Freesurfer

freesurfer@nmr.mgh.harvard.edu

8 participants
30078 discussions

Re: [Freesurfer] Samseg dice is low
by Cerri, Stefano 04 Sep '22

04 Sep '22

Hi Dilek, 0.2 Dice seems extremely low. Also, in my experience, a threshold of 0.05 on T1w-FLAIR scans will show up many FP lesions. We usually reported a Dice in the range of 0.50-0.65 on various datasets (MS and WMH, default threshold, T1w-FLAIR), so I'm surprised by a such low value. Can you share with us your run_samseg command? Stefano Date: Sun, 4 Sep 2022 15:53:17 +0300 From: Dilek ?zkan <dozkan521(a)gmail.com> Subject: To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <CAPQSyvLqkvjk7JFxFoAG8RcX7ff40TS70vzvF6uWWHwC6CgqEg(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Hello all, I use Freesurfer-Samseg for MS lesion segmentation(cross-sectional). I use the T1 and Flair for this. (just these are inputs) I registered *flair and t1 to DIR *for every patient. (My manual lesion masks are on DIR imaging.) I controlled the registrations, these are true. I created a binary lesion mask using *threshold 0.05. *(mri_binarize --i /data/projects/MS_MRI/posteriors/Lesions.mgz --o /data/projects/MS_MR/binarize/lesion_binary.mgz --min 0.05) I checked the dice score with ground truth values with python. *threshold *0.05= *dice* 0,2 of the dataset Do you have any recommendations to increase the dice? # cvs_version 7.2.0 # sysname Linux # machine x86_64 Best regards

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Samseg dice is low
by Dilek Özkan 04 Sep '22

04 Sep '22

External Email - Use Caution Hello all, I use Freesurfer-Samseg for MS lesion segmentation(cross-sectional). I use the T1 and Flair for this. (just these are inputs) I registered *flair and t1 to DIR *for every patient. (My manual lesion masks are on DIR imaging.) I controlled the registrations, these are true. I created a binary lesion mask using *threshold 0.05. *(mri_binarize --i /data/projects/MS_MRI/posteriors/Lesions.mgz --o /data/projects/MS_MR/binarize/lesion_binary.mgz --min 0.05) I checked the dice score with ground truth values with python. *threshold *0.05= *dice* 0,2 of the dataset Do you have any recommendations to increase the dice? # cvs_version 7.2.0 # sysname Linux # machine x86_64 Best regards

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Re: [Freesurfer] Illegal Instruction (mri_segment_hypothalamic_subunits) - VM 7.2.0
by fsbuild 03 Sep '22

03 Sep '22

External Email - Use Caution Hello Randy, The mri_segment_hypothalamic_subunits command is a python script that uses tensorflow which in turn is coded to use AVX instructions.  If the VM host processor does not support AVX instructions, then you will get an illegal instruction error. You can check to see if AVX instructions are supported if this commands shows "avx" or "avx2" in the output (see screenshot for where that is the case). $ lscpu | grep avxIf AVX instructions are supported, then error can also happen if the command is incomplete. - R.

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Re: [Freesurfer] problem with autorecon2-cp
by Mostafa Fakhri 03 Sep '22

03 Sep '22

External Email - Use Caution Hi Doug, Thank You for your response I have a new problem I used -autorecon1 and autorecon2-cp: recon-all -sd /share/users/mfakhri/freeSurfer-analys/subjects -subject fastWM -i /share/users/mfakhri/freeSurfer-analys/100610_7T/T1w.nii.gz -autorecon1 -autorecon2-cp But process was stopped after half an hour with this error: $ cat /share/users/mfakhri/freeSurfer-analys/subjects/fastWM/mri/error.log mghRead(/share/users/mfakhri/freeSurfer-analys/subjects/fastWM/mri/norm.mgz, -1): could not open file Mostafa

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Request for 7 zip password VM_67
by Cristian Neira 02 Sep '22

02 Sep '22

External Email - Use Caution Hello, I just need a passcode to archive the zip folder for file FS_7_2_0_ubuntu_18_04_06.ova so that I can install a FreeSurfer virtual disk. Thanks, Cristian

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FreeView feature request
by Aaron Tanenbaum 02 Sep '22

02 Sep '22

External Email - Use Caution I am looking set up freesurfer to do two things. If they are not currently possible then I would like to submit two feature requests for freeview. Here they are When making voxel edits, it would be useful to see all voxels the mouse is pointing to. Currently the mouse looks like a pen pointing to one voxel. If my brush size is 5, it would be nice if all 25 voxels are highlighted. It would also be convenient to have the voxels that have been edited in a single brush stroke highlighted.. Frequently I will be making an edit to an image while another image is overlaid on top of it. So I can not see my edits. forcing me to toggle between images. Thank you

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Postdoc: Brain networks, development, and mental illness risk
by Signe Bray 02 Sep '22

