Freesurfer

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30131 discussions

trac-all -prep error
by Arman Avesta 02 Dec '21

02 Dec '21

External Email - Use Caution Hi gang, I'm trying to run trac-all -prep on a number of cases, and I'm getting an error. I've attached the config and log files for two cases. I would really appreciate your help. Best,Arman

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Postdoctoral Fellowship at MGH/HMS in *Advanced Ultra High-Field Imaging and Analysis of Brain Vasculature*
by Polimeni, Jonathan R. 02 Dec '21

02 Dec '21

POSTDOCTORAL RESEARCH FELLOW — ADVANCED ULTRA HIGH-FIELD IMAGING AND ANALYSIS OF BRAIN VASCULATURE Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital (MGH) Harvard Medical School A post-doctoral research fellowship in Ultra-High Field MRI data analysis and acquisition is available at the Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital (MGH). The successful candidate will be working in the High-Resolution and Ultra-High-Field Functional Imaging Group led by Dr. Jonathan Polimeni to both develop and apply advanced methods for imaging brain vasculature. This NIH-funded project seeks to improve segmentation accuracy of fine-scale features of the neurovasculature, including mesoscale blood vessels and regional capillary density. The focus of this fellowship will be to build upon existing analytic methods developed in our laboratory, however there will be opportunities to improve upon high-resolution, quantitative in vivo vascular imaging acquisition methods as well. The vascular imaging data will mainly be based on MRI, however there will be opportunities for applying these tools to microscopy and histology data. These vascular data will be utilized to characterize the basic anatomy of brain vasculature, to compare the vascular anatomy across patient groups, and to use these data to help interpret high-resolution functional MRI. Thus, candidates with an interest in developing clinical applications of vascular imaging using Ultra-High-Field MRI, and in integrating multi-modal neuroimaging data, are strongly encouraged to apply. The successful candidate will be a highly motivated researcher with a desire to begin an independent career related to or involving advanced human neuroimaging. The ideal candidate would have a strong analytical background and a high level of creativity. The ideal candidate would also hold a Ph.D. degree in Neuroscience, MR Physics, Biomedical Engineering, or a related field; however, strong candidates with other scientific backgrounds will also be considered. First-hand experience with conducting human MRI experiments is highly desired, and skills in image segmentation and training in fMRI data analysis are also desired; knowledge of cerebrovascular anatomy and human neuroscience are also highly desired. Interested candidates with electrical engineering or computer science and a strong background in medical imaging may also apply, and are welcome to inquire about suitability beforehand. ADDITIONAL SKILLS/ABILITIES/COMPETENCIES Candidates should be enthusiastic about working in a fast-paced, interdisciplinary environment. The successful candidate will be able to work both independently and collaboratively in a large multi-institutional project. Strong written and oral English communication skills are required. APPLICATION Interested applicants should send a cover letter describing research experience, interests, and future research and career goals, as well as an up-to-date curriculum vitae and contact information for three references, to Jonathan Polimeni, Ph.D., by email: jonp(a)nmr.mgh.harvard.edu. Questions regarding this position and informal inquiries should be directed to Jonathan Polimeni, Ph.D., by email: jonp(a)nmr.mgh.harvard.edu. This position is full-time with benefits and is available immediately. The Massachusetts General Hospital and Harvard Medical School are an equal opportunity employer, and all qualified applicants will receive consideration for employment without regard to race, color, religion, sex, national origin, disability status, protected veteran status, gender identity, sexual orientation, pregnancy and pregnancy-related conditions or any other characteristic protected by law. Jonathan R. Polimeni, Ph.D. Assistant Professor of Radiology, Harvard Medical School Assistant in Biomedical Engineering, Massachusetts General Hospital Affiliated Faculty, Harvard-MIT Division of Health Sciences and Technology Director of Ultra-High-Field Imaging, Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth St. Suite 2301 Charlestown, MA 02129 USA tel: +1 617-724-4546 https://www.nmr.mgh.harvard.edu/lab/mr-pig

