Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

thalamic nuclei segmentation
by Sara PONTICORVO 08 Apr '21

08 Apr '21

External Email - Use Caution Hi Freesurfer experts, I processed ~150 subjects with freesurfer v6 (recon-all) and I was wondering if it is possible to use the script for the segmentation of the thalamic nuclei on these subjects. I know this part of the processing is now integrated in the v7 of freesurfer, but I'm thinking if there is a way to avoid re-run all the reconstruction with the new version. I looked in the wiki page, and it seems that there was a way to integrate the scripts in the fs-v6, but I don't find any downloadable package or scripts. Thanks for your help, Sara -- Sara Ponticorvo, PhD Department of Medicine Surgery and Dentistry University of Salerno

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Re: [Freesurfer] Virtual Box Account Password
by fsbuild 07 Apr '21

07 Apr '21

External Email - Use Caution Sending this to your posted email address in a few minutes. - R..On Apr 7, 2021, at 05:45, Banu Femir <banu.femir(a)gmail.com> wrote:        External Email - Use Caution        Dear Freesurfer Developers,I downloaded Virtual Box on my Windows following the steps on: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/11Q8tziq_44pDhv3UNtqG-Qaqy_JvvV_aM6BwG…, when I try to turn on the virtual linux, it asks for a password of an account named "developer". I tried to find a password on the internet but could not. This question was asked by someone else on May, 2020, the reply is like " You may check *brain.map* " but I could not find anything about it. I would be so happy if you can help me because I am stuck with my data analysis. I am sending the picture in the attachment. Many thanks!Banu<IMG_3862.jpg>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Virtual Box Account Password
by Banu Femir 07 Apr '21

07 Apr '21

External Email - Use Caution Dear Freesurfer Developers, I downloaded Virtual Box on my Windows following the steps on: https://secure-web.cisco.com/1CyzUIZtRjJfdg7gYEEp3hkwAuc4pVU2M20x2njsr6thrr… However, when I try to turn on the virtual linux, it asks for a password of an account named "developer". I tried to find a password on the internet but could not. This question was asked by someone else on May, 2020, the reply is like " You may check *brain.map* " but I could not find anything about it. I would be so happy if you can help me because I am stuck with my data analysis. I am sending the picture in the attachment. Many thanks! Banu

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Re: [Freesurfer] Freesurfer Website Ports
by fsbuild 06 Apr '21

06 Apr '21

External Email - Use Caution Hello Hannah, While the freesurfer group does not control the port(s) numbers exposed on the public facing web servers that host the freesurfer web pages, I’ve been told by IT that you should not need to access the ftp port and you should only need to setup the VPN to allow outgoing connections to port 443 on surfer.nmr.mgh.harvard.edu   - R. On Apr 6, 2021, at 10:45, Swearingen, Hannah <hannah_swearingen1(a)brown.edu> wrote:        External Email - Use Caution        We are wanting to connect to the site in the need of support from the freesurfer website (i.e. the manual pages) while behind our closed system.On Tue, Apr 6, 2021 at 9:29 AM Douglas N. Greve <dgreve(a)mgh.harvard.edu> wrote:why do you need to connect to the web site? that is not needed to run FSOn 4/5/2021 3:20 PM, Swearingen, Hannah wrote:        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  SERVICE21/tcp  open   ftp80/tcp  open   http443/tcp open   httpsOur 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-- _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1mpRMRdRVUkGiydkfChj9bLezWcQrfs3mS3ulkDqlybYpV… mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1PUXz56CZ6qGrl8q9bmwZYfsR2A1_vtHJuPlUw… SwearingenHannah.Swearingen@va.gov Hannah_Swearingen1@brown.edu401-273-7100 x14449_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh..harvard.edu/mailman/listinfo/freesurfer

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Postdoc opportunity - fMRI and EEG in childhood leukemia
by Mark Wagshul 06 Apr '21

