Freesurfer February 2022

freesurfer@nmr.mgh.harvard.edu

83 participants
132 discussions

sulc surface error: unit mismatch between FreeSurfer 5.3.0 and 6.0.1
by Guerreiro Fernandes-3, F.D. (Francisco David) 20 Feb '22

20 Feb '22

External Email - Use Caution Dear FreeSurfer Developers, I'm attempting to correlate the sulcal depth information present in the ?h.sulc files with activation in particular brain regions during an overt language task in an fMRI paradigm. For this matter, a dataset was gathered throughout the years with several subjects and the cortical reconstruction process (as described in: https://secure-web.cisco.com/1nqW39ubw2AyrvIfDDZNWB66KB47XSeO6tS5QZO8RBYGIE…) was performed at the time of data acquisition. However, for subjects where recon-all was run in different FreeSurfer versions (5.3.0 or 6.0.1), I get an order of magnitude difference in the sulc values in the ?h.sulc volumes. I've searched the list and the official FreeSurfer Release Notes (https://secure-web.cisco.com/1vUPpLJpZFWtBAPAZsBnTOCfqihx6dgklkyFygBvPMdyx7…) and found no information of a change of magnitude in sulc values. Does anyone have any thoughts on how to trouble-shoot this one? 1) FreeSurfer versions: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 & freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a 2) Platform: Linux blue 3.16.0-4-amd64 #1 SMP Debian 3.16.7-ckt11-1+deb8u3 (2015-08-04) x86_64 GNU/Linux Kind Regards, Francisco D. Guerreiro Fernandes [Description: Universitair Medisch Centrum Utrecht] Francisco David Guerreiro Fernandes, PhD Candidate | BCI Group | UMC Utrecht Brain Center Dept. Neurology & Neurosurgery | University Medical Center Utrecht Room STR 4.119 | Heidelberglaan 100 | 3584CX Utrecht | The Netherlands Email: F.GuerreiroFernandes-3(a)umcutrecht.nl<mailto:F.GuerreiroFernandes-3@umcutrecht.nl> | Tel: +31 88 75 50080 De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. Denk s.v.p aan het milieu voor u deze e-mail afdrukt. This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197. Please consider the environment before printing this e-mail.

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Running recon-all in parallel error: cannot find sub-101_ses-BL_T1w.nii
by Yuan, Ye 19 Feb '22

19 Feb '22

External Email - Use Caution Dear FreeSurfer Developers, I hope this email finds you well. I'm an MRes student from Imperial College London. I'm attempting to run recon-all in parallel, as described in the FreeSurfer tutorial of Andy's brain book: https://secure-web.cisco.com/1f8N_u253wnYss7NsLFujqzigTyBNU3U_hugHrybuTHK9C… The appropriate way would be: ls .. | grep sub- > subjList.txt # here I deleted the special character of subject number manually, the right format would be `sub-101` for sub in `cat subjList.txt`; do cp ../${sub}/ses-BL/anat/*.gz . done gunzip *.gz SUBJECTS_DIR=`pwd` ls *.nii | parallel --jobs 8 recon-all -s {.} -i {} -all -qcache # the last step However, when running the last step, I've got the following error: ERROR: cannot find sub-101_ses-BL_T1w.nii Linux nhp-System-Product-Name 4.15.0-142-generic #146~16.04.1-Ubuntu SMP Tue Apr 13 09:27:15 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub-101_ses-BL_T1w exited with ERRORS at 2022 02 18 Friday 10:49:24 CST For more details, see the log file To report a problem, see http://secure-web.cisco.com/1TEXQ5EYB9LOX23P4f0QsCWsgDayARXAUE94TZk30GfILIE… In addition, I have attached the dataset that has been processed except for the last step in my last email, the recon-all.log weren't generated in this case. Does anyone have any thoughts on how to trouble-shoot this issue? 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Platform: CentOS release 6.7 (Final) 3) uname -a: Linux nhp-System-Product-Name 4.15.0-142-generic #146~16.04.1-Ubuntu SMP Tue Apr 13 09:27:15 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: were not generated Many thanks in advance! Best regards, Ye

