Freesurfer April 2021

freesurfer@nmr.mgh.harvard.edu

104 participants
144 discussions

aparc+aseg to native space issue
by Larson, Kathleen E 15 Apr '21

15 Apr '21

External Email - Use Caution Hi, I am having an issue converting the aparc+aseg segmentation into the native space. I have tried using both of the following commands: mri_label2vol --seg aparc+aseg.mgz --temp rawavg.mgz --o aparc+aseg_native.mgz --regheader mri_vol2vol --mov aparc+aseg.mgz --targ rawavg.mgz --regheader --nearest --o aparc+aseg_native.mgz In both cases, the output segmentation in native space is slightly offset along the x axis (given x,y,z coordinates). In fact, mri_label2vol is offset in the opposite direction as mri_vol2vol. All outputs have the same origin as the original native space, so I am wondering if it's a problem with the interpolation. Do you have any advice for how to fix this issue? Thank you! Kathleen Larson (she/her) Medical Image Computing Lab (MedICL) Biomedical Engineering | Ph.D. Candidate Vanderbilt University

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Surface registration problem
by Manenti, Giorgio 15 Apr '21

15 Apr '21

External Email - Use Caution Dear Experts, I’m encountering a problem when running the preproc-sess on my functional data. When using the flag -surface subject hemi i am getting ":ERROR: source volume is neither source nor target of the registration”. The source is a template.nii file present in the bold folders, while the destination file is the mri/orig.mgz from the “subject” folder (after Longitudinal recon-all). I am not sure if the problem could be connected with the mc-sess,stc-sess or topup (where i need to crop out 1 slice to get an even volume) steps, that i’m running before preproc-sess, or if i’m missing an extra flag. Here the command i’m running: preproc-sess -s f10_sess01new -fsd bold -i my_hifi_images -nostc -nomc -surface hum_15721.long.long010 lhrh -mni305 -fwhm 4 -per-run Many thanks for your time and support, Best Regards Giorgio

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Re: [Freesurfer] Freesurfer Digest, Vol 206, Issue 6
by zalewk 15 Apr '21

15 Apr '21

External Email - Use Caution Hi Doug, Sorry for the late reply, and thanks for all your help. Attached is the text file of the output. This was testing autorecon-pial, but the bug is the same no matter if it's autorecon2-wm, autorecon3, or any place it hits the "if ( $ud" statement. Best, Kody Run it with -debug as the first option, capture the output, and send it to us. On 4/1/2021 8:29 PM, zalewk wrote: > > ????????External Email - Use Caution > > Hi Freesurfer team, > > My lab recently switched over from FS6 to FS7 and I think I've > encountered a bug with recon-all. > I'm running subjects stepwise and editing them, running recon-all with > the -autorecon2 and -autorecon3 flags initially are no problem, they > run fine.? Trying to re-run them or use the -autorecon2-wm, > -autorecon-pial etc. flags lead to crashing at certain parts of the > program. The error message I get is "if: expression syntax". Digging > into the code, it seems to crash when it hits a line of code "if($ud > || $ForceUpdate)". The syntax superficially looks right (I don't know > tcsh), checking the variables it seems like $ForceUpdate is never set, > but removing it from recon-all doesn't fix the problem. > It seems the $ud variable is for checking if updates are needed for a > set of volumes passed to the program. I don't know why that would be a > problematic argument, removing that part seems to fix it, but this > also seems like an important variable and I don't know enough about > tcsh to understand why it works after removing it. Can one of the > folks who wrote the recon-all script help me out? I'm running the > commands step-wise as a work-around, but that is much less convenient. > > Best, ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of freesurfer-request(a)nmr.mgh.harvard.edu <freesurfer-request(a)nmr.mgh.harvard.edu> Sent: Tuesday, April 6, 2021 6:41 AM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: Freesurfer Digest, Vol 206, Issue 6 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://secure-web.cisco.com/12RCdM4nvnTq08RfLMdhWLNUwwCLn6K8WftCJlAbuQ-Iak… or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Freesurfer Website Ports (Swearingen, Hannah) 2. mris_average_surface fails (?????????) 3. Re: 2mm thick image for hippocampal segmentation. (Ramesh Babu) 4. Re: fMRIPrep BOLD Output (Douglas N. Greve) 5. Re: mri_glmfit error (Douglas N. Greve) 6. Re: Regarding recon all (Douglas N. Greve) 7. Re: retaining label ids (Douglas N. Greve) 8. Re: recon-all bug (Douglas N. Greve) 9. Re: mris_label2annot - make all command exiting with errors (Douglas N. Greve) 10. Re: recon-all bug (Douglas N. Greve) 11. Re: Dicom Tag Problem Reconall (Douglas N. Greve) 12. unsubscribe (Coleman, Katherine) 13. Re: mri_gtmpvc error Checking tissue type ERROR: CheckSegTissueType() tissue type for seg (Douglas N. Greve) 14. Re: Problem with freesurfer measures (Douglas N. Greve) 15. Re: Freesurfer Website Ports (Douglas N. Greve) 16. Re: mris_average_surface fails (Douglas N. Greve) 17. Re: 2mm thick image for hippocampal segmentation. (Douglas N. Greve) 18. Freesurfer Versions - Zeros in the Cortex (Daniel Gutstein) 19. Re: mri_gtmpvc error Checking tissue type ERROR: CheckSegTissueType() tissue type for seg (Bahar Hazal Yal??nkaya) ---------------------------------------------------------------------- Message: 1 Date: Mon, 5 Apr 2021 15:20:31 -0400 From: "Swearingen, Hannah" <hannah_swearingen1(a)brown.edu> Subject: [Freesurfer] Freesurfer Website Ports To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <CAG+grQp1wJ8ywX0StrT4VJO38JYtwfxivTNvdH3KwQrhtwiRGw(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Hi, I am setting up an Access Control List for an isolated VLAN in which my center's neuroimaging computing workstations will be connected to our hospital's network for data back-up. We want to be able to connect to Freesurfer's website while connected to the VLAN, and we need to supply which ports the website accesses. I used nmap to scan and see which ports are open, and I found this: PORT STATE SERVICE 21/tcp open ftp 80/tcp open http 443/tcp open https Our hospital's IT is unsure if the FTP port can be opened without a security breach, and they are wondering if we will still be able to access the website without the 21/FTP port opened? Can anyone provide me with that information? Thanks, Hannah --

