at iteration 3. Initial and final likelihoods: 414.3136, 414.5143. Region 4436: Convergence at iteration 4. Initial and final likelihoods: 517.1163, 518.8835. Region 4445: Convergence at iteration 4. Initial and final likelihoods: 371.1772, 376.3281. Region 4456: Convergence at iteration 3. Initial and final likelihoods: 419.4101, 420.2904. Region 4374: Convergence at iteration 20. Initial and final likelihoods: 909.2794, 1054.2007. Region 4387: Convergence at iteration 3. Initial and final likelihoods: 434.6045, 434.8105. Region 4394: Convergence at iteration 3. Initial and final likelihoods: 305.6105, 306.3464. Region 4407: Convergence at iteration 4. Initial and final likelihoods: 441.8864, 443.5837. Region 4414: Convergence at iteration 6. Initial and final likelihoods: 407.173, 417.2559. Region 4427: Convergence at iteration 4. Initial and final likelihoods: 296.9316, 299.3968. Region 4434: Convergence at iteration 3. Initial and final likelihoods: 361.5294, 362.2747. Region 4447: Convergence at iteration 3. Initial and final likelihoods: 438.7214, 438.9005. Region 4454: Convergence at iteration 3. Initial and final likelihoods: 414.2992, 414.4532. Aproximate percentage of fitted locations: 100% Parallel pool using the 'local' profile is shutting down. Summary:

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Postdoctoral Fellowship in advanced multi-parametric imaging in Parkinson’s disease, Alzheimer’s disease, and healthy aging
by Maurizio Bergamino 10 Nov '20

10 Nov '20

External Email - Use Caution My Lab, at Barrow Neurological Institute (Phoenix, AZ), is looking for a Postdoc. For more information email to: Ashley M. Stokes, Ph.D. Assistant Professor // Division of Neuro-Imaging Research Barrow Neurological Institute *Ashley.Stokes(a)BarrowNeuro.org* and/or Ryan R. Walsh, M.D., Ph.D., FAAN Associate Professor // Muhammad Ali Parkinson Center Department of Neurology // Barrow Neurological Institute *Ryan.Walsh(a)BarrowNeuro.org* A postdoctoral fellowship position (fully funded for up to three years) is available at Barrow Neurological Institute (BNI) working with Ashley Stokes, PhD, and Ryan R. Walsh, MD, PhD, as part of a rapidly growing collaborative research effort between the Division of Neuro-Imaging Research, Department of Neurology, and Muhammad Ali Parkinson Center. The position will primarily focus on the development, application, and analysis of advanced MRI methods in the context of both Parkinson’s disease and Alzheimer’s disease, as well as dementia with Lewy bodies and healthy cognitive aging, expanding upon recent novel approaches developed by this multi-modal lab. These methods include advanced functional, diffusion, perfusion, and structural imaging methods, with an emphasis on novel mathematical/signal processing approaches to provide a more comprehensive understanding of neurodegenerative diseases and normal brain aging across structural, functional, and perfusion signatures, including their mutual interdependence. BNI is the world’s largest dedicated neurological disease treatment and research institution, and the Muhammad Ali Parkinson Center at BNI is a recognized leader in the field. Outstanding institutional resources, including 1.5T and 3T Philips clinical MRI, a research-dedicated Philips 3T MRI, a 7T preclinical Bruker MRI, microCT, microPET, and optical imaging scanners are available at BNI. The Division of Neuro-Imaging Research has a strong history of imaging excellence and is currently expanding. BNI is a major hub for neuroscience research, including both basic and translational neuroscience, with a wide range of internationally-recognized neurology subspecialties. Barrow Neurological Foundation provides robust philanthropic support exceeding $18M per annum, 100% of which benefits patient care, research and education at BNI. Applicants should have a PhD in physics, engineering, mathematics, computer science, or a related discipline. Competitive candidates will have expertise in signal processing and/or functional MRI and be interested in developing novel approaches to analysis of MRI-based signals. This position is available immediately and offers competitive compensation and benefits. Phoenix is the 5th largest metropolitan in the United States and the 2nd fastest growing city. Phoenix is a beautiful place to live and work, boasting more days of sunshine and a lower cost of living than most comparable cities. A rich culture, including theatre, concerts, museums, sports, and great food, are easily found in Phoenix. With a moderate climate most of the year, many Phoenicians enjoy an active lifestyle of hiking, cycling, rock climbing, swimming, and golf. Interested applicants should send a current CV, including the names of three references, to both: *Ashley M. Stokes, Ph.D.Assistant Professor // Division of Neuro-Imaging Research Barrow Neurological Institute Ashley.Stokes(a)BarrowNeuro.org* *Ryan R. Walsh, M.D., Ph.D., FAANAssociate Professor // Muhammad Ali Parkinson Center Department of Neurology // Barrow Neurological Institute Ryan.Walsh(a)BarrowNeuro.org*

