Freesurfer

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30076 discussions

Ubuntu 16.04 solution?
by NIELS JANSSEN . 20 Oct '16

20 Oct '16

Dear users, I have Ubuntu 16.04 (64bit) and I would like to use freesurfer. I first installed version 5.3 but got the well-known 'nu_correct' error: nu_correct: crashed while running nu_estimate_np_and_em (termination status=65280) Some searching revealed that this error is also described here: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg47050.html In this thread it was recommended to either downgrade perl to some earlier version (not which one), or to download the development version. I downloaded two development versions: freesurfer-Linux-centos6_x86_64-dev (on oct 10) and freesurfer-Linux-centos6_x86_64-stable-v6-beta-20161019-e582155 (on oct 19) But for both versions I get the same error when trying to test if the installation was correct: nielsj@nielsj-XXXX-D2H-USB3:/usr/local/freesurfer/subjects$ mri_convert sample-001.mgz ~/sample-001.nii.gz mri_convert.bin sample-001.mgz /home/nielsj/sample-001.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from sample-001.mgz... -------------------------------------------------------------------------- ERROR: Invalid FreeSurfer license key found in license file /usr/local/freesurfer/license.txt If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu/registration.html to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. -------------------------------------------------------------------------- I copied the same license.txt file as for the 5.3 version, where it worked, so I know the license.txt file is OK. One observation: after untarring the user:group properties of the files in /usr/local/freesurfer look weird and are 8481:1590 for all files, except the license.txt which is root. Is this normal? Can I install freesurfer on my machine or should I revert to Ubuntu 14.04? Thank you. -- Niels Janssen Cognitive Neuroscience Laboratory Institute of Biomedical Technologies Center for Biomedical Research of the Canary Islands University of La Laguna Tenerife, Spain http://www.neurocog.ull.es/en

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Postdoc Position at the Dynamic Memory Lab at UC Davis
by Frank Hsieh 20 Oct '16

20 Oct '16

Postdoctoral Researcher: The Dynamic Memory Lab (C. Ranganath, PI) at the University of California, Davis, now has an open position for a funded postdoctoral researcher. We currently are running studies that involve multimodal imaging (EEG, fMRI, ECoG, Diffusion Imaging, MR Spectroscopy) as well as concurrent transcranial electrical stimulation (tDCS/tACS). The lab is located at the UC Davis Center for Neuroscience, which houses a 3T Siemens Skyra MRI scanner, an MR-compatible tDCS/tACS system, and EEG systems both at the lab and in-scanner. Start date is flexible and can be delayed to accommodate defense and publication of thesis work. In addition to lab funding, candidates might be eligible for funding from the NIA T32 grant on the Neuroscience of Cognitive Aging (collaboration with Charles DeCarli) or from a joint R01 to examine memory in schizophrenia (collaboration with J. Daniel Ragland and Cam Carter). Qualifications: Candidates must have completed a Ph.D. in Psychology, Neuroscience, or a related field and have first-authored publications that reflect familiarity with neuroscience techniques (e.g., EEG, fMRI, tDCS/tACS, TMS, etc.). For this position, successful candidates will need to have strong analytical skills in multivariate analysis of fMRI, EEG, or other neurophysiological data. Strong preference will be given to candidates with research background in learning and memory and expertise in probabalistic tractography, model-based analysis, representational similarity analysis, or pattern classification of fMRI data, time-frequency analysis, cortical source estimation and/or multivariate analysis of EEG or MEG in humans, or corresponding LFP analyses in animal models. Beyond experience, we are looking for someone who is resourceful, collaborative, resilient, productive, honest, and enthusiastic about mentoring junior lab members. Prof. Charan Ranganath will go through applicant information starting Nov. 1st, 2016, until position is filled. Interested individuals please send your CV and names of 3 references to DML Lab Manager Nichole Bouffard ( nrbouffard(a)ucdavis.edu)

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Freesurfer Matlab scripts for reading and writing files
by Keefe, Sarah 19 Oct '16

19 Oct '16

Hi, I am part of the Freesurfer anonymization project mentioned in an earlier thread- sorry to start a new thread but I was unable to reply to the previous one. We are trying to find out how to remove all provenance information from .mgh files. I am having trouble reading .mgh files into Matlab in order to remove the tags at the end of the file. How would we read and write the tags section of an mgh file in Matlab? Would that be done using any of the Freesurfer Matlab scripts? I haven't had success with viewing or removing tags using load_mgh or MRIread - MRIread displays header information only. Thanks so much, Sarah ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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adding control points and pial editing
by miracle ozzoude 19 Oct '16