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Decompressed problem during reconall
by Banu Femir 15 Apr '21

15 Apr '21

External Email - Use Caution Dear FreeSurfer Developers, I've a problem that cannot solve for the last week. I am using virtual box, FS7 on my windows. I run reconall for Bert and checked that it is working.I have an MRI scan of sepstic patients that I got via CD, these are DICOM files but does not end with .dcm. When I try to run reconall, for dcm images I got the following error (the longer version is in the attachment) ........ Loading pixel data JPEG compressed, decompressing cd /home/developer/Documents/7.1.0-1/subjects/sepsis2 fsdcmdecompress --i /home/developer/Documents/7.1.0-1/subjects/D_000001/F_000001 --o /tmp/developer.tmp.decompressed.dcm.0oOV4x --jpeg >& /tmp/developer.tmp.decompressed.dcm.0oOV4x.dcmdjpeg.out ERROR: 512, see /tmp/developer.tmp.decompressed.dcm.0oOV4x.dcmdjpeg.out for more details Command exited with non-zero status 1 @#@FSTIME 2021:04:08:08:29:16 mri_convert N 2 e 1.97 S 1.19 U 0.60 P 91% M 9200 F 2 R 999 W 0 c 174 w 356 I 32240 O 0 L 0.55 0.33 0.41 @#@FSLOADPOST 2021:04:08:08:29:18 mri_convert N 2 0.55 0.33 0.41 Linux developer-VirtualBox 5.3.0-53-generic #47~18.04.1-Ubuntu SMP Thu May 7 13:10:50 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sepsis2 exited with ERRORS at Thu Apr 8 08:29:18 EDT 202 I converted files to nii, this time I decided to run reconall on nii images, it took more time but again failed on talairach transform. I tried to run on different shells but ended up with the same problem. Is it related with my MRI data or computer, how can I understand that? Many thanks! Banu

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Regarding xhemi comparison of hemispheres of the same subject
by Ghassemieh, A. (Anna) 15 Apr '21

15 Apr '21

External Email - Use Caution Dear all, I'm currently working on comparing left with right hemisphere activation for individual subjects and using version 7.1.1. Since it is on an individual level, we would like to register the left hemisphere of each subject to their mirrored right hemisphere (or vice versa). When looking at the way this is described in the wiki (https://secure-web.cisco.com/1b80Mej4E9rovgmSCJq2Tz2wDNVe2geAoqeHRggKKORugG…) we started to wonder the following: It is suggested to register to the symmetrical template for each subject. However, it is unclear to us why this is necessary since there is already a matched registration via the spherical reg file for each subject. Does anyone know if it is possible to use this for the purpose somehow instead? Kind regards! ------------------------------------------------------------------------------ De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. Denk s.v.p aan het milieu voor u deze e-mail afdrukt. ------------------------------------------------------------------------------ This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197. Please consider the environment before printing this e-mail.

