Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30081 discussions

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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b0dc flag for Freesurfer7
by Manenti, Giorgio 06 Apr '21

06 Apr '21

External Email - Use Caution Dear Experts, I am wondering if there is additional documentation about the -b0dc flag for mkanalysis-sess. This flag is applying field distortion correction. Is it possible to use my topup information in order to correct it or it s a different field correction? Many thanks, Best Giorgio

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Fwd: Failed tissue type check {Disarmed}
by Julie Ottoy 06 Apr '21

06 Apr '21

External Email - Use Caution Hi Doug, Did you have a chance to look at this subject ? Thanks a lot, Julie ---------- Forwarded message --------- From: Julie Ottoy <julie.jj.ottoy(a)gmail.com> Date: Thu, 18 Mar 2021 at 13:08 Subject: Re: [Freesurfer] Failed tissue type check {Disarmed} To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Hi Doug I upload the files on the server, see subject_ottoy.tar.gz thanks a lot! Julie On Tue, 16 Mar 2021 at 12:03, Douglas N. Greve <dgreve(a)mgh.harvard.edu> wrote: > I don't know. Can you upload the data so I can take a look? Instructions > are below. I'd need both the anatomical data (output of recon-all) and > input.nii.gz and PET.lta > > From the linux command line, > Create the file you want to upload, eg, > cd $SUBJECTS_DIR > tar cvfz subject.tar.gz ./subject > Now log into our anonymous FTP site: > ftp surfer.nmr.mgh.harvard.edu > It will ask you for a user name: use "anonymous" (no quotes) > It will ask you for a password: use "anonymous" (no quotes) > cd transfer/incoming > binary > put subject.tar.gz > Send an email that the file has been and the name of the file. > > > > On 3/8/2021 11:47 AM, Julie Ottoy wrote: > > External Email - Use Caution > Hi Doug, > > Any other suggestions I could try? It seems to be only an issue with the > non-pvc data. > > Thanks > Julie > > On Tue, 2 Feb 2021 at 11:10, Julie Ottoy <julie.jj.ottoy(a)gmail.com> wrote: > >> Hi Doug, >> >> I tried these fixes but they still give me the error message below. I did >> replace it in the gtmseg.ctab though -- should it be perhaps the seg.ctab >> in the aux folder ? >> >> Thanks, >> Julie >> >> On Tue, 12 Jan 2021 at 10:37, Julie Ottoy <julie.jj.ottoy(a)gmail.com> >> wrote: >> >>> Hi Doug >>> >>> I tried that as well but getting the same error as with --replace 29 3. >>> >>> ERROR: CTABpruneCTab(): ctab does not have segid 2 >>> >>> >>> Thanks, >>> julie >>> >>> On Tue, 12 Jan 2021 at 10:35, Greve, Douglas N.,Ph.D. < >>> DGREVE(a)mgh.harvard.edu> wrote: >>> >>>> Try using --replace 29 2 >>>> >>>> >>>> On 12/29/2020 12:48 PM, Julie Ottoy wrote: >>>> >>>> External Email - Use Caution >>>> Hi Doug >>>> >>>> Thanks for your reply. I tried both your suggestions, but it seems as >>>> though they both ran into an error. >>>> >>>> For your first suggestion, i.e. adding --replace 29 3 to