Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30070 discussions

3T Intensity Normalization (Re-Submission)
by David S Lee 29 Jun '18

29 Jun '18

External Email - Use Caution Hello Experts, I believe -3T Flag can be used with "recon-all" on scans collected by 3T scanners. I believe it performs intensity normalization to set white matter intensity threshold at 110. I am hoping to learn more about the flag option as it produces slightly better output for me. Would you be able to guide me to a documentation on this -3T flag? Thank you! -- David S. Lee Associate Research Specialist Center for Healthy Minds University of Wisconsin - Madison (608) 890-1115

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Poor occipital signal and low contrast
by Chawla, Megha 28 Jun '18

28 Jun '18

External Email - Use Caution Hi, I have scans for ~60 participants, and for some reason the scans are of visibly poor quality when I convert them to .mgz (blurry, very low contrast). The white boundary also seems to exclude considerable white matter in the occipital in about half of the scans. Because of the extremely low contrast, I am unable to manually add control points as I cannot visibly tell the difference between wm and gm. I am attaching orig.mgz for one participant here. Acquisition parameters for these scans were: High-resolution T1-weighted anatomical images (1 × 1 × 1 mm3) were acquired with an MPRAGE pulse sequence (TI=900 ms, sagittal slices, 256 × 256 matrix) using a Siemens Allegra 3T head-only scanner. I tried running more iterations of during the nu_correct (as suggested here: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2008-November/008985…) using the following command: mc2835% recon-all -autorecon1 -nuintensitycor -nuiterations 10 -subjid 30026_FS but got the following error: ERROR: Flag -nuiterations unrecognized. -autorecon1 -nuiterations 10 -subjid 30026_FS Darwin Ifats-Mac-Pro.med.yale.internal 16.7.0 Darwin Kernel Version 16.7.0: Thu Jun 15 17:36:27 PDT 2017; root:xnu-3789.70.16~2/RELEASE_X86_64 x86_64 recon-all -s exited with ERRORS at Tue Jun 19 14:56:04 EDT 2018 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Is there any way to salvage this data for analysis? Any help will be really appreciated. Thank you! Megha

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Errors in scans
by Nasiriavanaki, Zahra 28 Jun '18