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trac-all -bedp error after successful -prep
by Michele Valotti 10 Nov '20

10 Nov '20

External Email - Use Caution Hi all, I am trying to run tract segmentation on a scan and after running trac-all -prep without errors, trac-all -bedp can't run because it can't find dmri/data. Checking the dir I see a data.nii.gz but it looks like it's a broken link, even though the dwi.nii.gz image (which data.nii.gz should link to in my understanding) is in the folder. I have attached the log which I have skimmed through without seeing any obvious problems. Any help is greatly appreciated, Thank you, Michele

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Re: [Freesurfer] Freesurfer 7.1.0 on CentOS 8.1 {Disarmed}
by fsbuild 10 Nov '20

10 Nov '20

External Email - Use Caution Hello Ali, The swrast error can happen if Nvidia grpahics drivers were installed using Nvidia’s own packages/download and then subsequently, your CentOS8 kernel was updated via the CentOS package management tools, i.e. the Nvidia software may then be incompatible with the upgraded system.  I think there are Nvidia packages in the CentOS package repos, and using those to re-install the Nvidia software could fix those kinds of errors. Currently the freesurfer RPM install path is not relocatable.  I’m not sure relocation would help as I think admin/root privileges would still be needed to for the installation process to download and install any system system dependent packages the freesurfer RPM indicates are needed. I would ask your IT folks (with root/admin privileges) to look into updating the Nvidia software and also install the freesurfer RPM for you.  They may already have a way to share/mount/mirror what the freesurfer RPM will install under the unique path /usr/local/freesurfer/7.1.1 from one machine to another. -R. On Nov 6, 2020, at 09:29, Snedden, Ali <Ali.Snedden(a)nationwidechildrens.org> wrote:        External Email - Use Caution        Hello, Thank you for the response.  I am working on a computer cluster where we install all user software on a shared filesystem.  Looking at the RPM, it does not seem that I can install it in a path of my choosing (i.e. not in /usr). i.e.$ rpm -qpi freesurfer-CentOS8-7.1.0-1.x86_64.rpm | head -15 | grep RelocationsRelocations : (not relocatable) Is there a strategy for installing the rpm in a custom path? Best,Ali  From: fsbuild <fsbuild@contbay.com>Date: Thursday, November 5, 2020 at 11:47 PMTo: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>Cc: "Snedden, Ali" <Ali.Snedden@nationwidechildrens.org>Subject: Re: [Freesurfer] Freesurfer 7.1.0 on CentOS 8.1 Hello Ali, I would try using the RPM installer which should at least check some dependencies on X packages, system libraries, etc.,  MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.1.1/freesurfer-C… R.  On Nov 5, 2020, at 22:39, Snedden, Ali <Ali.Snedden(a)nationwidechildrens.org> wrote:         External Email - Use Caution         Hello,  I’ve seen a couple mentions on the list-serv about difficulties using Freesurfer on CentOS 8.   My issue is likely similar, but I have a few more details.  I downloaded freesurfer-linux-centos8_x86_64-7.1.0.tar.gz.   When I launch `freeview`, it pops up a white/empty X window for a moment and then quickly disappears.   E.g. $ freeviewMESA-LOADER: failed to open swrast (search paths /usr/lib64/dri)libGL error: failed to load driver: swrastAborted (core dumped) I vaguely recall that the libGL errors _aren’t_ fatal.  I’ve seen them with other X applications.  Digging around the abort logs, I found the stack trace (see end of email).  Do you have thoughts on this?  I thought it might be a VTK compatibility issue, but that is a guess at best. Best regards,Ali  ###################### The stack trace ######################## [ccpp-2020-11-05-09:15:34-22241]# cat core_backtrace{   "signal": 6,   "executable": "/gpfs0/export/apps/opt/freesurfer/7.1.0/bin/freeview",   "only_crash_thread": true,   "stacktrace":      [ {   "crash_thread": true        ,   "frames":              [ {   "address": 140352624871839                ,   "build_id": "f796584f6ea7bb2e49cfd09412b9c6ec86eaf0fc"                ,   "build_id_offset": 227743                ,   "function_name": "raise"                ,   "file_name": "/usr/lib64/libc-2.28.so"                }              , {   "address": 140352624782581                ,   "build_id": "f796584f6ea7bb2e49cfd09412b9c6ec86eaf0fc"                ,   "build_id_offset": 138485                ,   "function_name": "abort"                ,   "file_name": "/usr/lib64/libc-2.28.so"                }              , {   "address": 140352824105729                ,   "build_id": 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"file_name": "/gpfs0/export/apps/opt/freesurfer/7.1.0/bin/freeview"                } ]        } ]} _______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_____________… mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