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Skull stripping with T2
by Rohan Bareja 15 Apr '21

15 Apr '21

External Email - Use Caution Hello, I am doing skull stripping with free surfer v6.0, and have tried various watershed cut-offs to do skull stripping on T2 scans. But, it removes a lot of brain portion. Here are my commands: mri_convert /Applications/freesurfer/subjects/patient_20_t2/mri/T2_age_reg_bias.nii.gz /Applications/freesurfer/subjects/patient_20_t2/mri/001.mgz recon-all -s patient_20_t2 -autorecon1 ## to be used only when increasing or decreasing threshold of skull stripping. recon-all -skullstrip -wsthresh 25 -clean-bm -s patient_12_t2 Is there any way that I can improve upon this and get better results if I am missing something? Thanks, Rohan

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Re: [Freesurfer] retaining label ids
by miracle ozzoude 15 Apr '21

15 Apr '21

External Email - Use Caution [image: image1.png] [image: image2.png] Hello Doug, Thanks for the reply. I've a parcellation of the gm and wm with different label ids (see screenshot 1). I did like to extract a *non-binarised* wm to look like screenshot 2. mri_extract_label and mri_binarize don't keep the different colours. Is there a freesurfer command to achieve this? On Tue, Apr 6, 2021 at 2:07 PM miracle ozzoude <miracooloz(a)gmail.com> wrote: > Hello Doug, > > Thanks for the reply. > > I've a parcellation of the gm and wm with different label ids (see > screenshot 1). I did like to extract a *non-binarised* wm to look like > screenshot 2. > > mri_extract_label and mri_binarize don't keep the different colours. > > Is there a freesurfer command to achieve this? > > Many thanks > [image: image.png] > [image: image.png] > > On Tue, Apr 6, 2021 at 12:07 PM miracle ozzoude <miracooloz(a)gmail.com> > wrote: > >> Hello Doug, >> >> Thanks for the reply. >> >> I've a parcellation of the gm and wm with different label ids (see >> screenshot 1). I did like to extract a *non-binarised* wm to look like >> screenshot 2. >> >> mri_extract_label and mri_binarize don't keep the different colours. >> >> Is there a freesurfer command to achieve this? >> [image: image.png] >> [image: image.png] >> >> >> On Thu, Apr 1, 2021 at 2:00 PM miracle ozzoude <miracooloz(a)gmail.com> >> wrote: >> >>> Hello Experts, >>> >>> I did like to extract wm whilst retaining the label ids. I tried >>> mri_extract_labels but it didn't work. >>> >>> Any help would be appreciated. >>> >>> Many thanks, >>> Paul >>> >>

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Re: [Freesurfer] Install issue
by fsbuild 15 Apr '21

15 Apr '21

External Email - Use Caution Hello Pal, Could be because tar archive contains hard links - which I don’t believe are supported when running a linux VM on top of a Windows OS (error from the first hard link it encountered and tried to write - and then quit). You could try expanding the tar archive ignoring *all*links* with the following using the *star* (pre-cursor to tar) command (cut and paste below and change tar archive name if need be), $ star -x  f=freesurfer-linux-centos7_x86_64-7.1.0.tar.gz  -find ! -type l - R. On Apr 15, 2021, at 02:35, Pål Gunnar Larsson <pall(a)ous-hf.no> wrote:        External Email - Use Caution        Thank you for the response.The computer runs Win10 pro and are under AD-control. May be there are something there out of my reach. Funny that it is almost only unpacking of some man-pages giving errorsI’ll try your suggestions. Pål Dr. philos. Pål G. LarssonOverlegeNevrokirurgisk avdelingOslo UniversitetssykehusPostboks 4950 Nydalen0424 Oslo  Tlf.:  23074407Mobil: 93429791 E-mail: pall@ous-hf.no Denne meldingen innholder ikke sensitiv informasjon som bryter med Ous sine regler for taushetsplikt Fra: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] På vegne av Hoopes, AndrewSendt: 14. april 2021 19:42Til: Freesurfer support listEmne: Re: [Freesurfer] Install issue I’m not totally sure of the answer here. Could be filesystem limitations or a permissions issue. Have you tried untar’ing without the -p flag, or ensuring that you can write to /usr/local? BestAndrew From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Pål Gunnar Larsson <pall@ous-hf.no>Date: Tuesday, April 13, 2021 at 8:57 AMTo: freesurfer@nmr.mgh..harvard.edu <freesurfer@nmr.mgh.harvard.edu>Subject: [Freesurfer] Install issue        External Email - Use Caution        Today I tried to set up a new Freesurfer instance.It is on a Win10 system with Vmware 6.0 and Ubuntu 18 LTS. I have tried a local install and to /usr/local, but I get the same error  “cannot hardlink to….” And then a row of protocol errors (see attachment). What is the issue? Pål G. Larsson M.D., PhD.Department of NeurosurgeryDivision of Surgery and Clinical Neuroscience not sensitive _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Install issue
by Pål Gunnar Larsson 15 Apr '21