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Queries on DK Atlas and No of regions
by Koustav Chatterjee 01 Dec '21

01 Dec '21

External Email - Use Caution Dear all, I had an understanding that Desikan-Killiiany atlas can parcellate total of 68 regions from both hemispheres. However, after running recon-all -all, I can see total of 62 regions. I am afraid if you could help me understanding these discrepancies.. Thank you for your help. Regards, KC

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Re: [Freesurfer] trac-all -prep error
by fsbuild 01 Dec '21

01 Dec '21

External Email - Use Caution Hello Arman, The first error indicates there is a file missing from under fsl/bin, /usr/local/fsl/bin/eddy_correct: line 95: /usr/local/fsl/bin/imglob: No such file or directory - which makes me think something may not be correct with how fsl is setup/installed on your machine. - R. On Dec 1, 2021, at 10:35, Arman Avesta <avesta.arman(a)yahoo.com> wrote:        External Email - Use Caution        Hi gang,I'm trying to run trac-all -prep on a number of cases, and I'm getting an error. I've attached the config and log files for two cases.. I would really appreciate your help.Best,Arman<dmrirc1.txt><dmrirc2.txt><trac-all.log><trac-all.log>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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2x2 ANOVA, tp2-tp1 is not an option for study design
by stdp82＠virgilio.it 01 Dec '21

01 Dec '21

External Email - Use Caution Hi list, I have two groups undergoing two different treatments: one's placebo (n=12), one's drug (n=12). Two timepoints, at baseline (T1, no treatment) and at treatment (T2). 2x2 ANOVA, repeted measures has been applied by following the guidlines and mailing list. to compute tp2-tp1, as reported in the fsgd example, is not an option for study design because we aiming to assess the interaction time-x-group.treatment Please chech the design matrix, the command line produces an error. GroupDescriptorFile 1 Title 2x2_repeted_measures Class Subject1 Class Subject2 Class Subject3 Class Subject4 Class Subject5 Class Subject6 Class Subject7 Class Subject8 Class Subject9 Class Subject10 Class Subject11 Class Subject12 Class Subject13 Class Subject14 Class Subject15 Class Subject16 Class Subject17 Class Subject18 Class Subject19 Class Subject20 Class Subject21 Class Subject22 Class Subject23 Class Subject24 Variables tp1-vs-tp2.drug tp1-vs-tp2.plb Input CODE01_tp1 Subject1 1 0 Input CODE02_tp1 Subject2 1 0 Input CODE03_tp1 Subject3 1 0 Input CODE05_tp1 Subject4 1 0 Input CODE06_tp1 Subject5 0 1 Input CODE07_tp1 Subject6 0 1 Input CODE09_tp1 Subject7 0 1 Input CODE10_tp1 Subject8 1 0 Input CODE11_tp1 Subject9 1 0 Input CODE12_tp1 Subject10 0 1 Input CODE13_tp1 Subject11 0 1 Input CODE14_tp1 Subject12 1 0 Input CODE15_tp1 Subject13 1 0 Input CODE16_tp1 Subject14 1 0 Input CODE17_tp1 Subject15 0 1 Input CODE18_tp1 Subject16 1 0 Input CODE19_tp1 Subject17 0 1 Input CODE20_tp1 Subject18 0 1 Input CODE21_tp1 Subject19 0 1 Input CODE22_tp1 Subject20 1 0 Input CODE23_tp1 Subject21 0 1 Input CODE24_tp1 Subject22 0 1 Input CODE25_tp1 Subject23 1 0 Input CODE26_tp1 Subject24 0 1 Input CODE01_tp2 Subject1 -1 0 Input CODE02_tp2 Subject2 -1 0 Input CODE03_tp2 Subject3 -1 0 Input CODE05_tp2 Subject4 -1 0 Input CODE06_tp2 Subject5 0 -1 Input CODE07_tp2 Subject6 0 -1 Input CODE09_tp2 Subject7 0 -1 Input CODE10_tp2 Subject8 -1 0 Input CODE11_tp2 Subject9 -1 0 Input CODE12_tp2 Subject10 0 -1 Input CODE13_tp2 Subject11 0 -1 Input CODE14_tp2 Subject12 -1 0 Input CODE15_tp2 Subject13 -1 0 Input CODE16_tp2 Subject14 -1 0 Input CODE17_tp2 Subject15 0 -1 Input CODE18_tp2 Subject16 -1 0 Input CODE19_tp2 Subject17 0 -1 Input CODE20_tp2 Subject18 0 -1 Input CODE21_tp2 Subject19 0 -1 Input CODE22_tp2 Subject20 -1 0 Input CODE23_tp2 Subject21 0 -1 Input CODE24_tp2 Subject22 0 -1 Input CODE25_tp2 Subject23 -1 0 Input CODE26_tp2 Subject24 0 -1 a) groupxtime.mtx 0 0 1 -1 b) tp1-vs-tp2.Mod.mtx 0 0 1 0 c) tp1-vs-tp2.Plb.mtx 0 0 0 -1 mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --surface fsaverage rh --glmdir repeted_measures.wls --nii.gz --fsgd Repeted_measure.fsgd --C Tp1-vs-Tp2.Mod.mtx --C Tp1-vs-Tp2.Plb.mtx --C groupxtime.mtx ERROR: dimension mismatch between X and contrast Tp1-vs-Tp2.Mod.mtx X has 72 cols, C has 4 cols