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Re: [Freesurfer] FreeSurfer Issue
by fsbuild 17 Feb '22

17 Feb '22

External Email - Use Caution Hello Anna, You could try the bash shell commands below … freeview should open an empty window. Those commands are documented for the bash shell and also csh/tcsh shells on the help page, https://secure-web.cisco.com/1HXGi2MgGyKrnZsUEDporX-UQ3IrQRAR1UaZSL_m2PtlLk… - R. % bash The default interactive shell is now zsh.To update your account to use zsh, please run `chsh -s /bin/zsh`.For more details, please visit https://secure-web.cisco.com/1Tcz7fGutzZau6blDkstZVkR5nPiyXBdbX07yX4PuhMcNr… you@Host-Mac:~> export FREESURFER_HOME=/Applications/freesurfer/7.2.0 you@Host-Mac:~> source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME   /Applications/freesurfer/7.2.0FSFAST_HOME       /Applications/freesurfer/7.2.0/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR      /Applications/freesurfer/7.2.0/subjectsMNI_DIR           /Applications/freesurfer/7.2.0/mni you@Host-Mac:~> freeview On Feb 17, 2022, at 18:44, Pusok, Anna <anna.pusok(a)yale.edu> wrote:        External Email - Use Caution        Hi,Sorry but this did not fix the issues- could I ask you to help with Freesurfer? I tried to get it work many times, with no success and what you recommended also did not work.Thank you.From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Tim Schäfer <ts+ml@rcmd.org>Sent: Thursday, February 17, 2022 2:10 PMTo: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>Subject: Re: [Freesurfer] FreeSurfer Issue         External Email - Use Caution        Dear Anna,You should use 'setenv' (for tcsh and related shells) or 'export' (for BASH) when defining environment variables, as listed here:    MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsecure-… setenv FREESURFER_HOME /Applications/freesurfer/7.2.0You should also source (instead of executing) the SetUpFreeSurfer.csh script:    source $FREESURFER_HOME/SetUpFreeSurfer.cshBest,Tim> On 02/17/2022 5:32 PM Pusok, Anna <anna.pusok(a)yale.edu> wrote:> >  > External Email - Use Caution        > > Hi there,> I hope this email finds you well!> I ran into some issues when I tried to use freesurfer. This is the error message I get in my terminal. Could you help me with this issue? If we could set up a Zoom meeting to discuss the issue, that would be helpful as well!> Thank you,> Anna> _______________________________________________> Freesurfer mailing list> Freesurfer(a)nmr.mgh.harvard.edu> MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsecure-…. Tim SchäferPostdoc Computational NeuroimagingDepartment of Child and Adolescent Psychiatry, Psychosomatics and PsychotherapyUniversity Hospital Frankfurt, Goethe University Frankfurt am Main, Germany_______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_____________… mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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autorecon2-wm not reflecting edits in white matter segmentation (7.1.1, 7.2.0)
by Edan Daniel 17 Feb '22

17 Feb '22

External Email - Use Caution We have been having issues with recreating the final surfaces after editing the white matter segmentation, which used to work smoothly in version 6. After running a subject through recon-all (version 7.1.1 *without* the parallel flag) and then editing the white matter, we run the following command (w v7.1.1): recon-all -autorecon2-wm -autorecon3 -subjid ' freesurferfoldername ' -cc-crs ' num2str(corpus_point) The ribbon file and surfaces do update *very slightly* but it’s largely ignoring our (sometimes large) edits. This pipeline worked well for us in version 6- do you have any idea what might be going on? Would love to hear your thoughts about this. Many thanks!! Edan, Braindevlab@Princeton

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FreeSurfer Issue
by Pusok, Anna 17 Feb '22

