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30076 discussions

Passcode VM
by Marius Zeinhofer 05 May '22

05 May '22

External Email - Use Caution Hi, I am interested in the passcode for the VM as explained on the Freesurfer website. Thank you very much. Best, Marius

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recon-all -long error (the third step of the longitudinal pipeline)
by FONG, manson CM [CBS] 05 May '22

05 May '22

External Email - Use Caution Hello Experts, I'm attempting to run the longitudinal pipeline, as described in this tutorial page (https://secure-web.cisco.com/1Ixk7gG7cuuWHkljgthBFn12YPhnTaeVaFK7XUh0r8RABW…) I've tried the pipeline on 13 subjects (from the Alzheimer Disease Neuroimaging Initiative), each with varying number of time points. For all of them, I succeeded in the first two steps ( [CROSS] & [BASE] ), but recon-all threw an error for all subjects & for all time-points midway through the third step ( [LONG] ). For example, for the subject 128_S_4832, I've run the cross-sectional step for all time points, resulting in corresponding folders called $SUBJECTS_DIR/128_S_4832_Ses01 and so on, and a template in the folder $SUBJECTS_DIR/128_S_4832 (from the [BASE] step). The exact command that exited with ERRORS was: recon-all -long 128_S_4832_Ses01 128_S_4832 -all -parallel -openmp 16 Like in the first two step, I was using parallel computing with 16 cores. From recon-all.log in the folder $SUBJECTS_DIR/128_S_4832_Ses01.long.128_S_4832/scripts, it appears that the last command that reported no issue was: mris_curvature -seed 1234 -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated After this step, recon-all threw an error. The last four lines in my log file are: Usage: reconbatchjobs logfile cmdfile1 [cmdfile2 ...] See recon-all script for examples. Linux ubda-d050 3.10.0-693.21.1.el7.x86_64 #1 SMP Wed Mar 7 19:03:37 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 128_S_4832_Ses01.long.128_S_4832 exited with ERRORS at Sat Apr 30 22:10:07 HKT 2022 I've searched the list and no similar errors have been reported. 1) FreeSurfer version: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b 2) Platform: CentOS Linux 7 (Core) 3) recon-all.log & recon-all.error: see attached Many thanks for your advice in advance! Best regards, Manson Fong [https://secure-web.cisco.com/1RCpfhD31IvrvhPAqouiPEccsev2Meg7QPUJ7MSltmEQqz…] Disclaimer: This message (including any attachments) contains confidential information intended for a specific individual and purpose. If you are not the intended recipient, you should delete this message and notify the sender and The Hong Kong Polytechnic University (the University) immediately. Any disclosure, copying, or distribution of this message, or the taking of any action based on it, is strictly prohibited and may be unlawful. The University specifically denies any responsibility for the accuracy or quality of information obtained through University E-mail Facilities. Any views and opinions expressed are only those of the author(s) and do not necessarily represent those of the University and the University accepts no liability whatsoever for any losses or damages incurred or caused to any party as a result of the use of such information.

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segmentHA_T1, mri_segstats: How can I get the PVC uptake for amygdalar nuclei?
by Tun, Samantha 05 May '22

05 May '22

External Email - Use Caution Hello Freesurfer Devs! I am attempting to extract the tau uptake in the amygdalar segmentations. I ran this command: mri_segstats --seg rh.hippoAmygLabels-T1.v21.FS60.FSvoxelSpace.mgz --i anat_resliced.mgz --sum rHA_stats.dat to try and calculate the tau uptake. I was able to get an output, but I am unsure how to proceed from here. I basically want to get the pvc uptake of the amygdalar and hippocampal subfields scaled to the pons. I don't think I can run the mri_gtmpvc command, so if you had any insight on how to calculate the scaled uptake of tau in the subfields, let me know! Best, Samantha

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Scalable recon workflow
by Horn, Mitchell Jacob 05 May '22

05 May '22

Hi Experts, If I have 100s of subjects to recon and have access to an HPC with both GPU and CPU options what is the recommended flags to maximize speed performance? Is … -parallel -openmp 4 … still the best approach? And if so, is 2GB memory/core best (keeping it 8GB memory/subject) or is there some better arrangement? Best, Mitch

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"B0 distortion correction with reverse-polarity DWIs"
by Gonzalo Rojas Costa 04 May '22

