Freesurfer June 2021

freesurfer@nmr.mgh.harvard.edu

97 participants
140 discussions

which file is freesurfer autoseg result?
by 1248742467 15 Jun '21

15 Jun '21

External Email - Use Caution hello, FSI do the brain region parcellation, I have label(ground truth) for each subject. I want to use my own neural network segmentation results and Freesurfer automatic segmentation results comparison, to get a qualitative and quantitative results? Which file in the label folder is the result of automatic segmentation? And how do I get quantitative results? As seen in some articles, the result of automatic segmentation by Freesurfer is 84.39 for DICE and 85.19 for ACC.

2 1

Re: [Freesurfer] T1 hippocampal subfields exited with ERRORS
by 林鈺庭 15 Jun '21

15 Jun '21

External Email - Use Caution Dear Eugenio, We checked the RAM setting of the Docker container and found it was default using 2GB RAM! Then we set the Maximum RAM up to 16GB and work all done!! Thank you for your patience helping so much! Wish you have a great day! Best regards, Josephine <freesurfer-request(a)nmr.mgh.harvard.edu> 於 2021年6月12日週六上午12:01寫道： > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://secure-web.cisco.com/1_MhR_xuFQQ6f3qyQNiH1uM9hERvO8xgb2j3Rov_l0il6h… > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. Re: T1 hippocampal subfields exited with ERRORS > (Iglesias Gonzalez, Juan E.) > 2. Open Position: Postdoc or PhD Student for Deep Learning based > Lesion Recognition in human MRI (Dr. rer. nat. Johannes Jungilligens) > 3. Finding equivalent vertices on fsaverage_sym lh and rh > surfaces (Tim Sch?fer) > 4. Re: memory allocation error (Bernardoni, Fabio) > 5. Issues with recon-all hanging (Michael Datko) > 6. Re: how to visualize statistical maps in FS7.1? > (Bernardoni, Fabio) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 11 Jun 2021 11:52:08 +0000 > From: "Iglesias Gonzalez, Juan E." <JIGLESIASGONZALEZ(a)mgh.harvard.edu> > Subject: Re: [Freesurfer] T1 hippocampal subfields exited with ERRORS > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <2E162B79-9558-4942-8B6E-55A7B384D524(a)mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > Dear Josephine, > This is unusual. Could it be possible that you are running out of RAM > memory? Do you have 16GB or more available? > Cheers, > /Eugenio > > On 11 Jun 2021, at 01:39, ??? <ytlin923(a)g.ntu.edu.tw<mailto: > ytlin923(a)g.ntu.edu.tw>> wrote: > > > External Email - Use Caution > > Dear Developer and Eugenio, > > We encounter the error at the end of the analysis,it looks like this: > > Smoothing mesh collection with kernel size 0.750000 > .../usr/local/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: > line 40: 499 Killed > /usr/local/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML S013 /data > 0.333333333333333333333333333333333333 > /usr/local/freesurfer/average/HippoSF/atlas/AtlasMesh.gz > /usr/local/freesurfer/average/HippoSF/atlas/AtlasDump.mgz > /usr/local/freesurfer/average/HippoSF/atlas/compressionLookupTable.txt 0.05 > right L-BFGS v21 '/usr/local/freesurfer/bin/fs_run_from_mcr > /usr/local/freesurfer/bin/' 0 > Linux f8e6a6f8a44a 5.10.25-linuxkit #1 SMP Tue Mar 23 09:27:39 UTC 2021 > x86_64 x86_64 x86_64 GNU/Linux > > T1 hippocampal subfields exited with ERRORS at Thu Jun 10 10:22:54 UTC 2021 > > I've attached the log file here, could you help us with this error? Thank > you so much! > > Best regards, > Josephine > > <hippocampal-subfields-T1.log>_______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://secure-web.cisco.com/1_MhR_xuFQQ6f3qyQNiH1uM9hERvO8xgb2j3Rov_l0il6h… > >

2 1

In Freesurfer, the sulc value of the gyrus is NOT positive, on the contrary, they are negative?
by 1248742467 15 Jun '21

15 Jun '21

External Email - Use Caution Hello, Fs  In Freesurfer, the sulc value of the gyrus is NOT positive, on the contrary, they are negative？ by the way, how the mean curvature reflects the degree of fold? Since the mean curvature is a local measurement, does the mean curvature map reflects the fold degree? 

