Freesurfer June 2021

freesurfer@nmr.mgh.harvard.edu

97 participants
140 discussions

freesurfer-7.1.1 :: show_tal ::mri_show: Command not found
by Eric Deveaud 03 Jun '21

03 Jun '21

External Email - Use Caution Hello freesurfer-7.1.1 installed from rpm on centos8 show_tal tries to call mri_shown a non existing program in /usr/local/freesurfer/7.1.1/bin regards Eric

1 1

freesurfer-7.1.1 :: rebuild_gca_atlas.csh :: missing subjects.csh
by Eric Deveaud 03 Jun '21

03 Jun '21

External Email - Use Caution subjects.csh is not installed but rebuild_gca_atlas.csh requires it best regards Eric

1 0

mritotal for talairach registration in FS7
by Gabor Perlaki 03 Jun '21

03 Jun '21

External Email - Use Caution This email was sent 22 hours ago, but somehow it haven't appeared on the forum yet. I post it again. Gabor Perlaki <petzinger.gabor(a)gmail.com> ezt írta (időpont: 2021. jún. 2., Sze, 12:11): > The default talairach registration is wrong in ~20% of our subjects and > thus eTIV is also quite inaccurate (e.g. <1000 cc in certain cases). I > tried -use-mritotal which resulted in much more accurate talairach > registration. > My questions: > Q1, I think it's not a good idea to mix talairach_avi and mritotal > registrations in a single study, because they can consequently result in > different eTIV values or initialization parameters affecting the final > segmentations. Therefore it would be easier to run the whole analysis again > with mritotal as default rather than correcting the talairach registration > and rerunning the analysis in separate steps for each subject. Is the > following command OK for this purpose? > recon-all -s SUBJ -i input_dicom_file -use-mritotal -all > > Q2, Is mritotal only used to calculate talairach.xfm or are there any > other hidden analysis steps which may perform worse (even though > talairach.xfm is more accurate) when using it instead of talairach_avi? > > Q3, Is it more accurate to use sbTIV instead of eTIV? > > Thanks, > Gabor >

1 0

'help: aparcstats2table'
by Zeynep Boz 02 Jun '21

02 Jun '21

External Email - Use Caution Hello, I am using Ubuntu 18.05 version and Freesurfer6 version. I've completed all the recon-all parts without any problems, but I'm having trouble with the "aparcstats2table" part. The command "aparcstats2table --subject H1_deneme --hemi lh --meas thickness --tablefile lh.thicknes.xlsx" gives the following error: File "/usr/local/freesurfer/bin/aparcstats2table", line 156 print 'ERROR: atleast 1 subject must be provided' On the command "asegstats2table --subjects H1_deneme H1 --common-segs --meas volume --stats = aseg.stats --table = segstats.txt" gives the following error: File "/usr/local/freesurfer/bin/asegstats2table", line 195 print 'ERROR: subjects are not specified (use --subjects SUBJECTS)' Thank you in advance for your support Dr.Zeynep YÜKSEL Ondokuz Mayis University Vocational School of Health Services, Medical İmaging 55139, Atakum, Samsun, Turkey Tel: +903623121919 Ext:5261

2 1

mris_fix_topology taking ages
by Ellen Ji 02 Jun '21

02 Jun '21

External Email - Use Caution Dear experts, mris_fix_topology has been running for several hours now and the log suggests many more defects than normal. I tried to follow Bruce's advice from the thread here https://secure-web.cisco.com/11N_pSFTUOEZsMU7wtMNfIhMmRNWqmvsxTQeTGxdl-E3X_…, but wasn't able to load the &h.defect_labels as I received the error below. Attached is part of the recon-all.log (starting from mris_fix_topology). Is there any other way to check/visualize what might have gone wrong? FYI, I'm running recon-all thru the HCP Pipeline. Thanks! tksurfer avoss_01 lh defect_labels subject is avoss_01 hemi is lh surface is defect_labels surfer: current subjects dir: /home/eji/newdata/projects/avoss/HCP/subjects/avoss_01/T1w surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /mnt/newdata/projects/avoss/HCP/subjects/avoss_01/T1w/avoss_01/surf checking for nofix files in 'defect_labels' Reading image info (/home/eji/newdata/projects/avoss/HCP/subjects/avoss_01/T1w/avoss_01) Reading /home/eji/newdata/projects/avoss/HCP/subjects/avoss_01/T1w/avoss_01/mri/orig.mgz surfer: Reading header info from /home/eji/newdata/projects/avoss/HCP/subjects/avoss_01/T1w/avoss_01/mri/orig.mgz nquads=4063237, nvertices=664 ERROR: MRISread: file '/home/eji/newdata/projects/avoss/HCP/subjects/avoss_01/T1w/avoss_01/surf/lh.defect_labels' has many more faces than vertices! Probably trying to use a scalar data file as a surface! No such file or directory