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Anova 2x2 longitudinal
by stdp82＠virgilio.it 30 Nov '21

30 Nov '21

External Email - Use Caution Hi list, I have two groups undergoing two different treatments: one's placebo (n=12), one's drug (n=12). Two timepoints, at baseline (T1, no treatment) and at treatment (T2). 2x2 ANOVA, repeted measures has been applied by following the guidlines and mailing list. to compute tp2-tp1 is not an option for study design. Please chech the design matrix, the command line produces an error. GroupDescriptorFile 1 Title 2x2_repeted_measures Class Subject1 Class Subject2 Class Subject3 Class Subject4 Class Subject5 Class Subject6 Class Subject7 Class Subject8 Class Subject9 Class Subject10 Class Subject11 Class Subject12 Class Subject13 Class Subject14 Class Subject15 Class Subject16 Class Subject17 Class Subject18 Class Subject19 Class Subject20 Class Subject21 Class Subject22 Class Subject23 Class Subject24 Variables tp1-vs-tp2.drug tp1-vs-tp2.plb Input CODE01_tp1 Subject1 1 0 Input CODE02_tp1 Subject2 1 0 Input CODE03_tp1 Subject3 1 0 Input CODE05_tp1 Subject4 1 0 Input CODE06_tp1 Subject5 0 1 Input CODE07_tp1 Subject6 0 1 Input CODE09_tp1 Subject7 0 1 Input CODE10_tp1 Subject8 1 0 Input CODE11_tp1 Subject9 1 0 Input CODE12_tp1 Subject10 0 1 Input CODE13_tp1 Subject11 0 1 Input CODE14_tp1 Subject12 1 0 Input CODE15_tp1 Subject13 1 0 Input CODE16_tp1 Subject14 1 0 Input CODE17_tp1 Subject15 0 1 Input CODE18_tp1 Subject16 1 0 Input CODE19_tp1 Subject17 0 1 Input CODE20_tp1 Subject18 0 1 Input CODE21_tp1 Subject19 0 1 Input CODE22_tp1 Subject20 1 0 Input CODE23_tp1 Subject21 0 1 Input CODE24_tp1 Subject22 0 1 Input CODE25_tp1 Subject23 1 0 Input CODE26_tp1 Subject24 0 1 Input CODE01_tp2 Subject1 -1 0 Input CODE02_tp2 Subject2 -1 0 Input CODE03_tp2 Subject3 -1 0 Input CODE05_tp2 Subject4 -1 0 Input CODE06_tp2 Subject5 0 -1 Input CODE07_tp2 Subject6 0 -1 Input CODE09_tp2 Subject7 0 -1 Input CODE10_tp2 Subject8 -1 0 Input CODE11_tp2 Subject9 -1 0 Input CODE12_tp2 Subject10 0 -1 Input CODE13_tp2 Subject11 0 -1 Input CODE14_tp2 Subject12 -1 0 Input CODE15_tp2 Subject13 -1 0 Input CODE16_tp2 Subject14 -1 0 Input CODE17_tp2 Subject15 0 -1 Input CODE18_tp2 Subject16 -1 0 Input CODE19_tp2 Subject17 0 -1 Input CODE20_tp2 Subject18 0 -1 Input CODE21_tp2 Subject19 0 -1 Input CODE22_tp2 Subject20 -1 0 Input CODE23_tp2 Subject21 0 -1 Input CODE24_tp2 Subject22 0 -1 Input CODE25_tp2 Subject23 -1 0 Input CODE26_tp2 Subject24 0 -1 a) groupxtime.mtx 0 0 1 -1 b) tp1-vs-tp2.Mod.mtx 0 0 1 0 c) tp1-vs-tp2.Plb.mtx 0 0 0 -1 mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --surface fsaverage rh --glmdir repeted_measures.wls --nii.gz --fsgd Repeted_measure.fsgd --C Tp1-vs-Tp2.Mod.mtx --C Tp1-vs-Tp2.Plb.mtx --C groupxtime.mtx ERROR: dimension mismatch between X and contrast Tp1-vs-Tp2.Mod.mtx X has 72 cols, C has 4 cols