the command >>>> line of gtmpvc, I get the error: >>>> >>>> Loading seg for gtm 057_S_5295re/mri/gtmseg.mgz >>>> >>>> Loading seg ctab 057_S_5295re/mri/gtmseg.ctab >>>> >>>> Reading 057_S_5295re/mri/gtmseg.lta >>>> >>>> Replacing 19 >>>> >>>> Pruning ctab >>>> >>>> ERROR: CTABpruneCTab(): ctab does not have segid 3 >>>> >>>> >>>> For your second suggestion, i.e. I replaced the following line in the >>>> ctab: >>>> >>>> 29 Left-undetermined 135 206 235 0 -1 >>>> >>>> ==> replaced by: 29 Left-undetermined 135 206 235 0 >>>> 3 >>>> >>>> >>>> I get the error: >>>> >>>> Computing Seg in input space >>>> >>>> Building GTM DoVoxFracCor=0 >>>> >>>> ERROR: creating region for nthseg=12, segid=29, Left-undetermined >>>> >>>> It may be that there are no voxels for this seg when mapped into the >>>> input space. >>>> >>>> Check 057_S_5295/057_S_5295.gtmnopvc.output.pons/aux/seg.nii.gz and the >>>> registration >>>> >>>> Build time 5.9690, err = 1 >>>> >>>> >>>> Thank you, >>>> >>>> Julie >>>> >>>> On Wed, 23 Dec 2020 at 12:48, Greve, Douglas N.,Ph.D. < >>>> DGREVE(a)mgh.harvard.edu> wrote: >>>> >>>>> You can use the fix from my previous email or you can add the >>>>> following line any were into the gtmseg.ctab file: >>>>> 29 Left-undetermined 135 206 235 0 3 >>>>> >>>>> >>>>> On 12/18/2020 11:06 PM, Julie Ottoy wrote: >>>>> >>>>> External Email - Use Caution >>>>> Sorry I would like to correct my previous post. The subject also >>>>> failed with PVC. >>>>> I see now that the issue is happening during the gtm seg stage where >>>>> it gives the error: WARNING: segid 29 Left-undetermined tissue type is >>>>> not set. >>>>> For your information: I ran the standard FS and petsurfer pipeline as >>>>> outlined on the wiki. I tried two gtm seg commands: >>>>> gtmseg --s ${id} --xcerseg --keep-hypo --subsegwm --subseg-cblum-wm >>>>> gtmseg --s ${id} --keep-cc --no-xcerseg --keep-hypo --subsegwm >>>>> --subseg-cblum-wm >>>>> >>>>> Thank you for your help, >>>>> Julie >>>>> >>>>> On Fri, 18 Dec 2020 at 00:09, Julie Ottoy <julie.jj.ottoy(a)gmail.com> >>>>> wrote: >>>>> >>>>>> External Email - Use Caution >>>>>> Dear Doug, >>>>>> >>>>>> I have the same issue as the people below. I was wondering if this >>>>>> was solved in the meantime. >>>>>> >>>>>> I ran petsurfer gtmpvc with the psf 0 and no-tfe flags to not do PVC >>>>>> and got the following error in only one of my subjects. When I ran the same >>>>>> subject with PVC and specified psf, it did run fine. >>>>>> >>>>>> $Id: mri_gtmpvc.c,- >>>>>> setenv - >>>>>> cd - >>>>>> mri_gtmpvc --i /input.nii.gz --reg PET.lta --psf 0 --no-tfe --seg >>>>>> gtmseg.mgz --default-seg-merge --auto-mask 10 0.01 --mgx 0.01 --o >>>>>> /gtmnopvc.output.ceregrey --rescale 8 47 >>>>>> sysname Linux >>>>>> hostname - >>>>>> machine - >>>>>> user - >>>>>> vgthresh 0.001000 >>>>>> nReplace 18 >>>>>> 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 >>>>>> 24 avail.processors, using 1 >>>>>> Creating output directory /gtmnopvc.output.ceregrey >>>>>> Loading seg for gtm /ID/mri/gtmseg.mgz >>>>>> Loading seg ctab /ID/mri/gtmseg.ctab >>>>>> Reading /ID/mri/gtmseg.lta >>>>>> Replacing 18 >>>>>> Pruning ctab >>>>>> Checking tissue type >>>>>> ERROR: CheckSegTissueType() tissue type for seg 29 Left-undetermined >>>>>> not set >>>>>> Failed tissue type check >>>>>> >>>>>> Any suggestions would be appreciated! >>>>>> Thank you, >>>>>> Julie >>>>>> >>>>>> Re: [Freesurfer] mri_gtmpvc error: failed tissue type check >>>>>> <https://secure-web.cisco.com/1-AfjZga-sPrQL2DD6_knJ0CVtb1mQnm-139FdXZgREjGD…> >>>>>> 2017-11-25 >>>>>> <https://secure-web.cisco.com/1wmX-yI5dbw4l_pxYy3eoVUJqMBCtBczIUKuXvmoQaLof8…> >>>>>> Thread >>>>>> <https://secure-web.cisco.com/1H-6HNMBxeDbZPyhVbOH9A2eLQckCsYtW7MQ3G9W6kDVwa…> >>>>>> Douglas Greve >>>>>> <https://secure-web.cisco.com/1WfAMB3Ad9t1D_s6Buw38joSkwdCcFg-F8c6cN0W9n84zV…> >>>>>> >>>>>> sorry, can you send me the details again? >>>>>> >>>>>> >>>>>> On 11/21/17 10:24 AM, Klein, Gregory wrote: >>>>>> >>>>>> Hello Donatas and Douglas, >>>>>> >>>>>> Did you ever find a cause and solution for this problem? I too >>>>>> occasionally get this error message, and cannot get the results of >>>>>> mri_gtmpvc for certain subjects. >>>>>> >>>>>> >>>>>> Any suggestions are welcome. >>>>>> Thanks, >>>>>> Greg >>>>>> >>>>>> -- >>>>>> Gregory Klein, PhD >>>>>> Principal Scientist, Biomarker Experimental Medicine Leader >>>>>> F. Hoffmann-La Roche Ltd. >>>>>> Bldg 01, Floor 16, N445 >>>>>> Grenazacherstrasse 170, >>>>>> 4070 Basel, Switzerland >>>>>> Mobile: +41 79 572 97 89 >>>>>> Office Phone: +41 61 682 07 59 >>>>>> email: gregory.kl...(a)roche.com >>>>>> >>>>>> Roche Products Limited, 6 Falcon Way, Shire Park, Welwyn Garden City, >>>>>> AL7 1TW Registration No:100674 >>>>>> >>>>>> >>>>>> Confidentiality note: This message is intended for the use of the >>>>>> named recipient(s) only and may contain confidential and / or >>>>>> privileged information. If you are not the intended recipient, please >>>>>> contact the sender and delete this message. Any unauthorized use of >>>>>> the information contained in this message is prohibited. >>>>>> >>>>>> >>>>>> ___ >>>>>> Freesurfer mailing listFreesurfer(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/1sA96g6MVXhTKqyIohE7iDpAeVudtNSoraQRr6PoymCFS6… <https://secure-web.cisco.com/1Aj-KIXWBSRBh4QYhiT5lPQzukbBDpNzMoSUI14TDJiN4-…> >>>>>> >>>>>> >>>>>> The information in this e-mail is intended only for the person to whom it is >>>>>> addressed. If you believe this e-mail was sent to you in error and the e-mail >>>>>> contains patient information, please contact the Partners Compliance HelpLine at*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/1pcd3R17cw9CUmO-RFZqcKXMAKlR9Hi_f5yRd0WcMyKMI2V… <http://secure-web.cisco.com/1Kuqledw2eJViDlbH8MA0_r7jBLVXWD3VreLVXqKwRqHFX1…> . If the e-mail was sent to you in error >>>>>> but does not contain patient information, please contact the sender and properly >>>>>> dispose of the e-mail. >>>>>> >>>>>> >>>>>> >>>>>> Re: [Freesurfer] mri_gtmpvc error: failed tissue type check >>>>>> <https://secure-web.cisco.com/1vNIDvkxU5C3l-uZggX6Oz-MWAWokjyVkJCUVlEhq9XKRo…> >>>>>> 2016-11-09 >>>>>> <https://secure-web.cisco.com/1VugCXXwalKKVT7bLxwwxB0wUwO_LQ0hZG5P6oNAE9_RkA…> >>>>>> Thread >>>>>> <https://secure-web.cisco.com/1H-6HNMBxeDbZPyhVbOH9A2eLQckCsYtW7MQ3G9W6kDVwa…> >>>>>> Douglas N Greve >>>>>> <https://secure-web.cisco.com/1M-leUu9vjxLEhQIgnl6dfbF3d7ST4-ULxvVl3JoB7UDa6…> >>>>>> >>>>>> Donatas, please remember to include previous correspondence so that we >>>>>> have everything in one email. Can you upload your freesurfer subject so >>>>>> that I can debug it further? upload to >>>>>> >>>>>> *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1eGgq3MtUZinN6YC13LiaDErXWJN9vgi9QwYQxtVWBl6Ea… <https://secure-web.cisco.com/1IYyWkyzVzqvMHe5CQVU03U4UqcuGDMK5jId9qWFaW81r6…> >>>>>> >>>>>> >>>>>> On 11/09/2016 12:17 PM, Donatas Sederevicius wrote: >>>>>> > >>>>>> > I followed the processing workflow as described in PETSurfer wiki >>>>>> > and gtmseg.mgz was created using gtmseg script as described. I >>>>>> > ran this processing for over 100 subjects and only one has failed. >>>>>> > >>>>>> > >>>>>> > >>>>>> > ___ >>>>>> > 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/1sA96g6MVXhTKqyIohE7iDpAeVudtNSoraQRr6PoymCFS6… <https://secure-web.cisco.com/1Aj-KIXWBSRBh4QYhiT5lPQzukbBDpNzMoSUI14TDJiN4-…> >>>>>> >>>>>> -- >>>>>> Douglas N. Greve, Ph.D. >>>>>> MGH-NMR Centergr...(a)nmr.mgh.harvard.edu >>>>>> Phone Number: 617-724-2358 >>>>>> Fax: 617-726-7422 >>>>>> >>>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://secure-web.cisco.com/18hglveD2QhtSJ7bQFM9F3sXBln9p2f7eLtue0lnyouc5FB…> >>>>>> FileDrop: *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1eGgq3MtUZinN6YC13LiaDErXWJN9vgi9QwYQxtVWBl6Ea… <https://secure-web.cisco.com/1IYyWkyzVzqvMHe5CQVU03U4UqcuGDMK5jId9qWFaW81r6…>*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/1En2sExPLORX4J1w9LZmBmOFgR3GA3uFmBVMOMf2e7NMCyv… <http://secure-web.cisco.com/19vdC8-giAFd6ifd70PmXkEzKNFxO_PL9uIhgUKTBRjgXJM…> >>>>>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>>>> >>>>>> ___ >>>>>> Freesurfer mailing listFreesurfer(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/1sA96g6MVXhTKqyIohE7iDpAeVudtNSoraQRr6PoymCFS6… <https://secure-web.cisco.com/1Aj-KIXWBSRBh4QYhiT5lPQzukbBDpNzMoSUI14TDJiN4-…> >>>>>> >>>>>> >>>>>> The information in this e-mail is intended only for the person to whom it is >>>>>> addressed. If you believe this e-mail was sent to you in error and the e-mail >>>>>> contains patient information, please contact the Partners Compliance HelpLine at*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/1pcd3R17cw9CUmO-RFZqcKXMAKlR9Hi_f5yRd0WcMyKMI2V… <http://secure-web.cisco.com/1Kuqledw2eJViDlbH8MA0_r7jBLVXWD3VreLVXqKwRqHFX1…> . If the e-mail was sent to you in error >>>>>> but does not contain patient information, please contact the sender and properly >>>>>> dispose of the e-mail. >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> Re: [Freesurfer] mri_gtmpvc error: failed tissue type check >>>>>> <https://secure-web.cisco.com/1yv39xApOHJ3FS6xDcFycnMnbHtStZeNBiLl3QzfL8G4yu…> >>>>>> 2016-11-09 >>>>>> <https://secure-web.cisco.com/1VugCXXwalKKVT7bLxwwxB0wUwO_LQ0hZG5P6oNAE9_RkA…> >>>>>> Thread >>>>>> <https://secure-web.cisco.com/1H-6HNMBxeDbZPyhVbOH9A2eLQckCsYtW7MQ3G9W6kDVwa…> >>>>>> Donatas Sederevicius >>>>>> <https://secure-web.cisco.com/1JNZMWhSBxxqZ4whfRrQXZBTWg88CVAVN7kKCidcLVIRKl…> >>>>>> >>>>>> I followed the processing workflow as described in PETSurfer wiki and >>>>>> gtmseg.mgz was created using gtmseg script as described. I ran this processing >>>>>> for over 100 subjects and only one has failed. >>>>>> ___ >>>>>> Freesurfer mailing listFreesurfer(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/1sA96g6MVXhTKqyIohE7iDpAeVudtNSoraQRr6PoymCFS6… <https://secure-web.cisco.com/1Aj-KIXWBSRBh4QYhiT5lPQzukbBDpNzMoSUI14TDJiN4-…> >>>>>> >>>>>> >>>>>> The information in this e-mail is intended only for the person to whom it is >>>>>> addressed. If you believe this e-mail was sent to you in error and the e-mail >>>>>> contains patient information, please contact the Partners Compliance HelpLine at*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/1pcd3R17cw9CUmO-RFZqcKXMAKlR9Hi_f5yRd0WcMyKMI2V… <http://secure-web.cisco.com/1Kuqledw2eJViDlbH8MA0_r7jBLVXWD3VreLVXqKwRqHFX1…> . If the e-mail was sent to you in error >>>>>> but does not contain patient information, please contact the sender and properly >>>>>> dispose of the e-mail. >>>>>> >>>>>> >>>>>> >>>>>> Re: [Freesurfer] mri_gtmpvc error: failed tissue type check >>>>>> <https://secure-web.cisco.com/1vPxlf-9EcToYjQ2NcohNFPvheryGJhjZq4nxdkmbOKRg2…> >>>>>> 2016-11-09 >>>>>> <https://secure-web.cisco.com/1VugCXXwalKKVT7bLxwwxB0wUwO_LQ0hZG5P6oNAE9_RkA…> >>>>>> Thread >>>>>> <https://secure-web.cisco.com/1H-6HNMBxeDbZPyhVbOH9A2eLQckCsYtW7MQ3G9W6kDVwa…> >>>>>> Douglas Greve >>>>>> <https://secure-web.cisco.com/1WfAMB3Ad9t1D_s6Buw38joSkwdCcFg-F8c6cN0W9n84zV…> >>>>>> >>>>>> Was gtmseg.mgz created with the gtmseg script? >>>>>> >>>>>> >>>>>> On 11/9/16 4:43 AM, Donatas Sederevicius wrote: >>>>>> >>>>>> >>>>>> Dear Freesurfer community, >>>>>> >>>>>> An error has occured while applying PET partial volume correction >>>>>> using mri_gtmpvc. A snippet from the log file: >>>>>> >>>>>> >>>>>> Reading /projects/PET/recon/ID247/mri/gtmseg.lta >>>>>> Replacing 18 >>>>>> ERROR: CheckSegTissueType() tissue type for seg 29 Left-undetermined >>>>>> not set >>>>>> >>>>>> Failed tissue type check >>>>>> >>>>>> gtmseg was run as: gtmseg --s ID247 and completed without errors. >>>>>> >>>>>> mri_gtmpvc was run as: >>>>>> >>>>>> mri_gtmpvc --i /projects/PET/processed/ID247/ID247_PIBStatic.nii.gz >>>>>> --psf 2 --no-rescale --seg /projects/PET/recon/ID247/mri/gtmseg.mgz >>>>>> --reg /projects/PET/processed/ID247/PET2MRI.lta --default-seg-merge >>>>>> --o /projects/PET/processed/ID247/gtmpvcYES.output/SGTM/non_scaled >>>>>> --save-input --km-ref 8 47 --km-hb 11 12 13 50 51 52 >>>>>> >>>>>> >>>>>> How could this