06 Apr '21

External Email - Use Caution Postdoctoral Fellow position available at Albert Einstein College of Medicine in NYC The departments of Neuroscience (Dr. Elyse Sussman) and Radiology (Dr. Mark Wagshul) at the Albert Einstein College of Medicine in New York City are seeking a full-time postdoctoral research associate to work on an NIH-funded project exploring the neural bases of chemotherapy-induced cognitive deficits (chemobrain) in survivors of childhood leukemia. The project employs both EEG-based and fMRI-based methods to elucidate the cognitive pathways driving chemo-related cognitive dysfunction in children ages 5 - 12 years. The position is available starting June 2021; candidates are expected to be able to commit to join for the duration of the project through March 2025. Successful candidates for the position will have a PhD in physics, biomedical engineering, neuroscience or a related discipline, a strong background in either cognitive neuroscience or MRI physics, expertise in image and EEG data processing, as well as data and statistical analysis. Programming experience should include the commonly used packages for image and EEG processing, such as C++, Matlab, and FSL. The candidate should have significant experience in event-related potential (ERP) data collection and analysis methods and/or imaging in a clinical setting and a strong background in the development and/or application of novel methods for human brain imaging, such as DTI / fMRI / structural MRI data analyses. Candidates with experience only in EEG-based or fMRI-based methods will be considered if they can demonstrate through experience or letters of reference that they are able to quickly and independently master new techniques and methods of analysis. The candidate will allocate equal amounts of time to the EEG and MRI labs. Prior experience with auditory-based ERP/fMRI is not necessary, but candidates with such experience will be given preference. A strong work ethic, excellent organizational and communication skills, and ability to work independently is expected. Previous experience working with child populations is a plus. The candidate will be expected to be involved in all aspects of the project, including EEG, image and data analysis, statistical analysis, as well as interfacing with the clinical team. Competitive salary and benefits will be offered based on qualifications. The Gruss MRRC is located on the main campus of the Albert Einstein College of Medicine in Bronx, NY. The Center has a multinuclear 3.0 Tesla Whole Body Philips Elition human system and a 9.4 T Direct Drive Varian animal system. Image processing facilities including a computing cluster, multiple Linux workstations and PCs with imaging and general software installed. Please visit our website for more details (http://secure-web.cisco.com/1GGPHY7tcK4iQ7uhuzlRsC2wStBZnZ-wk-MUQxbdrTpcNFZ…) The Albert Einstein College of Medicine is a leading academic institution, with over $170M in NIH funding. The candidate will have access to state-of-the-art brain imaging (MRI, EEG) and computing facilities. Einstein is one of the nation's premier institutions for medical education, basic research and clinical investigation. It is home to some 2,000 faculty members, 750 M.D. students, 350 Ph.D. students attending the Sue Golding Graduate Division - including 125 in the combined M.D./Ph.D. program - and 325 postdoctoral investigators training at our Belfer Institute for Advanced Biomedical Studies. More than 7,000 Einstein alumni are among the nation's foremost clinicians, biomedical scientists and medical educators. Interested candidates should send their CV, a brief statement of their research interests and career goals, and the names and phone numbers of three references to: Mark Wagshul (mark.wagshul(a)einsteinmed.org) or Elyse S. Sussman (elyse.sussman(a)einsteinmed.org) Review of applications will begin immediately and continue until the position is filled. The Albert Einstein College of Medicine is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, age, protected veteran or disabled status, or genetic information. Einstein seeks candidates whose skills, and personal and professional experience, have prepared them to contribute to our commitment to diversity and excellence, and the communities we serve.

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"ERROR: crypt() returned null with 4-line file"
by Cook, Philip 06 Apr '21

06 Apr '21

External Email - Use Caution Dear FreeSurfer developers, I have also encountered the error that Katja Zoner reported in https://secure-web.cisco.com/1HqVP4_2gCSsHuuEFWzIN0yTWdDhhIeKNpc8cqD9BfBOmm… We work on different servers within the same institution and have been in contact with our administrators, we are sure at this point that the error is caused by FIPS 140 compliance on some of our systems. It is unrelated to Singularity. The crypt() function, as called in freesurfer/utils/chklc.cpp, returns NULL with errno == EPERM on machines booted in FIPS mode. I believe these users have encountered the same problem https://secure-web.cisco.com/1-z_qWpPYjwD6UccsUQP4XQEVo4YMH5WkF2I0eRZ2Z2G-7… https://secure-web.cisco.com/1D8Zt97JISxcqWsV-6sX9O6GUs5X59E2NOYaxNQqkDBr8t… As one of the above users noted, certain institutions (such as the Veterans Administration) require FIPS mode, as do studies using sensitive data. Our administrators have agreed to provide some "insecure" machines to run FreeSurfer binaries and containers for the time being, but we're concerned about the sustainability of this longer term. I think the issue could be resolved by using a FIPS-compliant algorithm in the call to crypt(). For example, I've tested crypt() with the SHA-512 algorithm in FIPS mode, and this works crypt_gkey = crypt(gkey, "$6$FS"); but this would require the license file to contain an SHA-512 encrypted gkey in addition to the DES one that currently exists. Alternatively, we can check if errno == EPERM after the call to crypt(), and bypass the encryption check in that case. I understand that these solutions are non-trivial and could raise backwards compatibility or license compliance issues. Unfortunately, I've not been able to find any other workaround. Thanks

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"ERROR: crypt() returned null with 4-line file" when running via Singularity
by Zoner, Katja 06 Apr '21