4 7

Time courses and Yeo’s boundaries
by stdp82＠virgilio.it 02 Jun '21

02 Jun '21

1 0

Recon-all error :Segmentation fault (core dumped)
by liub 02 Jun '21

02 Jun '21

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to recon-all my NIfTI-1 data ,while after a few minutes of running,there was an error: mris_calc -o /dev/shm/tmp.mri_nu_correct.mni.897826/nu0.mgz /dev/shm/tmp.mri_nu_correct.mni.897826/nu0.mgz mul Segmentation fault (core dumped) Command exited with non-zero status 1 Also when I ran the command "recon-all -all -s bert" using the official data in */freesurfer/subjects/bert ,it raised the same error. I googled this error,but there's still no answer.I've attached the recon-all.log. The recon-all.log is belong to bert and recon-all(1).log is belong to my data. Here is my operating system info : uname -a: Linux HEUBME.com 4.18.0-193.28.1.el8_2.x86_64 #1 SMP Thu Oct 22 00:20:22 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux Platform: CentOS Linux release 8.3.2011 FreeSurfer version: freesurfer-Linux-centos8_x86_64-7.1.1 Thank you for your kind help. Best regards.

2 5

Freeview mghRead error
by Duvnjak, Aleksandar 02 Jun '21

02 Jun '21

External Email - Use Caution Dear Freesurfer Developers, I have recently switched to a Mac for ease of use and have encountered an error upon trying to view output files from a previous data cohort which were processed on a remote computing server and copied to this Mac's local drive. I am able to view all surfaces and volumes of the native bert tutorial set, however am unable to view my own outputs. In the terminal I receive the following error: Katarinas-MacBook-Pro:mdc026 kduvnjak$ freeview -v /Applications/freesurfer/subjects/mdc026/mri/wm.mgz mghRead(/Applications/freesurfer/subjects/mdc026/mri/wm.mgz, -1): could not open file MRIread failed: Unable to read from /Applications/freesurfer/subjects/mdc026/mri/wm.mgz mghRead(/Applications/freesurfer/subjects/mdc026/mri/wm.mgz, -1): could not open file 2021-06-02 11:07:49.903 Freeview[6760:441577] modalSession has been exited prematurely - check for a reentrant call to endModalSession: Please find below any additional relevant information: Freesurfer version: freesurfer-i386-apple-darwin11.4.2-stable6-20170119 (freesurfer-Darwin-OSX-stable-pub-v6.0.0.dmg<https://secure-web.cisco.com/13d8iRus52q-OHqUT-mKsxtr9lAYTVlnK-JKuHKACZf9jO…>) Platform: macOS Sierra Version 10.12.6 uname -a: Darwin Katarinas-MacBook-Pro.local 16.7.0 Darwin Kernel Version 16.7.0: Thu Dec 20 21:53:35 PST 2018; root:xnu-3789.73.31~1/RELEASE_X86_64 x86_64 I am also strangely unable to attach the recon-all file to this email. Perhaps this is some sort of permissions issue, although I have sudo chown for this user on the dir and that didn't seem to help. Kind regards, Aleksandar

1 0

FW: [All] Postdoctoral position at the Multicultural Alzheimer's Prevention Program
by Fischl, Bruce 01 Jun '21