19 Oct '16

Hello Freesurfer, I have 100 participants for my study and I would like to add control points and edit the pial for all of them. Is there a command that can automatically do both or do I have to manually inspect all 100 participants and add control point/ pial edit where necessary. thanks. Best, Paul

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Question regarding: Binary label map to skull strip brains
by Karmacharya, Sarina 19 Oct '16

19 Oct '16

Dear Freesurfer team, I have a questions for you regarding the binary masks (labels maps) that freesufer uses to skull strip the brain in the first part of recon-all. I was wondering if freesurfer stores/saves this label mask that it uses to skullstrip? If so what would be the naming convention of this label map/mask and the location of the label map/mask in the freesurfer folder. I will be waiting to hear back from you. Best Regards, Sarina

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Re: [Freesurfer] Problem in upload file through ftp
by Cong 19 Oct '16

19 Oct '16

Hi Dear Bruce Thanks for your reply. Do you mean change to source directory in my computer? but I can’t, It appears 550 Failed to change directory. I find I can only change to / directory. I did some try but all failed. Name (surfer.nmr.mgh.harvard.edu:Brainwaver): anonymous 331 Please specify the password. Password: 230 Login successful. Remote system type is UNIX. Using binary mode to transfer files. ftp> cd /Users/Brainwaver/Desktop 550 Failed to change directory. ftp> cd / 250 Directory successfully changed. ftp> put /Cong2Bruce.zip local: /Cong2Bruce.zip remote: /Cong2Bruce.zip 229 Entering Extended Passive Mode (|||37894|). 553 Could not create file. ftp> put Cong2Bruce.zip local: Cong2Bruce.zip remote: Cong2Bruce.zip ftp: Can't open `Cong2Bruce.zip': No such file or directory ftp> cd /Cong2Bruce.zip 550 Failed to change directory. ftp> cd / 250 Directory successfully changed. ftp> cd transfer/incoming 250 Directory successfully changed. ftp> put /Cong2Bruce local: /Cong2Bruce remote: /Cong2Bruce ftp: Can't open `/Cong2Bruce': No such file or directory ftp> put /Cong2Bruce.zip local: /Cong2Bruce.zip remote: /Cong2Bruce.zip 229 Entering Extended Passive Mode (|||37856|). 553 Could not create file. ftp> Best Wishes Cong Chen > Date: Mon, 17 Oct 2016 23:16:52 -0400 > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > > Try changing dir into the source directory then do the put with only the file name and no path > Cheers > Bruce > >> On Oct 17, 2016, at 10:33 PM, Cong <3110103623(a)zju.edu.cn> wrote: >> >> Hi Bruce >> full session is listed. Thank you very much. >> >> Best Wishes >> Cong >> >> BrainwaverdeMacBook-Pro:~ Brainwaver$ ftp surfer.nmr.mgh.harvard.edu >> Connected to surfer.nmr.mgh.harvard.edu. >> 220-This is the Martinos Center Anonymous FTP service. Use of this site >> 220-shows implicit consent to our Acceptable Use Policy outlined at >> 220-http://www.nmr.mgh.harvard.edu/martinos/userInfo/computer/nmr-aup.php >> 220- >> 220-OPERATIONAL NOTE: If, when doing a GET or PUT, you encounter either >> 220- >> 220-229 Entering Extended Passive Mode >> 220- >> 220- and nothing happens OR >> 220- >> 220-229 Entering Extended Passive Mode >> 220-500 Bad EPRT protocol. >> 220- >> 220- try issuing the EPSV command prior to GET or PUT. >> 220- >> 220 >> Name (surfer.nmr.mgh.harvard.edu:Brainwaver): anonymous >> 331 Please specify the password. >> Password: >> 230 Login successful. >> Remote system type is UNIX. >> Using binary mode to transfer files. >> ftp> cd transfer/incoming >> 250 Directory successfully changed. >> ftp> put /Users/Brainwaver/Desktop/Cong2Bruce.zip >> local: /Users/Brainwaver/Desktop/Cong2Bruce.zip remote: /Users/Brainwaver/Desktop/Cong2Bruce.zip >> 229 Entering Extended Passive Mode (|||37896|). >> 553 Could not create file. >> ftp> epsv >> EPSV/EPRT on IPv4 off. >> ftp> put /Users/Brainwaver/Desktop/Cong2Bruce.zip >> local: /Users/Brainwaver/Desktop/Cong2Bruce.zip remote: /Users/Brainwaver/Desktop/Cong2Bruce.zip >> 227 Entering Passive Mode (132,183,202,158,147,230). >> 553 Could not create file. >> ftp> >> >>> Date: Sun, 16 Oct 2016 16:04:12 -0400 (EDT) >>> From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >>> >>> Hi Cong >>> >>> can you send us your full session history - what exact commands did you >>> type and what was the screen output? >>> >>> cheers >>> Bruce >>>> On Sun, 16 Oct 2016, Cong wrote: >>>> >>>> Dear freesurfer experts? ? When I use command "put path/to/my/file?,?it?s >>>> always appear an error "229 Entering Extended Passive Mode (|||37867|). >>>> 553 Could not create file?, if I use epsv?command before put, then comes an >>>> error "227 Entering Passive Mode (132,183,202,158,147,237).?553 Could not >>>> create file?. Could you give me some advices? >>>> >>>> Best Wishes >>>> Cong Chen