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Which file should be used as the result of automatic freesurfer segmentation?
by 1248742467 30 Nov '21

30 Nov '21

External Email - Use Caution I am going to use Freesurfer to compare the results of automatic segmentation with our proposed method. The label I use is lh.label.DKT31.manual.annot in the mindboggle dataset, so which automatic segmentation result should be used? In addition, are there any references that have relevant segmentation results that I can use directly?

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Information on anova 2x2 longitudinal design
by stdp82＠virgilio.it 30 Nov '21

30 Nov '21

External Email - Use Caution Hi list, I have two groups undergoing two different treatments: one's placebo (n=12), one's drug (n=12). Two timepoints, at baseline (T1, no treatment) and at treatment (T2). 2x2 ANOVA, repeted measures has been applied by following the guidlines and mailing list. Please chech the design matrix, the command line produces an error. GroupDescriptorFile 1 Title 2x2_repeted_measures Class Subject1 Class Subject2 Class Subject3 Class Subject4 Class Subject5 Class Subject6 Class Subject7 Class Subject8 Class Subject9 Class Subject10 Class Subject11 Class Subject12 Class Subject13 Class Subject14 Class Subject15 Class Subject16 Class Subject17 Class Subject18 Class Subject19 Class Subject20 Class Subject21 Class Subject22 Class Subject23 Class Subject24 Variables tp1-vs-tp2.drug tp1-vs-tp2.plb Input CODE01_tp1 Subject1 1 0 Input CODE02_tp1 Subject2 1 0 Input CODE03_tp1 Subject3 1 0 Input CODE05_tp1 Subject4 1 0 Input CODE06_tp1 Subject5 0 1 Input CODE07_tp1 Subject6 0 1 Input CODE09_tp1 Subject7 0 1 Input CODE10_tp1 Subject8 1 0 Input CODE11_tp1 Subject9 1 0 Input CODE12_tp1 Subject10 0 1 Input CODE13_tp1 Subject11 0 1 Input CODE14_tp1 Subject12 1 0 Input CODE15_tp1 Subject13 1 0 Input CODE16_tp1 Subject14 1 0 Input CODE17_tp1 Subject15 0 1 Input CODE18_tp1 Subject16 1 0 Input CODE19_tp1 Subject17 0 1 Input CODE20_tp1 Subject18 0 1 Input CODE21_tp1 Subject19 0 1 Input CODE22_tp1 Subject20 1 0 Input CODE23_tp1 Subject21 0 1 Input CODE24_tp1 Subject22 0 1 Input CODE25_tp1 Subject23 1 0 Input CODE26_tp1 Subject24 0 1 Input CODE01_tp2 Subject1 -1 0 Input CODE02_tp2 Subject2 -1 0 Input CODE03_tp2 Subject3 -1 0 Input CODE05_tp2 Subject4 -1 0 Input CODE06_tp2 Subject5 0 -1 Input CODE07_tp2 Subject6 0 -1 Input CODE09_tp2 Subject7 0 -1 Input CODE10_tp2 Subject8 -1 0 Input CODE11_tp2 Subject9 -1 0 Input CODE12_tp2 Subject10 0 -1 Input CODE13_tp2 Subject11 0 -1 Input CODE14_tp2 Subject12 -1 0 Input CODE15_tp2 Subject13 -1 0 Input CODE16_tp2 Subject14 -1 0 Input CODE17_tp2 Subject15 0 -1 Input CODE18_tp2 Subject16 -1 0 Input CODE19_tp2 Subject17 0 -1 Input CODE20_tp2 Subject18 0 -1 Input CODE21_tp2 Subject19 0 -1 Input