problem be solved? >>>>>> >>>>>> Thank you. >>>>>> >>>>>> Best regards, >>>>>> >>>>>> Donatas >>>>>> >>>>>> >>>>>> >>>>>> ___ >>>>>> Freesurfer mailing listFreesurfer(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/1sA96g6MVXhTKqyIohE7iDpAeVudtNSoraQRr6PoymCFS6… <https://secure-web.cisco.com/1Aj-KIXWBSRBh4QYhiT5lPQzukbBDpNzMoSUI14TDJiN4-…> >>>>>> >>>>>> >>>>>> ___ >>>>>> Freesurfer mailing listFreesurfer(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/1sA96g6MVXhTKqyIohE7iDpAeVudtNSoraQRr6PoymCFS6… <https://secure-web.cisco.com/1Aj-KIXWBSRBh4QYhiT5lPQzukbBDpNzMoSUI14TDJiN4-…> >>>>>> >>>>>> >>>>>> The information in this e-mail is intended only for the person to whom it is >>>>>> addressed. If you believe this e-mail was sent to you in error and the e-mail >>>>>> contains patient information, please contact the Partners Compliance HelpLine at*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/1pcd3R17cw9CUmO-RFZqcKXMAKlR9Hi_f5yRd0WcMyKMI2V… <http://secure-web.cisco.com/1Kuqledw2eJViDlbH8MA0_r7jBLVXWD3VreLVXqKwRqHFX1…> . If the e-mail was sent to you in error >>>>>> but does not contain patient information, please contact the sender and properly >>>>>> dispose of the e-mail. >>>>>> >>>>>> >>>>>> >>>>>> [Freesurfer] mri_gtmpvc error: failed tissue type check >>>>>> <https://secure-web.cisco.com/1-KTvEDdAuFhtSF_p9XP0T2HYXV7p_VXGloR253IuV-slW…> >>>>>> 2016-11-09 >>>>>> <https://secure-web.cisco.com/1VugCXXwalKKVT7bLxwwxB0wUwO_LQ0hZG5P6oNAE9_RkA…> >>>>>> Thread >>>>>> <https://secure-web.cisco.com/1H-6HNMBxeDbZPyhVbOH9A2eLQckCsYtW7MQ3G9W6kDVwa…> >>>>>> Donatas Sederevicius >>>>>> <https://secure-web.cisco.com/1JNZMWhSBxxqZ4whfRrQXZBTWg88CVAVN7kKCidcLVIRKl…> >>>>>> >>>>>> Dear Freesurfer community, >>>>>> >>>>>> >>>>>> >>>>>> An error has occured while applying PET partial volume correction using >>>>>> mri_gtmpvc. A snippet from the log file: >>>>>> >>>>>> >>>>>> >>>>>> Reading /projects/PET/recon/ID247/mri/gtmseg.lta >>>>>> Replacing 18 >>>>>> ERROR: CheckSegTissueType() tissue type for seg 29 Left-undetermined not set >>>>>> Failed tissue type check >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> gtmseg was run as: gtmseg --s ID247 and completed without errors. >>>>>> >>>>>> mri_gtmpvc was run as: >>>>>> >>>>>> mri_gtmpvc --i /projects/PET/processed/ID247/ID247_PIBStatic.nii.gz --psf 2 >>>>>> --no-rescale --seg /projects/PET/recon/ID247/mri/gtmseg.mgz --reg >>>>>> /projects/PET/processed/ID247/PET2MRI.lta --default-seg-merge --o >>>>>> /projects/PET/processed/ID247/gtmpvcYES.output/SGTM/non_scaled --save-input >>>>>> --km-ref 8 47 --km-hb 11 12 13 50 51 52 >>>>>> >>>>>> >>>>>> >>>>>> How could this problem be solved? >>>>>> >>>>>> >>>>>> >>>>>> Thank you. >>>>>> >>>>>> >>>>>> >>>>>> Best regards, >>>>>> >>>>>> Donatas >>>>>> ___ >>>>>> Freesurfer mailing listFreesurfer(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/1sA96g6MVXhTKqyIohE7iDpAeVudtNSoraQRr6PoymCFS6… <https://secure-web.cisco.com/1Aj-KIXWBSRBh4QYhiT5lPQzukbBDpNzMoSUI14TDJiN4-…> >>>>>> >>>>>> >>>>>> The