3 3

Error/shifting in cortical parcellation
by Helena-Céline Stevelt 15 Jun '21

15 Jun '21

External Email - Use Caution Dear Freesurfer Community, I wish to manually reassign/edit cortical parcellation performed by FS. We use the cortical parcellation done by FS and it has worked very well for most of our subjects. However, we have two subjects where the parcellation has not been done correctly. It seems that the central sulcus has been mis-classified to be one sulcus too far posterior in the brain - this has resulted in incorrect labeling of surrounding gyri. Curiously, it is only one hemisphere for both subjects (rh for one and lh for the other), where the other hemisphere is correctly parcellated. In our two mis-parcellated subjects, how might we manually reassign or guide FS to correctly classify the central sulcus and thus correctly label the surrounding gyri? I have attached a picture of an erroneous parcellation. Freesurfer version: freesurfer-linux-centos6_x86_64-dev-20201011-4d2b06a Platform: Ubuntu 16.04 Best, Helena-Céline Stevelt Danish Research Centre for Magnetic Resonance

2 2

HIRING: Postdoc and Research Tech
by Zollei, Lilla,Ph.D. 15 Jun '21

15 Jun '21

I am hiring at the Martinos Center, MGH. For details, see 1. Postdoc: https://scholar.harvard.edu/lillazollei/jobs 2. Research technician: https://partners.taleo.net/careersection/ghc/jobdetail.ftl?job=3156502 If you have any questions, let me know. Best, Lilla

1 0

the white matter surface is from the individual sMRI?
by 1248742467 14 Jun '21

14 Jun '21

External Email - Use Caution Hello, Fs can I get the white matter surface from individual smri？

2 1

can the white matter surface is from the individual sMRI?
by 1248742467 14 Jun '21

14 Jun '21

External Email - Use Caution Hello, Fs can I get the white matter surface from individual smri？

1 0

FreeSurfer cortical thickness
by Rosalia Dacosta Aguayo 14 Jun '21

14 Jun '21

External Email - Use Caution Dear Freesurfer's experts, I run FreeSurfer and I got the following stats: rosalia@rosalia-Lenovo-Y520-15IKBN /media/rosalia/Nuevo_vol/ARTICO/derivatives/freesurfer/sub-003/stats $ ls aseg.stats lh.BA_exvivo.thresh.stats rh.aparc.stats lh.aparc.a2009s.stats lh.curv.stats rh.BA_exvivo.stats lh.aparc.DKTatlas.stats lh.w-g.pct.stats rh.BA_exvivo.thresh.stats lh.aparc.pial.stats rh.aparc.a2009s.stats rh.curv.stats lh.aparc.stats rh.aparc.DKTatlas.stats rh.w-g.pct.stats lh.BA_exvivo.stats rh.aparc.pial.stats wmparc.stats rosalia@rosalia-Lenovo-Y520-15IKBN /media/rosalia/Nuevo_vol/ARTICO/derivatives/freesurfer/sub-003/stats $ A part from the aseg.stats file, which one should I consider if I am interested in cortical thickness. Should I run any other step for this? Best, Rosie

2 1

Samseg pallidum issue
by Russo, Andrew William 14 Jun '21

14 Jun '21

Hello FreeSurfer Developers, I ran longitudinal samseg on a group of subjects with MS (each with 5 MRI timepoints over 2 years) and found that the average volume of the pallidum increased over time, while other subcortical volumes (caudate, putamen, thalamus) decreased. I also tried longitudinal samseg using the --pallidum-separate flag and had similar results. As the putamen gets smaller it looks like the pallidum volume grows to fill in the space. Have you encountered this issue before? I am using enhanced T1 images (made from T1, FLAIR, and FA data) as the input for run_samseg_long (FreeSurfer v7). Thank you, Andrew Andrew Russo Clinical Research Coordinator Multiple Sclerosis Imaging Lab Massachusetts General Hospital 149 13th Street | Boston, MA 02129 617-726-7531

2 1

TRACULA trac-all cores/threads
by Drucker, Daniel 13 Jun '21

13 Jun '21

trac-all (TRACULA) seems to use multiple threads/cores. Is there a way to either (a) limit the number, or (b) determine how many it will use, so it can behave appropriately in a cluster? -- Daniel M. Drucker, Ph.D. Director of IT McLean Hospital Imaging Center Harvard Medical School

2 1

← Newer
1
...
6
7
8
9
10
11
12
13
14
Older →

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer June 2021