Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30086 discussions

VM ubuntu developer password
by FAIRS Amie 18 Jun '20

18 Jun '20

External Email - Use Caution Dear Freesurfer mailing list, I have just downloaded the virtual machine + ubuntu package, as outlined on the website when running a VM in windows. However, ubuntu is asking for a developer password to open within the VM. I see on the help page (on the website) that the log in ID could be in the README doc, but I can't actually get the VM open to get there. Does anyone know the password so I can set up the VM and get started with freesurfer? Thanks so much in advance! Best, Amie ------------------ Dr. Amie Fairs Post-doctorant Aix-Marseille Université Laboratoire Parole et Langage (LPL) | CNRS UMR 7309 | 5 Avenue Pasteur | 13100 Aix-en-Provence Email : amie.fairs(a)univ-amu.fr<mailto:amie.fairs@univ-amu.fr> While I may send this email outside of typical working hours, I have no expectation to receive an email outside of your typical hours.

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Correcting recon-all output (missing parts in pial surface)
by Michael 17 Jun '20

17 Jun '20

External Email - Use Caution Hello, I ran recon-all on a post-surgery MRI scan. Because of the resection area FreeSurfer did not include certain parts which should be included. What is the correct way of correcting this? I thought about editing the wm.mgz file by adding missing white matter using a brush value of 255 and erase white matter with a value of 1. Followed by re-creating the surfaces using: recon-all -autorecon2-wm -autorecon3 -subjid ... Thank you very much. Best Regards, Michael [image: fs.png]

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version 7 docker container
by David Pagliaccio 17 Jun '20

17 Jun '20

External Email - Use Caution Hello I was wondering if Freesurfer version 7 will be released as a container on docker hub?

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Re: [Freesurfer] Freesurfer license file error
by Hoopes, Andrew 17 Jun '20

17 Jun '20

Hi Mason, My guess is that freesurfer is still grabbing the initial license. Have you been sure to remove the original one? It might be hiding as a .license file Best Andrew From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Mason Wells <WellsMT1(a)cardiff.ac.uk> Reply-To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> Date: Wednesday, June 17, 2020 at 5:34 AM To: "freesurfer-bounces(a)nmr.mgh.harvard.edu" <freesurfer-bounces(a)nmr.mgh.harvard.edu>, FS Help <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Freesurfer license file error External Email - Use Caution Hi Expets, I am trying to work with the Ciftify package, a great tool for converting non-HCP data into cifti format. I am running the following docker command. However, I get an error with the return code 255 sudo docker run --entrypoint ciftify_recon_all -ti --rm -v /home/masontwells/Documents/Data/freesurfer/subjects:/data:ro -v /home/masontwells/Documents/Ciftify/HCP/outputs:/out tigrlab/fmriprep_ciftify:1.1.8-2.1.1 --surf-reg FS --fs-subjects-dir /data --ciftify-work-dir /out PPT_1x cmd: mri_convert /data/PPT_1x/mri/T1.mgz /out/PPT_1x/T1w/T1w.nii.gz Failed with returncode 255 At the bottom of the ciftify recon-all log it says the below. However, I downloaded the license as advised, placed it in the correct directory (usr/local/freesurfer). I have also added the path to the license to my bashrc. Have you seen this type of error before? GNU libc version: 2.23 ERROR: Systems running GNU glibc version greater than 2.15 require a newly formatted license file (it's free). Please download a new one from the following page: http://surfer.nmr.mgh.harvard.edu/registration.html -------------------------------------------------------------------------- Cheers, Mason Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK Email: WellsMT1(a)cardiff.ac.uk<mailto:WellsMT1@cardiff.ac.uk> Tel: 02920 879628 Web: Cardiff University webpage<https://www.cardiff.ac.uk/people/research-students/view/974214-> Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau’r Golwg & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU E-bost: WellsMT1(a)caerdydd.ac.uk<mailto:WellsMT1@caerdydd.ac.uk> Ffôn: 02920 879628

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total vertices does not match between results and labels
by Marina Fernández 17 Jun '20

17 Jun '20

External Email - Use Caution Dear experts, I am using the mri_surfcluster function to cluster the surface results: mri_surfcluster --subject fbb_average --mask mask.mgh --hemi lh --olab label --in sig_results_tvalues.mgh --thmin 0.000000000000001 When I count vertices different than 0 in the results file that I give as input (which contains only the significant vertex t values) I get a value (for example, total= 6237 vertices). The problem is that when I add the vertices of the output labels, the total number of vertices is less (for example: total=6152 vertices). Why does the number of total vertices not match? Is the function I use correct? Thank you very much in advance. Marina

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Ventricular location
by Ian 17 Jun '20

17 Jun '20

External Email - Use Caution Hi Freesurfers. I'm looking to find the center of the various Ventricles. Are they included in the freesurfer segmentation images with a specific code? If not, what approach would you use? Thanks, Ian -- *Ian Hardingham*

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freeview of freesurfer 7.1 incompatible with merged overlays
by Nick Blauch 17 Jun '20

17 Jun '20

External Email - Use Caution Hello Freesurfer experts, I recently upgraded to Freesurfer 7.1. Many nice changes so thanks for that. I often work with merged gifti files and the previous stable version of Freesurfer/Freeview (6.0) had no issue with them. Now, Freeview can view my unmerged overlays but not the merged ones. I get this error: Number of vertices in overlay data (1 or 1) does not match with surface (327684). The (very simple) matlab code used for merging giftis is here: https://github.com/viscog-cmu/bids_gen/blob/master/merge_fs_hemi_overlays.m . It simply concatenates left and right overlays into a single one which i plot on a merged surface. Wondering if anybody has any ideas? I have confirmed on an identical system using all the same files that this issue is specific to Freesurfer 7. The merged overlays work fine in python, matlab, etc. thanks, Nick -- *Nicholas M. Blauch* Ph.D. Student, Program in Neural Computation Carnegie Mellon University pronouns: he/him/his