information in this e-mail is intended only for the person to whom it is >>>>>> addressed. If you believe this e-mail was sent to you in error and the e-mail >>>>>> contains patient information, please contact the Partners Compliance HelpLine at*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/1pcd3R17cw9CUmO-RFZqcKXMAKlR9Hi_f5yRd0WcMyKMI2V… <http://secure-web.cisco.com/1Kuqledw2eJViDlbH8MA0_r7jBLVXWD3VreLVXqKwRqHFX1…> . If the e-mail was sent to you in error >>>>>> but does not contain patient information, please contact the sender and properly >>>>>> dispose of the e-mail. >>>>>> >>>>>> _______________________________________________ >>>>>> 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/1sA96g6MVXhTKqyIohE7iDpAeVudtNSoraQRr6PoymCFS6… >>>>>> <https://secure-web.cisco.com/14NSCNEWI-E5xedPGXzQlT7gdo_k2vDQZC-njeqsKjvbqv…> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing listFreesurfer(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/1sA96g6MVXhTKqyIohE7iDpAeVudtNSoraQRr6PoymCFS6… <https://secure-web.cisco.com/1VZK27znP4ziWcnYrbJVNYOFT_9_5WAe5nVeyQOdMJhBJq…> >>>>> >>>>> >>>>> _______________________________________________ >>>>> 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/1sA96g6MVXhTKqyIohE7iDpAeVudtNSoraQRr6PoymCFS6… >>>>> <https://secure-web.cisco.com/1VZK27znP4ziWcnYrbJVNYOFT_9_5WAe5nVeyQOdMJhBJq…> >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing listFreesurfer(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/1sA96g6MVXhTKqyIohE7iDpAeVudtNSoraQRr6PoymCFS6… <https://secure-web.cisco.com/1DOc6HK09tTHDCTRe3zaykFn4umMUwn8-y6MGj0gOXqv_Q…> >>>> >>>> >>>> _______________________________________________ >>>> 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/1sA96g6MVXhTKqyIohE7iDpAeVudtNSoraQRr6PoymCFS6… >>>> <https://secure-web.cisco.com/1DOc6HK09tTHDCTRe3zaykFn4umMUwn8-y6MGj0gOXqv_Q…> >>> >>> > _______________________________________________ > Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://secure-web.cisco.com/1sA96g6MVXhTKqyIohE7iDpAeVudtNSoraQRr6PoymCFS6…

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Freesurfer Versions - Zeros in the Cortex
by Daniel Gutstein 06 Apr '21

06 Apr '21

External Email - Use Caution Hello, We are looking at the vertex-wise thickness measures for participants within the fsaverage space. There are a number of indices within the cortex that have thickness values of 0 in the thickness.fsaverage.mgh surface files. In FreeSurfer version 5.1, those same indices no longer have thickness 0 in the corresponding rh and lh fwhm smoothed thickness surface files due to the smoothing effect. However, in versions 6 and 7.1.1, the indices with 0 values remain 0 even in the fwhm smoothed files. Do you know why it was chosen that smoothing should have no impact on zeros in the later versions of FreeSurfer? Also, if we are interested in impacting the zeros from the later versions, is there a methodology which you would recommend? Thanks, Daniel

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