28 Jun '18

Hi Freesufer developers We are getting some errors in our resting state and ASL scans. Everything goes fine while we are scaning the subjects, but when we look at the data in BORGET, some of them come out with errors. I copied one of the scaninfo files, so you can see the errors. Is there anyway to not get errors? Or shall we just unpack the ok data and go on? Thanks 1 localizer_64ch ok 512 512 3 1 MR.1.3.12.2.1107.5.2.43.67026.2018062716282052566788535 2 AAHead_Scout ok 160 160 128 1 MR.1.3.12.2.1107.5.2.43.67026.2018062716283612565588717 3 AAHead_Scout ok 162 162 5 1 MR.1.3.12.2.1107.5.2.43.67026.2018062716284031754889708 4 AAHead_Scout ok 162 162 3 1 MR.1.3.12.2.1107.5.2.43.67026.2018062716284031832189712 5 AAHead_Scout ok 162 162 3 1 MR.1.3.12.2.1107.5.2.43.67026.2018062716284031887889715 6 MEMPRAGE ok 256 256 176 4 MR.1.3.12.2.1107.5.2.43.67026.2018062716353836176490274 7 MEMPRAGE ok 256 256 176 4 MR.1.3.12.2.1107.5.2.43.67026.2018062716353836150890273 8 MEMPRAGE ok 256 256 176 1 MR.1.3.12.2.1107.5.2.43.67026.2018062716353850258890299 9 fMRI_DistortionMap_PA ok 92 92 57 1 MR.1.3.12.2.1107.5.2.43.67026.2018062716372672952394688 10 fMRI_DistortionMap_AP ok 92 92 57 1 MR.1.3.12.2.1107.5.2.43.67026.2018062716380680499794923 11 ep2d_bold_SMS3_PAT2_2p5iso ok 92 92 57 180 MR.1.3.12.2.1107.5.2.43.67026.2018062716403982376595295 12 ep2d_bold_SMS3_PAT2_2p5iso ok 92 92 57 180 MR.1.3.12.2.1107.5.2.43.67026.2018062716480447089626419 13 ep2d_bold_SMS3_PAT2_2p5iso ok 92 92 57 180 MR.1.3.12.2.1107.5.2.43.67026.2018062716552453255257555 14 ep2d_bold_SMS3_PAT2_2p5iso ok 92 92 57 180 MR.1.3.12.2.1107.5.2.43.67026.2018062717024484181988697 15 ep2d_bold_SMS3_PAT2_2p5iso ok 92 92 57 180 MR.1.3.12.2.1107.5.2.43.67026.2018062717100568938419838 16 ep2d_bold_SMS3_PAT2_2p5iso ok 92 92 57 180 MR.1.3.12.2.1107.5.2.43.67026.2018062717172417291250987 17 ep2d_bold_SMS3_PAT2_2p5iso ok 92 92 57 180 MR.1.3.12.2.1107.5.2.43.67026.2018062717244528886782134 18 ep2d_bold_SMS3_PAT2_2p5iso ok 92 92 57 180 MR.1.3.12.2.1107.5.2.43.67026.2018062717320619207913274 19 ep2d_bold_SMS3_PAT2_2p5iso ok 92 92 57 180 MR.1.3.12.2.1107.5.2.43.67026.201806271739232204744422 20 tgse_pcasl_optBS_M0_PLD2000 ok 96 96 1 22 MR.1.3.12.2.1107.5.2.43.67026.2018062717460555193775829 21 tgse_pcasl_optBS_M0_PLD2000 err 96 96 1 1 MR.1.3.12.2.1107.5.2.43.67026.2018062717461445002086101 22 HCP_CMRR_SpinEchoFieldMap_AP ok 104 104 72 3 MR.1.3.12.2.1107.5.2.43.67026.2018062717461591061986321 23 HCP_CMRR_SpinEchoFieldMap_PA ok 104 104 72 3 MR.1.3.12.2.1107.5.2.43.67026.2018062717461993800986977 24 HCP_CMRR_fMRI_rest_AP err 104 104 72 1 MR.1.3.12.2.1107.5.2.43.67026.201806271747377337919554 25 HCP_CMRR_fMRI_rest_AP err 104 104 72 216 MR.1.3.12.2.1107.5.2.43.67026.2018062717473793126919992 26 HCP_CMRR_fMRI_rest_PA err 104 104 72 1 MR.1.3.12.2.1107.5.2.43.67026.2018062717540945183412846 27 HCP_CMRR_fMRI_rest_PA ok 104 104 72 488 MR.1.3.12.2.1107.5.2.43.67026.2018062717541118019513248 Zahra (Mona) Nasiriavanaki Postdoctoral Research Fellow Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, 149-2615 Charlestown, MA, USA, 02129

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Moderation analysis in Freesurfer
by Mark Wagshul 28 Jun '18

28 Jun '18

External Email - Use Caution Dear Freesurfer experts, We are interested in looking at the moderating effect of grey matter thickness on a non-imaging outcome measure. Thus, the model would be: Outcome measure = Condition + GM thickness + Condition * GM thickness + covariates. where Condition is a categorical variable (1/2, for two conditions of the non-imaging measures). The Freesurfer GLM usually solves for the thickness as a function of some contrast, but is really just determining the voxel-wise statistical significant of a GLM, so should be doable even with the imaging variable on the RHS. Ideally, we would like to run this as a linear mixed model with subject as a random effect, and the condition as a repeated measure. Is this possible to do with the current Freesurfer software, and if so, how would I implement it? Thanks for any advice you can provide. Mark ____________________ Mark Wagshul, PhD Associate Professor Gruss Magnetic Resonance Research Center Albert Einstein College of Medicine Bronx, NY 10461 Ph: 718-430-4011 FAX: 718-430-3399 Email: mark.wagshul(a)einstein.yu.edu<mailto:mark.wagshul@einstein.yu.edu> [einstein-logo-rgb] This email message and any accompanying attachments may contain privileged information intended only for the named recipient(s). If you are not the intended recipient(s), you are hereby notified that the dissemination, distribution, and or copying of this message is strictly prohibited. If you receive this message in error, or are not the named recipient(s), please notify the sender at the email address above, delete this email from your computer, and destroy any copies in any form immediately.