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Freesurfer 7.1 processing error MacOS, manual fix code not working
by Annelies Vant Westeinde 17 Jun '20

17 Jun '20

External Email - Use Caution Dear all, As evidently experienced by others, a certain percentage of subjects failed to run on freesurfer 7.1 version, stopping at the segmentation step, while they could run in version 6. I read that this is bug is present in Mac os, which I am using (high sierra). I tried to fix it, as advised, using the following lines of code suggested: cd $FREESURFER_HOME/bin sudo rm rca-long-tp-init sudo curl https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/rca-lon… -o rca-long-tp-init sudo chmod +x rca-long-tp-init The first line seems to work. However, I get the following errors when runnding the lines from sudo curl: anneliess-ipro:bin k6-anneva1-s$ sudo curl https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/rca-lon… -o rca-long-tp-init sudo chmod +x rca-long-tp-init % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 13012 100 13012 0 0 35881 0 --:--:-- --:--:-- --:--:-- 35944 curl: (6) Could not resolve host: sudo curl: (6) Could not resolve host: chmod curl: (6) Could not resolve host: +x curl: (6) Could not resolve host: rca-long-tp-init I had already given my sudo password in the first step. I might be doing something very basic wrong. Could somebody help? Thanks! Annelies Annelies van't Westeinde | PHD Candidate Department of Women's and Children's Health | Karolinska Institutet 171 77 Solna | Karolinskavägen 37A +46 760967499 annelies.vant.westeinde(a)ki.se | ki.se<http://ki.se/en/startpage> ______________________________________ Karolinska Institutet – a medical university När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://ki.se/medarbetare/integritetsskyddspolicy>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI’s processing of personal data here<https://ki.se/en/staff/data-protection-policy>.

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Freesurfer license file error
by Mason Wells 17 Jun '20

17 Jun '20

External Email - Use Caution Hi Expets, I am trying to work with the Ciftify package, a great tool for converting non-HCP data into cifti format. I am running the following docker command. However, I get an error with the return code 255 sudo docker run --entrypoint ciftify_recon_all -ti --rm -v /home/masontwells/Documents/Data/freesurfer/subjects:/data:ro -v /home/masontwells/Documents/Ciftify/HCP/outputs:/out tigrlab/fmriprep_ciftify:1.1.8-2.1.1 --surf-reg FS --fs-subjects-dir /data --ciftify-work-dir /out PPT_1x cmd: mri_convert /data/PPT_1x/mri/T1.mgz /out/PPT_1x/T1w/T1w.nii.gz Failed with returncode 255 At the bottom of the ciftify recon-all log it says the below. However, I downloaded the license as advised, placed it in the correct directory (usr/local/freesurfer). I have also added the path to the license to my bashrc. Have you seen this type of error before? GNU libc version: 2.23 ERROR: Systems running GNU glibc version greater than 2.15 require a newly formatted license file (it's free). Please download a new one from the following page: http://surfer.nmr.mgh.harvard.edu/registration.html -------------------------------------------------------------------------- Cheers, Mason Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK Email: WellsMT1(a)cardiff.ac.uk<mailto:WellsMT1@cardiff.ac.uk> Tel: 02920 879628 Web: Cardiff University webpage<https://www.cardiff.ac.uk/people/research-students/view/974214-> Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau’r Golwg & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU E-bost: WellsMT1(a)caerdydd.ac.uk<mailto:WellsMT1@caerdydd.ac.uk> Ffôn: 02920 879628

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MGN and LGN in ThalamicNuclei segmentation
by julienbesle 17 Jun '20

17 Jun '20

External Email - Use Caution Hello, I'm interested in locating the MGN and LGN using segmentationThalamicNuclei, but there is a mismatch between their location in the discrete segmentation (ThalamicNuclei.v10.T1.mgz) and the underlying probability maps obtained by setting environment variable WRITE_POSTERIORS to 1. While the LGN in the segmentation has many voxels within the corresponding area of maximum probability, many high-probability voxels are missing from it. For the MGN, the segmentation volume is restricted to a small number of voxels in the most lateral/posterior/superior part of the area of max probability, but most high-probability voxels are absent from the segmentation. Any reason why this could be happening? Is there anything I can do (parameters I can change in the script) to fix this? The defaut Freesurfer segmentation ("thalamus proper") is generally larger than the segmentation output by segmentThalamicNuclei, except in the area of the LGN, where the thalamic segmentation extends more laterally/inferiorly, as if it had been extended in order to include the LGN (although imperfectly). Unfortunately, this does not seem to be the case for the MGN (which is my primary area of interest). To solve the issue, I'm thresholding the posterior probability maps at p>0.2 for both LGN and MGN and adding these voxels to the discrete segmentation, but that's not very satisfactory. Actually, it wasn't very clear to me from the published paper how the discrete segmentation is obtained from the posterior probability maps and if any cut-off value is used to decide whether to include any voxel in the final discrete segmentation? (Note that I'm using T1-weighted MPRAGE data at a resolution of 0.7 mm isotropic) Thanks Julien

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