15 Apr '21

External Email - Use Caution Today I tried to set up a new Freesurfer instance. It is on a Win10 system with Vmware 6.0 and Ubuntu 18 LTS. I have tried a local install and to /usr/local, but I get the same error "cannot hardlink to...." And then a row of protocol errors (see attachment). What is the issue? Pål G. Larsson M.D., PhD. Department of Neurosurgery Division of Surgery and Clinical Neuroscience not sensitive

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New York City-based Neuroimaging Postdoctoral Position Available
by Sherry Simkovic 14 Apr '21

14 Apr '21

External Email - Use Caution The Psychiatry Research Institute at Montefiore Einstein (PRIME), a division of the Department of Psychiatry and Behavioral Sciences at Albert Einstein College of Medicine, is seeking a highly motivated postdoctoral scholar in the field of human neuroimaging. The focus of this position will be on analyzing fMRI data as well as related MR and biological measures. Candidates should either have completed or be near completing a PhD in neuroscience, psychology, cognitive science, radiology, engineering, or a related field, and should have a strong background in quantitative analysis. Proficiencies with at least one major neuroimaging software suite (e.g. FSL, AFNI, SPM, Freesurfer, Caret, Connectome workbench, etc.) and Unix/Linux environment are expected. Familiarity with Matlab, Python, and/or R programming languages is a plus. Under the mentorship of Vilma Gabbay, MD, this postdoctoral scholar will be expected to advance both clinical and methodological knowledge through their postdoctoral training. Dr. Gabbay is the Director of Research at PRIME, a unique program in the greater New York metropolitan area dedicated exclusively to the study and treatment of adolescent mood and anxiety disorders, utilizing innovative neuroimaging and immunological methodologies. The neuroimaging program features high-resolution data acquisition and analysis techniques modeled on the Human Connectome Project (HCP) and is dedicated to advancing the fields of magnetic resonance imaging and spectroscopy. Resources available on-campus and through long-standing collaborations include multiple research-dedicated 3T MRI scanners (Siemens Skyra, Philips Elition) with cutting-edge accelerated fMRI and edited MRS sequences, high-performance scientific computing clusters, and an extensive library of analytic and statistical software. The primary responsibility for this postdoctoral fellow will be to analyze neuroimaging data from several ongoing and recently concluded research projects. Dr. Gabbay is fully committed to fostering the trainee's research independence through publication of first-authored manuscripts in top journals and mentorship in grant applications. In addition to assisting with the PI’s proposals, the successful applicant will be highly encouraged to develop and pursue funding for their own research project through federal (e.g. NIH F32) or foundation grant programs by the end of their first year. The initial employment period for this position is two years, with the possibility of extension. Salary will be competitive and commensurate with experience and the cost of living in New York City. Subsidized housing close to the Einstein campus in the Morris Park neighborhood of The Bronx is available. Please send a CV, statement of interest, and contact information for three references to Dr. Ely (benjamin.ely(a)einsteinmed.org<mailto:benjamin.ely@einsteinmed.org>) and Dr. Qi Liu (qi.liu(a)einsteinmed.org<mailto:qi.liu@einsteinmed.org>). Albert Einstein College of Medicine is an equal opportunity employer, and all qualified candidates will be given equal consideration. Priority will be given to candidates available to start sooner. Best and thanks, Sherry Sherry Simkovic Study Coordinator Psychiatry Research Institute of Montefiore Einstein (PRIME) Pediatric Mood and Anxiety Disorders Program (PMAP) 1225 Morris Park Avenue, Bronx, NY 10461 TEL: (718) 839-7504 FAX: (718) 839-7575 EMAIL: sherry.simkovic(a)einsteinmed.org<mailto:sherry.simkovic@einsteinmed.org> [cid:image001.png@01D62891.B16B0C40]

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Freesurfer April 2021