17 Feb '22

External Email - Use Caution Hi there, I hope this email finds you well! I ran into some issues when I tried to use freesurfer. This is the error message I get in my terminal. Could you help me with this issue? If we could set up a Zoom meeting to discuss the issue, that would be helpful as well! Thank you, Anna

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mris_preproc error: no source hemi specified
by Koustav Chatterjee 17 Feb '22

17 Feb '22

External Email - Use Caution Dear FreeSurfer experts, I need your help. I am trying to run mris_preproc --fsgd in order to see the effect of cortical volume on velocity, accounting for the effects of eTIV in the analysis. My .fsgd file looks like GroupDescriptorFile 1 Title Vel_vol.glmdir MeasurementName volume Class Main Variables Velocity Totalintracranialvolume Input pt001 Main 57 1233150.571288 Input pt002 Main 44 1441659.580634 Input pt003 Main 60 1534770.256493 Input pt004 Main 55 1374671.330735 Input pt005 Main 29 1252775.397585 Input pt007 Main 42 1466033.251447 Input pt011 Main 82 1565625.985727 Input pt015 Main 30 1255088.0327 Input pt016.nii Main 79 1604469.84187 Input pt018.nii Main 45 1410265.173839 Input pt023 Main 70 1376261.088728 Input pt025 Main 49 1317185.172994 Input pt026 Main 45 1484779.378359 Input pt031 Main 53 1269043.642534 and .mtx file looks like 1 0 I am getting* e**rror: no source hemi specified.* Thanks, KC

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Reconstruct the white and pial from a single brain slice
by 陆玉恒 17 Feb '22

17 Feb '22

External Email - Use Caution Dear, I tried to reconstruct the white and pial surface from a sinlge brain slice (not MRI, it's a histology slice that converted to a nifti file) but failed when using the mris_make_surface. The white matter and grey matter were segmented by in-house tool. I generated the aseg.mgz, filled.mgz, wm.nii.gz from those segmentation masks and ran the "tessellate" "white" steps in "recon" but it reported error when making the ?h.white.I don't know why. I wonder if I could get the pial surface in this way, or you could tell me how to do so. I would appreciate it. Yuheng

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Re: [Freesurfer] Longitudinal Stream Error
by Douglas N. Greve 17 Feb '22

17 Feb '22

Does that file exist? ps. Please remember to post to the list. Thanks! On 2/15/2022 5:06 PM, Willett, Andrew Sunday wrote: > > Dr. Greve, > > I hope this email finds you well. Thank you for your response to my > listed question on Freesurfer’s mailing list on Sunday! I wanted to > reach out to followup re: longitudinal stream error. > > The main error I receive with the base code is as follows: > > SUBJECTS_DIR /PHShome/asw39/subjects > FREESURFER_HOME /PHShome/asw39/freesurfer > Loading source label. > Invalid argument > ERROR reading /PHShome/asw39/subjects/fsaverage/label/lh.BA1_exvivo.label > Linux rgs10.research.partners.org 2.6.32-696.28.1.el6.x86_64 #1 SMP > Thu Apr 26 04:27:41 EDT 2018 x86_64 x86_64 x86_64 GNU/Linux > > recon-all -s MSA12 exited with ERRORS at Tue Nov 30 20:43:37 EST 2021 > We got this error after we used Freesurfer v6.0 to process the data > cross-sectionally and then run the base template. Do you know whether > it is possible for v7.0 cross-sectional output to be run through v6.0 > longitudinal stream (as v6.0 is the most recent longitudinal stream > version)? > > Thanks, > > /Andee Sunday Willett, M.S./ > > / > > //_Pronouns_: they/them// > > / > // > > / > / > > /Research Assistant II/ > > /Department of Neurology, Division of Movement Disorders > / > > /Brigham and Women’s Hospital/ > // > > // > > //// > > /awillett(a)bwh.harvard.edu <mailto:jkim@bwh.harvard.edu>* > *brighamandwomens.org <http://www.brighamandwomens.org/>/ > > / > /