06 Apr '21

External Email - Use Caution Hi all, I am trying to run a single subject through FreeSurfer 7.1.1 via Singularity image (pulled from the FreeSurfer DockerHub) like this: export SINGULARITYENV_FS_LICENSE=/mnt/22Q/images/license.txt export SINGULARITYENV_SUBJECTS_DIR=/mnt/22Q/data/freesurfer singularity exec --cleanenv -B /project/bbl_projects/22Q/:/mnt/22Q \ /project/bbl_projects/22Q/images/freesurfer_7.1.1.sif \ recon-all -s sub-17867 -i /mnt/22Q/data/bids_directory/sub-17867/ses-22Q1/anat/sub-17867_ses-22Q1_T1w.nii.gz -all But it fails quickly with error message: ERROR: crypt() returned null with 4-line file Do you know what might be causing this error message? How can I address this? Additional info: 1. FreeSurfer version: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 2. uname -a: Linux singularity01 3.10.0-1127.8.2.el7.x86_64 #1 SMP Tue May 12 16:57:42 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux 3. recon-all.log: see attached See GitHub issue: https://secure-web.cisco.com/1ut10r0i0QuSlDil5z36vyz9khjKfY1Scbdqd9hofmPnzD… [https://secure-web.cisco.com/1TDcdfVeSPTzDeg0asgP7Yy7WKhWmvgHB9T_fyDNBmSSR4…<https://secure-web.cisco.com/1ut10r0i0QuSlDil5z36vyz9khjKfY1Scbdqd9hofmPnzD…> `ERROR: crypt() returned null with 4-line file` when running via Singularity image · Issue #848 · freesurfer/freesurfer<https://secure-web.cisco.com/1ut10r0i0QuSlDil5z36vyz9khjKfY1Scbdqd9hofmPnzD…> I am trying to run a single subject through FreeSurfer 7.1.1 via Singularity image like this: export SINGULARITYENV_FS_LICENSE=/mnt/22Q/images/license.txt export SINGULARITYENV_SUBJECTS_DIR=/mnt/22... github.com Thank you for any assistance! Katja Zoner

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mri_gtmpvc error Checking tissue type ERROR: CheckSegTissueType() tissue type for seg
by Bahar Hazal Yalçınkaya 06 Apr '21

06 Apr '21

External Email - Use Caution Hello Freesurfer"s Developers, I am trying to follow *PetSurfer* ( https://secure-web.cisco.com/1oGyZvXtztP0MX30hKqio2fJStw1wQuIW11p5b1b0CkNwS…) to apply PVC to Pet images. Default pipeline is working however, whenever i try to use another atlas, Schaefer parcellation, mri_gtmpvc command I get following error: WARNING: LTAconcat(): inverting LTA 1 to match geometry Replacing 18 Pruning ctab tissue type schema Checking tissue type ERROR: CheckSegTissueType() tissue type for seg 258 Head-ExtraCerebral not set Failed tissue type check I have searched to list several people who have issued similar errors but unfortunately i could not find any solution that works for me. Below you can find commands I used: $ gtmseg --s subject --o gtmseg.mgz --ctx-annot Schaefer2018_400Parcels_7Networks_order.annot 1000 2000 --ctab Schaefer2018_400Parcels_7Networks_order_LUT.txt $ mri_coreg --s subject --mov AbetaPre.nii.gz --reg AbetaPre.reg.lta $ mri_gtmpvc --i AbetaPre.nii.gz --psf 8 --reg AbetaPre.reg.lta --regheader --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --mgx .01 --km-ref 8 47 --o gtmpvc.output Also I checked the run of gtmseg via "*tkmeditfv*" where i can visualise 258 Head-ExtraCerebral, and additionally I checked *gtmseg.ctab *file also 258 Head-ExtraCerebral in the list. I will be happy to hear from you. Kind regards. -- Ph.D. Bahar Hazal Yalçınkaya

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Freesurfer Website Ports
by Swearingen, Hannah 06 Apr '21

06 Apr '21

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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2mm thick image for hippocampal segmentation.
by Ramesh Babu 06 Apr '21

06 Apr '21

External Email - Use Caution Dear Experts, For our project work, we particularly looking for hippocampal and its subfield volumes. Using GE 1.5T scanner, we tried a 3D BRAVO sequence with 1x1x1 resolution, 256x256x160 dimension with 8* flip angle which produced images with a lot of noise. Then we tried the same sequence with 1x1x2 resolution, and 256x256x80 FOV, which produced a clean image without noise. When we reformatted the images, it produces 0.5x0.5x1 resolution with 512x512x172 dimension. Is this sequence good for hippocampal volume estimation and subfield segmentation (also for whole-brain VBM analysis)? Could you please suggest to me a correct sequence for our project? Regards Ramesh

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