2 1

Editing Issues
by Harriet Cornwell 09 Nov '20

09 Nov '20

External Email - Use Caution Hi FreeSurfer team, Here are the details regarding the versions of FreeSurfer that my team are using: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 I have a couple of questions regarding editing. 1. Whilst editing one brain we discovered a small hole (see just above the cursor on Screenshot 1). Does this require any manual editing? If so, what would you recommend we do? 2. We are working with brains that were scanned at multiple sites. FreeSurfer seems to have a problem segmenting around the ventricles (see Screenshot 2) with a number of brains from one of the sites. Is this an issue that requires manual editing and if so, what do you recommend we do? If you need any further information, please let me know. Thank you in advance for any advice you can offer. Harriet PhD Student | University of Bath

2 1

BIDS-ASL request for comments - closes THIS Friday (11/13) {Disarmed}
by Franklin Feingold 09 Nov '20

09 Nov '20

External Email - Use Caution The BIDS community is preparing to merge the ASL (Arterial Spin Labeling) extension. The updated draft is available for review at: https://secure-web.cisco.com/19iI4s--bs7Y_Tdzvgf_eO4rOWt7fabvAARvcNytKJYcOi…, and comments and suggestions may be submitted on GitHub at: https://secure-web.cisco.com/1e1-qVFLFl7Vo9V2lZkAqUWA79qa_CZHfymhuxcQvkG9Oa…. The community review will close on Friday (Nov 13) at 11:59pm PT (pacific time) This BIDS extension seeks to establish how ASL data and additional metadata are organized within the BIDS structure. This encompasses the ASL sequences provided in the consensus paper [Alsop 2014], including single- and multi-time point pulsed and (pseudo)-continuous ASL. The final review entails a two week period for public commenting, with a possibility of extension for unresolved discussion. Once public comments are concluded, there will be a one week freeze, during which only critical issues will be considered. (For more details on the release protocol, see https://secure-web.cisco.com/18WQObGNOBtv6TPfRTvCtrEQv4TE4obqTEzfsuYxPZfeIy…) We look forward to hearing your feedback! The BIDS Team

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