04 May '22

External Email - Use Caution Hi: I tried to process a tractography with TRACULA. I got the error "ERROR: for B0 distortion correction with reverse-polarity DWIs. ERROR: or for model-based eddy-current distortion correction, ERROR: must specify PE direction". What does it mean? I read the webpage https://secure-web.cisco.com/1guG1MnfZf84DwQHfWaHHLuw6SMY7Z-tutMOyUkvQB8sNK…, but It was not clear to me how to solve the problem. Sincerely, Gonzalo Rojas Costa Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 http://secure-web.cisco.com/12GtciP9OUiW5DkspMfrRVy3WsQH7lo4AsKjg0Sj8uml6hm… https://secure-web.cisco.com/1MqLKS1F46RbplHUM6h_KNyjN0BiKcyL58vxd1gCfQMyaz… https://secure-web.cisco.com/1VYyKt8bpinu3O6RicUYTbOJmllqjZD8fa4vMdxnypEQay… https://secure-web.cisco.com/1cDJNj5GQNOJNQJmRBcgfx71cRT_O6MgqP1ftnJlfUY5Nu… http://secure-web.cisco.com/1FaAL_RhtLAORTKofMH0umP03Sz7z4fz1ix6_BxtTBFSkxZ… https://secure-web.cisco.com/1Chz4Nd2Gs4bv5UU_W7XXxgXJhQCBYB_9QHiTrY3XemPxP…

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TRACULA question
by Gonzalo Rojas Costa 04 May '22

04 May '22

External Email - Use Caution Hi: Is it possible to use input diffusion files in MOSAIC IMA Siemens file format directly? Or is it necessary to convert to nifti file format first? Sincerely, Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 https://secure-web.cisco.com/13PUT3U3zuLu0QBvcZiGdm18njGuoQr6dUsSQj9e5H3gOi… https://secure-web.cisco.com/1TdZ-Zm0eaCvN4RyCzzXuq6HNPTVfbbxwGyNTIGMGFiRfy… https://secure-web.cisco.com/1lJu3jBI0nOfv9_IwBeCbcBNGA2K6pj5tSumDqMfk3ZItR… http://secure-web.cisco.com/1vs-E3PvUdSdie9Xm5LpQNiLpowx1KB-bnADkKZ76Vp4VAN… https://secure-web.cisco.com/1FM_I0dgNRRtoYqJmIXPdHgx__9woRyRSo5bnLSxgt51fC…

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meanings of trac-all outputs
by Zeng, Qi 04 May '22

04 May '22

External Email - Use Caution Hi experts, Just want to check if dmri/dwi.nii.gz is the 4D dwi volumes after correction for B0 inhomogeneities, eddy current, and head motion? and dmri/nodif_brain_mask.nii.gz is the 3D ROI mask for the whole brain? and dmri/bvals and dmri/bvecs are rotated bvals and rotated bvecs? Thank you! Best, Qi

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Open research assistant position at Ohio State University (please share!)
by Osher, David E. 04 May '22

04 May '22

External Email - Use Caution The Cognition and Brain Circuitry Laboratory at the Ohio State University is recruiting a research assistant. Primary duties include: conducting neuroscience research on the functional and structural architecture of the human brain, and its role in cognition; programming, running, and analyzing behavioral and brain-imaging experiments using functional magnetic resonance imaging (fMRI), diffusion weighted imaging (DWI), functional connectivity, and behavioral assessments; scoring and coding data; performing statistical analyses using programs such as, MATLAB, Python, and shell scripting; recruiting research participants; maintaining participant databases; developing outreach letters. The position is available for one year with the possibility of extension based on satisfactory performance and availability of funds. Required qualifications include: Bachelor's degree in psychology, neuroscience, cognitive science, computer science, data science, engineering, physics, or math; conduct of social science research is required; experience in a social science research capacity. Highly desired: strong mathematical, statistical, and coding skills (e.g., MATLAB, Python, shell scripting); strong interpersonal skills for interacting with a diverse group of people; strong organizational skills. This position is an excellent opportunity for individuals considering future graduate studies in cognitive and computational neuroscience (every one of our research assistants has successfully been admitted into doctoral programs!). We are seeking an aspiring, self-motivated researcher with strong coding/programming skills who is excited about the brain, cognitive neuroscience, and/or clinical disorders and demonstrates evidence of a serious interest in a career in the field. If you are interested in being considered for these positions, please apply online at https://secure-web.cisco.com/1a8p8qGhoqso6oYBkudeXI8_eqsXtlC6hqmGfFmjR86taA… and submit a current CV and names of three references. If you have questions about the position or the lab, please contact Dr. David Osher at osher.6(a)osu.edu<mailto:osher.6@osu.edu> The Ohio State University is an equal opportunity employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation or identity, national origin, disability status, or protected veteran status. _____________________________________ David E. Osher, Ph.D. Assistant Professor of Psychology The Ohio State University davidosher.com<https://secure-web.cisco.com/1lqk_MmIM3fJEV2RfMCA4jAX9cFL53d2oDdw2rc_wWO1FR…>