2 1

error when running eddy_correct
by Куликова Софья Петровна 28 Jun '18

28 Jun '18

External Email - Use Caution Hello FreeSurfer Developers, I was trying to run dt_recon (on centos7 system) but have got an error at the eddy_correct stage, saying there is no $FSLDIR/bin/imglob file. Indeed, it is not there. However, I gave installed FSL according to their tutorial without any errors and have no problem with running dt_recon on another machine. Could you kindly tell me how can I deal with this issue? Best regards, Sofya Kulikova PhD Neuroscience, HSE-Perm

2 1

Hypothalamus
by 郑凤莲 27 Jun '18

27 Jun '18

External Email - Use Caution Hi FS experts, I want to study the volume changes of Hypothalamus in FS 6.0. However, I cannot find information about Hypothalamus in Wiki. Is there any description about Hypothalamus? I am looking forward to your reply. Thank you very much. Sincerely, Zheng | | 郑凤莲 | | 邮箱：zhengfenglian0105(a)163.com | 签名由网易邮箱大师定制

2 1

Best way to elaborate multiple .nii file for multiple subjects
by Ottavio Morciano 27 Jun '18

27 Jun '18

External Email - Use Caution Hi!I'am a student of medicine in Foggia,Italy.To elaborate a single .nii file for a single subjects i use "recon-all -i (name of .nii file) -s (name of subjects) -all -openmp 8(i have 8 core)"and to finish the work is necessary 8 hours. Now i want elaborate 10 .nii file for 10 subjects(a file for each subject).Is better to open 10 terminal and use the command recon-all in each terminal without -openmp,or with -openmp?Or to use this,Now i open 10 terminal BUT for every terminal i use the command Taskset to assign every terminal to a core of my cpus(2 core is busy with 2 recon-all....) Wich is the best way to finish the work more rapidly? Sorry for my bad english and i hope for a reply.Thanks Morciano Ottavio MD.Student

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Recon-all run time too long
by Ottavio Morciano 27 Jun '18

27 Jun '18

External Email - Use Caution Hi!I have a macbook pro MY 2014 with a Intel Core i7(quad core,2.7 ghz) and 16 gb of ram with El Capitan.This Macbook to run recon-all it takes 47 hours with -openmp 8 flag. A Dell with Intel Core i7 3632Q,8 GB RAM DDR3 1600mhz with Linux takes 8 hours...The same Dell on windows with linux virtualizated takes 13 hours. Why recon-all on mac is so slow? is the OS?the type of compilator used for each platform?freesurfer not optimized for El Capitan? the architecture of the cpu? Some Advice? Morciano Ottavio MD Student Università Di Foggia.Italy

1 0

Resting-State and Brain Connectivity in Montreal: Early registration deadline is July 10 (fwd)
by Bruce Fischl 26 Jun '18

26 Jun '18

FYI ---------- Forwarded message ---------- Date: Tue, 26 Jun 2018 22:35:08 +0000 From: "Amir Shmuel, Dr." <amir.shmuel(a)mcgill.ca> To: "Amir Shmuel, Dr." <amir.shmuel(a)mcgill.ca> Subject: Resting-State and Brain Connectivity in Montreal: Early registration deadline is July 10 External Email - Use Caution The Sixth Biennial Conference on Resting-State and Brain Connectivity Conference: September 26 - 28, 2018 Educational workshop: September 24 - 25, 2018 Montreal, QC, Canada · Early registration deadline: July 10, 2018 · Registration fees will increase substantially on July 11 · To receive notice of acceptance by July 9: submit an abstract by July 2 · Late abstract submission can be made until August 1, 2018 See the conference web-site: http://restingstate.com/2018/ Amir Shmuel Chair of the organizing committee http://restingstate.com/2018/wp-content/uploads/2017/06/resting-state-logo-…. jpg [IMAGE]

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questions about freeview quit unexpectly
by 姜时泽 26 Jun '18

26 Jun '18

External Email - Use Caution | | Dear fresurfer experts, I am currently using freeview 2.0 to check some data. I am not sure why it always quit unexpectedly when I try to load a volume. my freeview is installed on OS 10.11.3 system. Would you please help me to solve this problem. Thank you. Best wishes Shize -- Shize Jiang Fudan University, Department of neurosurgery, Huashan Hospital, Shanghai Medical College Shanghai,200032,P.R.China Mobile: (86)18317079839 E-Mail: sjiang13(a)fudan.edu.cn | | | |

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