Freesurfer March 2021

freesurfer@nmr.mgh.harvard.edu

106 participants
144 discussions

Autorecon1 failure
by Abdollahi, Shervin (NIH/NINDS) [C] 19 Apr '21

19 Apr '21

External Email - Use Caution Hello Freesurfer Developers, am trying to use run freesurfer that is configured inside smriprep.workflow.anatomical.py under init_anat_preproc_wf pipeline. this workflow, does the following: 1. T1w reference: realigning and then averaging T1w images 2. Brain Extraction and INU (bias field) correction (antsBrainExtraction.sh) 3. Brian tissue segmentation (@fsl_fast) 4. Spatial normalization to standard space (antsRegistration) 5. Surface reconstruction with Freesurfer When it gets to step 5, it takes skull-stripped t1, ants_segm, and bias_corrected image to use in freesurfer recon-all command. In the surface reconstruction section, it starts by running the following command: recon-all -autorecon1 -i /path-to /sub-03_ses-20140624_T1w.nii -T2 /path-to/sub-03_ses-20140624_T2w.nii -noskullstrip -hires -openmp 1 -subjid sub-03 -sd /Users/abdollahis2/Desktop/fcd_nipype/derivatives/freesurfer -expert /Users/abdollahis2/Desktop/fcd_nipype/single_subject_03/anat_preproc_wf/surface_recon_wf/_subject_id_03/autorecon1/expert.opts And surely soon, it gives me an error that it can not read mgh file (brainmask.mgz). looking into freesurfer/sub-03/mri directory I can see that brainmask.mgz is not created and I am not sure if this is because the option -noskullstrip was used? I have attached the recon-all.log file. I would appreciate any suggestion on how to debug this problem. 1. Freesurfer version: 7.1.1 (freesurfer-darwin-macOS-7.1.1-20200811-8b40551) 2. Platform: macOS Catalina, Version 10.15.7 3. uname -a: Darwin ndsd-eeg-cedar 19.6.0 Darwin Kernel Version 19.6.0: Tue Jan 12 22:13:05 PST 2021; root:xnu-6153.141.16~1/RELEASE_X86_64 x86_64 4. Recon-all.log: see attached

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Talairach Failed: Distorted T1
by Harkey, Thomas Jarrott 18 Apr '21

18 Apr '21

External Email - Use Caution Hello, My name is Thomas Harkey and I am conducting research using FreeSurfer. After running recon-all on this patient, the Talairach failed according to the .log file. No stats were calculated but loading the orig.mgz file into FreeView looks like this (see image attached). This DICOM file was successfully uploaded into other programs. How can I fix this error? Kind regards, -- Thomas Harkey University of Arkansas for Medical Sciences College of Medicine, Class of 2022 501-553-6318 TJHarkey(a)uams.edu<mailto:TJHarkey@uams.edu> ---------------------------------------------------------------------- Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.

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Tract endpoint density map surface overlay
by バキット・ムダシル 16 Apr '21

16 Apr '21

External Email - Use Caution Hi everyone, I need to confirm if the steps below are correct, so I would like to ask freesurfer experts help. By using the Left-Cerebral-White-Matter mask imported from freesurfer as a seed I created a tract end points density image of the arcuate fasciculus in a NIFTI format (first figure). I want to display the image on the same subject’s white matter surface. So, I wrote the command as follows mri_vol2surf --src DensityMAP.nii.gz --out filename.mgh --hemi lh --surf white --out_type mgh --regheader subject_id The output as seen in the second figure. Thanks Mudathir

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Failed tissue type check {Disarmed}
by Julie Ottoy 15 Apr '21

15 Apr '21

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@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 athttp://http://secure-web.cisco.com/1Kuqledw2eJViDlbH8MA0_r7jBLVXWD3VreLVX… . 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 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 > 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 FileDrop: https://secure-web.cisco.com/1ThbUNbSt9_UBVJvAmBRnAaRfVWyZ0ej5JxRkdyy8xuH36… Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 athttp://http://secure-web.cisco.com/1Kuqledw2eJViDlbH8MA0_r7jBLVXWD3VreLVX… . 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@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 athttp://http://secure-web.cisco.com/1Kuqledw2eJViDlbH8MA0_r7jBLVXWD3VreLVX… . 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@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 athttp://http://secure-web.cisco.com/1Kuqledw2eJViDlbH8MA0_r7jBLVXWD3VreLVX… . 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@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 athttp://http://secure-web.cisco.com/1Kuqledw2eJViDlbH8MA0_r7jBLVXWD3VreLVX… . 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.

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Re: [Freesurfer] striatal parcellation
by Marques Ana-raquel 14 Apr '21

14 Apr '21

External Email - Use Caution ? Dear Freesurfer Team, we would like to perform a volumetric analysis in Parkinson's disease using freesurfer, and we have previously used recon all to perform tha surface based analysis and automate segmentation. We would also like to extract the different volumes of striatal parcellation using the Choi2012_7Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz. However, we can't find how to perform this parcellation, and how to add it to the recon all steps? Thank you very much for your help! ? Ana Marques MD, PhD Service de Neurologie Hopital Gabriel-Montpied CHRU Clermont-Ferrand ar_marques(a)chu-clermontferrand.fr<mailto:ar_marques@chu-clermontferrand.fr> TEL: 04 73 751 600 FAX: 04 73 751 596

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make_average_subject error
by Jordan Mullins 14 Apr '21

14 Apr '21

External Email - Use Caution Hello, I am trying to create an average subject from a set of subjects, but keep getting an error that says "mghRead(mri/norm.mgz, -1): could not open file". I've read that several others have solved this issue by installing the patch available at http://secure-web.cisco.com/1holHARxUGo27ZLvlj5vX0sbezsRgmRaNdE1T-Z728EASqG…. I did this, but continue to get the same error. I'm working with Freesurver Version 6.0.0 and MacOS Big Sur Version 11.2.3. I've attached the recon-all.log below, but please let me know if you need additional information. Any insight on this would be appreciated! Thank you! Jordan -- *Jordan L. Mullins, B.A.* Doctoral Student, Department of Psychology University of California, Riverside http://secure-web.cisco.com/1mshZJHsrG2WjtWWNRNV7vunyA6LicMMo4DqXl-CgSaJWwH…

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How to edit GM when WM is ok
by Caroline Chwiesko 09 Apr '21

09 Apr '21

External Email - Use Caution Hello Freesurfer experts, i am doing some editing after recon-all. I have the issue that one gyrus is not captured by the pial surface. There is no wm that is wrong and that i could correct. It looks like this gyrus has a weird angle so there is actually no WM visible. How can such an error be corrected? I am happy to send a couple images if needed. Thank you very much in advance for any help! Cheers Carolin

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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

2 3

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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Freesurfer March 2021