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Probabilistic atlas of human thalamic nuclei
by Asa Borzabadi Farahani 03 May '22

03 May '22

External Email - Use Caution Dear Experts, I would really appreciate it if you could help me with this question: I would like to use the probabilistic atlas of human thalamic nuclei; provided by Iglesias et al. (2018); as a prior knowledge to locate the LGN within my subjects (prior knowledge would be the Atlas, the functional/structural data of subjects would be available and hence, I assume I would be able to get a better estimate for the location of LGN within the subjects). In order to do so, I need this probabilistic map to be available in the MNI or the fsaverage space. May I ask your opinion about this approach? Do you think it is feasible to have these probabilistic atlases in the MNI/fsaverage space? Best Regards, Asa Farahani

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Re: [Freesurfer] Permission denied error from -localGI
by Billah, Tashrif 02 May '22

02 May '22

Thank you Douglas. We took our time to install FreeSurfer 7.2 and retry. However, we ran into the same error: >> reading filled volume... /bin/bash: /scratch/tp44447785365264536.load_mgh.m.mgh: Permission denied ERROR: could not open /scratch/tp44447785365264536.load_mgh.m.mgh for reading ERROR: loading /data/pnl/FS_SUBJECTS_DIR/1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz as MGH Struct contents reference from a non-struct array object. Error in make_outer_surface (line 25) volume=vol.vol; >> ERROR: make_outer_surface did not create output file What can we do now? -Tashrif =================== Douglas N. Greve Wed, 27 Apr 2022 07:51:33 -0700 Can you just try it with 7.2? We had some problems at one point with temporary files in lGI that were fixed with 7.2 =================== On 4/27/2022 9:36 AM, Billah, Tashrif wrote: Sorry about missing your earlier question--our FreeSurfer is 7.1.0 We still need your help with this issue. Thank you, Tashrif Douglas N. Greve Sun, 27 Mar 2022 13:57:02 -0700 =================== What version of FS are you running? On 3/20/2022 8:47 PM, Billah, Tashrif wrote: It does not exist and cannot be created in a shared cluster. Is there a way to define a different folder for /scratch/tp24093955057547375.load_mgh.m.mgh? =============== Douglas N. Greve Wed, 09 Mar 2022 10:04:31 -0800 Do you have permission to /scratch? Does it exist? =============== Billah, Tashrif Wed, 02 Mar 2022 06:50:41 -0800 Hi all, We are trying to run recon-all with -localGI but running into an unknown permission denied error: $ recon-all -s sub-1001 -localGI ``` make_outer_surface('/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'); exit ================= < M A T L A B (R) > Copyright 1984-2017 The MathWorks, Inc. R2017a (9.2.0.556344) 64-bit (glnxa64) March 27, 2017 >> reading filled volume... /bin/bash: /scratch/tp24093955057547375.load_mgh.m.mgh: Permission denied ERROR: could not open /scratch/tp24093955057547375.load_mgh.m.mgh for reading ERROR: loading /path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz as MGH Struct contents reference from a non-struct array object. Error in make_outer_surface (line 25) volume=vol.vol; >> ERROR: make_outer_surface did not create output file '/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'! recon-all -s sub-1001 exited with ERRORS at Wed Mar 2 09:02:21 EST 2022 ``` Our MATLAB environment is properly setup and we regularly run other FreeSurfer-MATLAB commands. So I do not think that is causing the issue. Best, Tashrif

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