02 Sep '22

External Email - Use Caution Drs. Emma Towlson and Signe Bray at the University of Calgary are seeking applications for a postdoctoral scholar who will use c*omputational modeling of brain network alterations to study relationships to mental illness risk*. The project will involve working with neuroimaging data to build whole-brain simulations and examine network characteristics. Depending on interest, the postdoc may play a role in study design, data collection and processing, though the focus is modeling and data analysis. This is a 2-year position with the possibility of extension. Applicants should have interest in computational approaches to brain and mental health and have a background in network neuroscience, psychology, neurosciences, physics, biomedical engineering, or a related discipline. Experience with neuroimaging and strong data analytic skills are required. Calgary is a city of ~1.3M located a short-drive from Canada’s Rocky Mountains, offering outstanding outdoor recreation opportunities and more days of sunshine per year than any other major Canadian city. The postdoc will integrate with more than 300 Brain and Mental Health researchers at UCalgary and benefit from a new Computational Neuroscience Platform ( https://secure-web.cisco.com/17Kog-EAduJ6JkIBsDLKbEmlZaM8f3jyTiFiopeWtCLjVZ…) Interested candidates can find more details here https://secure-web.cisco.com/1UNSbOBLYUqexjCjYi1cQrH3hT9oGInSvtQKwe-O89g9Fp… and submit a letter of interest and CV to slbray(a)ucalgary.ca and emma.towlson(a)ucalgary.ca or reach out with any questions.

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TRACULA - Ball-and-stick model fit running time
by Liliana Wu 02 Sep '22

02 Sep '22

External Email - Use Caution Hi, I have successfully run the preprocessing steps for my DWI data, and I was wondering how long does bedpostx usually take to process DWI? I am running on a high-powered computer (cluster) and a multi-shell data 3 b-values of (b= 1000s/mm2, 34 directions; b= 1600s/mm2, 45 directions; and b= 2600s/mm2, 66 directions). Thank you, Liliana

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Re: [Freesurfer] Shift in cortical parcellation, issues with previously suggested solution
by Trolle, Carl 02 Sep '22

02 Sep '22

Hi, I believe so, I ran the following commands: mris_register -L subject/label/?h.central_sulcus.label $FREESURFER_HOME/average/?h.destrieux.simple.2009-07-29.gcs S_central subject/surf/?h.sphere $FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif subject/surf/?h.sphere.reg.new and then: mris_ca_label subject ?h subject/surf/?h.sphere.reg.new $FREESURFER_HOME/average/?h.destrieux.simple.2009-07-29.gcs subject/label/?h.aparc.a2009s.annot.new Overlaying the new annot-file over the inflated surface with the sulci visible moved the central sulcus to the designated spot (please see attached). This however seems to have caused the S_front_inf (yellow outline) to split into two. Kind regards, Carl

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Illegal Instruction (mri_segment_hypothalamic_subunits) - VM 7.2.0
by daedalus39＠aol.com 02 Sep '22

02 Sep '22

External Email - Use Caution Dear FreeSurfer developers, I cannot seem to get "mri_segment_hypothalamic_subunits" to work using the virtualbox installation of FS-7.2.0. I have a subject that ran to completion using recon-all, but when I tried to obtain the additional segmentation I keep getting "Illegal instruction (core dumped)". I have tried several permutations of the command (see below)(I did not include some of the extended syntax permutations (--sd, etc) in the list below, but I did try several - -> Illegal etc) It occurred to me that I should just attempt to see if the "help" command would work, so I simply copied the syntax directly from the wiki page mri_segment_hypothalamic_subunits -h... and as you can see below, that also returned "Illegal instruction (core dumped)". I even tried a direct copy of the syntax for "bert". No joy. Is this module actually implemented in the VM?Are there any suggestions regarding syntax, where the command is executed, etc.? Thanks in advance for any help you can offer. -Randy xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx developer@developer-VirtualBox:/$ lsbin dev initrd.img lib64 mnt root snap sys varboot etc initrd.img.old lost+found opt run srv tmp vmlinuzcdrom home lib media proc sbin swapfile usr vmlinuz.old developer@developer-VirtualBox:/$ mri_segment_hypothalamic_subunits --s WBI-FES_S_0862 --write_posteriorsIllegal instruction (core dumped)developer@developer-VirtualBox:/$ pwd/developer@developer-VirtualBox:/$ cd /usr/local/freesurfer/7.2.0/subjects/developer@developer-VirtualBox:/usr/local/freesurfer/7.2.0/subjects$ mri_segment_hypothalamic_subunits --s bertIllegal instruction (core dumped)developer@developer-VirtualBox:/usr/local/freesurfer/7.2.0/subjects$ mri_segment_hypothalamic_subunits --hIllegal instruction (core dumped)developer@developer-VirtualBox:/usr/local/freesurfer/7.2.0/subjects$ mri_segment_hypothalamic_subunits --helpIllegal instruction (core dumped)developer@developer-VirtualBox:/usr/local/freesurfer/7.2.0/subjects$ mri_segment_hypothalamic_subunits -helpIllegal instruction (core dumped)developer@developer-VirtualBox:/usr/local/freesurfer/7.2.0/subjects$ mri_segment_hypothalamic_subunits -hIllegal instruction (core dumped)developer@developer-VirtualBox:/usr/local/freesurfer/7.2.0/subjects$ mri_segment_hypothalamic_subunits --s WBI-WCM_S_0862 --write_posteriors --crop 1000Illegal instruction (core dumped)developer@developer-VirtualBox:/usr/local/freesurfer/7.2.0/subjects$ xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx -------- freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME /usr/local/freesurfer/7.2.0FSFAST_HOME /usr/local/freesurfer/7.2.0/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR /usr/local/freesurfer/7.2.0/subjectsMNI_DIR /usr/local/freesurfer/7.2.0/mnideveloper@developer-VirtualBox:~$

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