CODE22_tp2 Subject20 -1 0 Input CODE23_tp2 Subject21 0 -1 Input CODE24_tp2 Subject22 0 -1 Input CODE25_tp2 Subject23 -1 0 Input CODE26_tp2 Subject24 0 -1 a) groupxtime.mtx 0 0 1 -1 b) tp1-vs-tp2.Mod.mtx 0 0 1 0 c) tp1-vs-tp2.Plb.mtx 0 0 0 -1 mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --surface fsaverage rh --glmdir repeted_measures.wls --nii.gz --fsgd Repeted_measure.fsgd --C Tp1-vs-Tp2.Mod.mtx --C Tp1-vs-Tp2.Plb.mtx --C groupxtime.mtx ERROR: dimension mismatch between X and contrast Tp1-vs-Tp2.Mod.mtx X has 72 cols, C has 4 cols

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Re: [Freesurfer] Developer Password
by fsbuild 29 Nov '21

29 Nov '21

External Email - Use Caution Hello Art, Sending the login and update info to your email shortly. - R. On Nov 29, 2021, at 12:18, art.spam(a)web.de wrote:        External Email - Use Caution        Dear freesurfer team, following the instructions on installing the latest freesurfer version on a Windows hosted VirtualBox I'm asked for a developer password on booting.I couldn't find the password anywhere and saw in the archives that people ran into this before as well.Would you please forward me the login data?  Thanks in advance and kind regards, Art Sto _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Freeview.app crashing
by fsbuild 29 Nov '21

29 Nov '21

External Email - Use Caution Hello Christian, There is a posting on the freesurfer mail list talking about in general how to deal with freeview crashing on the Mac, but I will send it again to your email. https://secure-web.cisco.com/1e1jc_fAfWM9bqCzlGbCbme4yrpDt-91dbT3jRnUtzP-Lh… I you are working on macOS 11.X BigSur, then I would try getting a new license as older licenses have caused problems.  The link to the license form is, https://secure-web.cisco.com/19eqyrgyBwTeifm0ka9IWTt4P_siVrEJ-U2hnNgRBrwlvV… - R. On Nov 26, 2021, at 12:52, ChristianBauer <christian.bauer(a)ovgu.de> wrote:        External Email - Use Caution        Dear Freesurfer experts,I am having issues with opening Freeview. I am currently using Freesurfer v.7.2.0 and I had no problems setting up Freeusurfer and Freeview on my Desktop computer. However, I have had issues with Freeview crashing on my Mac laptop every now and then and now I cannot open Freeview at all  The error message I am getting is a s follows/Applications/freesurfer/7.2.0/bin/freeview: line 2:  3185 Segmentation fault: 11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@“I have tried downloading and reinstalling Freesurfer several times as well as trying the stand-alone version. I have also changed the license file as was previously suggested by one of your team. Any advice would be greatly appreciated.Thanks in advance,Christian_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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