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Re: [Freesurfer] mri_cvs_register quit for mris_resample: Command not found
by Cong 19 Oct '16

19 Oct '16

Hi Z K The contents of build-stamp.txt are freesurfer-Darwin-lion-stable-pub-v5.3.0. Best Wishes Cong Chen > Date: Tue, 18 Oct 2016 11:09:20 -0400 > From: Z K <zkaufman(a)nmr.mgh.harvard.edu> > > > Hello, > > Can you provide me with the contents of your > /Applications/freesurfer/build-stamp.txt file? > > > > On 10/18/2016 10:13 AM, Cong wrote: >> Dear freesufer experts >> I?m learning DTI image process according to steps in FsTutorial/ >> Diffusion_DtiIntegration. In Spatial Normalization I need create a >> .m3z morph file >> through mir_cvs_register. I used command mri_cvs_register --mov >> subjectname --template cvs_avg35. But it always stop for mris_resample: >> Command not found. I run freesurfer v5.3.0 in a MacBook Pro. Two log >> file in cvs folder are attached. Could you give me some advice? Thanks >> very much. >> >> Best Wishes >> Cong Chen

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MGZ file tag edit
by LaMontagne, Pamela 19 Oct '16

19 Oct '16

We have several data sharing efforts going on in which we would like to assign new Subject IDs and paths. We have identified the following mgz files that have provenance info including timestamps, dcm file name, subject ID (subject_name/assessors/session_name/DATA/subject_name/mri). aparc.a2009s+aseg.mgz aparc+aseg.mgz aseg.auto_noCCseg.mgz brain.mgz ctrl_pts.mgz filled.mgz norm.mgz rawavg.mgz T1.mgz wm.asegedit.mgz wm.mgz Questions: 1. Are we missing any files with provenance? - I do not see this information in the surf files 2. Will using gunzip then zip affect the integrity of the files for intended uses? Any suggestions would be gladly accepted on how to edit the mgz/mgh tags. Thanks, Pamela Pamela LaMontagne, PhD Clinical Research Coordinator Washington University School of Medicine Department of Radiology Phone: (314) 362-3487 Voice: (314) 669-4551 ________________________________ The material in this message is private and may contain Protected Healthcare Information (PHI). If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Optimal combination of MRI-sequences
by Erik Lindberg 18 Oct '16

18 Oct '16

Dear Freesufer experts, We are in the process of starting a large MRI project on normal aging and dementia. There has been a lot of discussions about what sequences to use. We are now thinking about combining several sequences. Is there an optimal combination of MRI sequences for Freesufer?

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Using "for" to run multiple subjects
by Farzaneh keyvanfard 18 Oct '16

18 Oct '16

Dear expert, I want to run recon-all for 100 subject simultaneously. I found the following link about it, but as I'm a beginner in this field, I don't understand how to use it. Would you please kindly give an example with a subject names, directory , etc. what should be written instead of * , or how could I define the number of subjects, ...? Thank you very much. https://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/Scripts/Two Best Regards F.Keyvanfard

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