01 Jun '21

Contact Dr. Quiroz If you are interested in the postdoc opportunity below Bruce From: all-bounces(a)nmr.mgh.harvard.edu <all-bounces(a)nmr.mgh.harvard.edu> On Behalf Of Quiroz, Yakeel T.,Ph.D. Sent: Tuesday, June 1, 2021 8:44 PM To: all(a)nmr.mgh.harvard.edu Subject: [All] Postdoctoral position at the Multicultural Alzheimer's Prevention Program Dear all, I hope everyone is doing well, I recently received another grant to use multimodal imaging and biomarkers to study cognitive decline in older Latinos, and I'm currently looking to recruit 1-2 postdoctoral fellows to join my group. I'd appreciate any help sharing this info with your colleagues! Any interested parties can contact me directly, Thanks in advance for the help! Yakeel T. Quiroz, PhD Associate Professor | Harvard Medical School MGH Research Scholar | Massachusetts General Hospital Departments of Psychiatry and Neurology Director, Familial Dementia Neuroimaging Lab Director, Multicultural Alzheimer's Prevention Program-MAPP Email: yquiroz(a)mgh.harvard.edu<mailto:yquiroz@mgh.harvard.edu> Phone: (617) 643-5944 @ytquiroz

1 0

Re: [Freesurfer] Freesurfer- subcortical group analysis
by Douglas N. Greve 01 Jun '21

01 Jun '21

There are not results to visualize, there is just a table. There should be a sig table in the output folder On 5/28/2021 9:37 AM, Aldinhas De Freitas Ferreira, Francisca wrote: > > External Email - Use Caution > > So so sorry to bother you again - hopefully the last time... > > I have followed your suggestion and that has worked, having used this > command > > mri_glmfit \--table aseg_stats.txt \--fsgd newCH_deblank3.fsgd dods > \--C groupdiff.mtx \--glmdir aseg.glmdir > > I am now trying to visualise the results according to FSwiki, used > this command > > freeview -f > /usr/local/freesurfer/subjects:annot=aparc.annot:annot_outline=1:overlay=/usr/local/freesurfer/subjects/aseg.glmdir/groupdiff/F.mgh:overlay_threshold=20,50 > -viewport 3d > > I get the following error > > ERROR: reading /usr/local/freesurfer/subjects > Read 0 bytes, expected 1 > Read 0 bytes, expected 1 > /freesurfer/subjects > MRISread failed > > I wonder is this means there is something wrong with the GLM I created > or if it is something wrong with my Freeview? > > Thanks a lot in advance! > Kind regards, > Francisca > > ------------------------------------------------------------------------ > *From:* Douglas N. Greve <dgreve(a)mgh.harvard.edu> > *Sent:* 27 May 2021 21:05 > *To:* Aldinhas De Freitas Ferreira, Francisca > <francisca.ferreira.16(a)ucl.ac.uk> > *Subject:* Re: Freesurfer- subcortical group analysis > Hi Francisca, if you run asegstats2table on your group to create a > group table (subjects on the rows, structures on the columns, each > element being the structure volume for that subject), then you can use > mri_glmfit with the --table option (instead of --y). You may want to > correct for intracranial volume by adding --etiv to the > asegstats2table command. > doug > > > On 5/27/2021 7:13 AM, Aldinhas De Freitas Ferreira, Francisca wrote: >> >> External Email - Use Caution >> >> Dear Dr Greve, >> >> My name is Francisca Ferreira, I am a neurosurgeon/neuroimaging PhD >> student at the FIL in UCL. I have recently contacted Eugenio >> Iglesias, who kindly pointed me in your direction. Sorry to bother >> you, I have been working with Freesurfer and I was hoping you would >> kindly give me your opinion? >> >> I am looking to compare responders vs non responders to deep brain >> stimulation of a subcortical structure called ventral tegmental area. >> I ran recon-all, and thought Freesurfer could be useful for this task >> as it now has a brainstem segmenting module that I’ve installed. >> >> I thought I could use brainstem or subcortical volumes/surfaces to do >> the glm group analysis? (in my case regressing out age and gender). >> It seems that all the options i found on mri_glm only allow >> surface-based analysis? (the flags available being - - cortex or - >> -non-cortex) is there any way around this? >> >> I am sorry for any lack of background knowledge- which stems from the >> fact that I am primarily a clinician... >> I’d be most grateful for any suggestions! >> >> Kind regards, >> Francisca > > 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 Mass > General Brigham Compliance HelpLine at > http://www.massgeneralbrigham.org/complianceline . 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. > > Please note that this e-mail is not secure (encrypted). If you do not > wish to continue communication over unencrypted e-mail, please notify > the sender of this message immediately. Continuing to send or respond > to e-mail after receiving this message means you understand and accept > this risk and wish to continue to communicate over unencrypted e-mail. >

2 2

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