Freesurfer

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TRACULA error wrt to dwi_orig_las.1.bvals file
by juergen.haenggi＠upd.unibe.ch 07 Dec '21

07 Dec '21

External Email - Use Caution Dear TRACULA experts I try to run TRACULA FS7.2 on a Linux machine and get the following error (see below). A similar problem has already been reported in the archives, but I found no solution. https://secure-web.cisco.com/15ekCi1WQB-CkH0WPGgECXGvPn99_mRmsow_C5M9nEA423… Because the file "dwi_orig_las.1.bvals“ was renamed to „dwi_orig_las.bvals“ earlier in the run mv -f /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.1.bvals /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.bvals it cannot be found by awk and as a result, I guess, the index.txt file is empty and therefore eddy_openmp terminated. How can I fix this problem? The terminal output, log and config files are attached. Thank you for any advise in advance Regards Jürgen —————— error ———— awk: fatal: cannot open file `/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.1.bvals' for reading (No such file or directory) eddy_openmp --imain=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.nii.gz --mask=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/lowb_orig_las_brain_mask.nii.gz --bvecs=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.bvecs --bvals=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi_orig_las.bvals --acqp=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/acqp.txt --index=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/index.txt --data_is_shelled --out=/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/dwi EddyInputError: Error when attempting to read --index file /mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_FS720/IPS_CO_007/dmri/index.txt Terminating program Linux upd-159253 4.15.0-147-lowlatency #151-Ubuntu SMP PREEMPT Fri Jun 18 20:06:19 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Wed Oct 27 13:41:49 CEST 2021 upd-159253:/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test> ——————

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FREESURFER issue making flatmap
by Alison McDonnell 06 Dec '21

06 Dec '21

External Email - Use Caution hi all, I was trying to open the inflated version after running recon all so i could make a patch and then make flatmap. when i ran mris_flatten lh.full.patch.3D lh.full.flat.patch.3D it gave an error saying there was no such file but i thought it should have been generated by recon all. them i just tried to open using freeview amd it said it couldnt determine the file type. if anyone has any idea whats going on that would be great. ive attached screenshot of the terminal showing the error messages and what i tried to do. it also took a very long time to run recon all but then ended with no errors so i dont know what problems came up then. thanks, Ali

2 15

follow-up on trac-all -prep -c error
by Salar Dini, Elaheh 04 Dec '21

04 Dec '21

External Email - Use Caution Hello Anastasia, Thank you so much for your response. It was very useful. I have changed the config file to the one I'm attaching to this message, but I'm still getting the same error: ERROR: for B0 distortion correction with reverse-polarity DWIs ERROR: or for model-based eddy-current distortion correction, ERROR: must specify PE direction I don't get any log for error file in this instance too. However, if I change the doeddy from default=2 to 1, it starts to work with an error later on. I'm attaching the log file, and error file for tra-all with doeddy=1 to this message too. Lastly, I wanted to ask if the fact that we ran recon-all with freesurfer version 6 and do the TRACULA with version 7.2.0 is problematic here? In other words, should the segmentation of T1 be done by same version of freesurfer as the one that trac-all is used from? Thanks again very much for your help. Ela

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trac-all -prep -c error
by Salar Dini, Elaheh 03 Dec '21

03 Dec '21

External Email - Use Caution Hi all, I am trying to run trac-all -prep -c dmrirc1.txt, with dmrirc1.txt being the configuration file. As soon as I attempt, I get the following error: ERROR: for B0 distortion correction with reverse-polarity DWIs ERROR: or for model-based eddy-current distortion correction, ERROR: must specify PE direction I am attaching the dmrirc1.txt to this message. The FreeSurfer segmentations of T1, produced by running Freesurfer recon-all, was done using freesurfer version 6. We try to run trac-all using freesurfer version 7.2.0. Interestingly, we don’t face the same error when we tried running trac-all using version 6 of freesurfer. Lastly, it is worth mentioning that no dmri folder has been made after running trac-all, and there is no trac-all log file in the script folder. 1) FreeSurfer version: freesurfer-CentOS7-7.2.0-1.x86_64.rpm. (Build-stamp text: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b) 2) Platform: CentOS7 Thank you and Kind regards, Ela Salardini

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TRACULA error
by Stephanie Otto 02 Dec '21

02 Dec '21

External Email - Use Caution Hello Freesurfer Team, I am trying to get TRACULA running on two different machines (Macbook Pro OS 11.6 and Mac desktop OS 10.14.6). I get the same error message on both devices, which is: domainname: Command not found. ERROR: for B0 distortion correction with reverse-polarity DWIs ERROR: or for model-based eddy-current distortion correction, ERROR: must specify PE direction I can't find an answer as to how to correct this in the email support archive or through Google. If anyone could assist me, I would greatly appreciate it. Thanks in advance for all your help. Best, Stephanie Otto Doctoral Candidate, Cognitive and Brain Sciences Program Department of Psychology, MSS 424/MS0296 University of Nevada, Reno sotto(a)nevada.unr.edu

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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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