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SAMSEG mesh format and content
by Martin Kavec 17 Feb '22

17 Feb '22

External Email - Use Caution Hi all, previous question from Florent triggered my interest in SAMSEG and I am running now couple of cases to see what it gives. I would like to ask - SAMSEG can also output a mesh. How is the mesh stored in file? - how can it be visualized (Paraview?) - what does the mesh represent. Individual structures? Thanks, Martin

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Re: [Freesurfer] FW: Problems with recon for manually fixed Talairach
by Douglas N. Greve 17 Feb '22

17 Feb '22

I'm a bit puzzled by this. Are you saving the xfm file to talairach.xfm? In the log file, it clearly says: INFO: transforms/talairach.xfm already exists! The new transforms/talairach.auto.xfm will not be copied to transforms/talairach.xfm This is done to retain any edits made to transforms/talairach.xfm Add the -clean-tal flag to recon-all to overwrite transforms/talairach.xfm and there is no command in the log that indicates that it was overwritten, and I cannot replicate this behavior here On 1/31/2022 10:33 AM, Goeckner, Bryna wrote: > External Email - Use Caution > > Sorry - Sending these directly since I tried to send these earlier, but they were blocked by the list-serve. > > Bryna Goeckner (she/her) > Graduate Student > Medical College of Wisconsin > Neuroscience Doctoral Program > > -----Original Message----- > From: Goeckner, Bryna > Sent: Friday, January 28, 2022 11:36 AM > To: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Problems with recon for manually fixed Talairach > > I'm attaching the two recon-all.logs. Both were generated for same subject using the same corrected talairach.xfm file, one with -notal-check and the other with -notalairach. Please let me know if you have any other questions. Thanks! > > Bryna Goeckner (she/her) > Graduate Student > Medical College of Wisconsin > Neuroscience Doctoral Program > > Subject: Re: [Freesurfer] Problems with recon for manually fixed > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <95652ab6-b36a-c708-edd7-b8734c1c7402(a)mgh.harvard.edu> > Content-Type: text/plain; charset=UTF-8; format=flowed > > Can you send the recon-all.log? > > On 1/27/2022 9:34 AM, Goeckner, Bryna wrote: >> External Email - Use Caution >> >> We are using FS 7.2 >> >> Bryna Goeckner (she/her) >> Graduate Student >> Medical College of Wisconsin >> Neuroscience Doctoral Program >> >> Date: Wed, 26 Jan 2022 16:43:44 -0500 >> From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> >> Subject: Re: [Freesurfer] Problems with recon for manually fixed >> Talairach >> To: freesurfer(a)nmr.mgh.harvard.edu >> Message-ID: <8e0752c5-13fa-755e-c416-4253ce5043b3(a)mgh.harvard.edu> >> Content-Type: text/plain; charset="utf-8" >> >> what version of FS are you using? >> >> On 1/21/2022 2:21 PM, Goeckner, Bryna wrote: >>> ????????External Email - Use Caution >>> >>> Hi, >>> >>> I am trying to decide how to proceed after manually updating a >>> talairach since various ways I?ve tried the recon process give me >>> different results. >>> >>> Our group used Freesurfer 7.2 for processing data with the T2 and 3T >>> flags as follows: >>> >>> recon-all -subject $1 -i $2/rawT1.ORIG.nii.gz -T2 >>> $2/rawT2.ORIG.nii.gz -T2pial -parallel -openmp 12 -3T -all >>> >>> After visual inspection, I made adjustments to the talairach using >>> tkregister2 and then used the code below to rerun the recon: >>> >>> recon-all -subject $1 -T2 $2/rawT2.ORIG.nii.gz -T2pial -parallel >>> -openmp 12 -3T? -all >>> >>> When this was done, the talairach.xfm file was restored to the >>> talairach from the original recon, while the talairach.xfm~ was still >>> the fixed version. At no point in this entire process did the >>> talairach (fixed or original) generate an error. >>> >>> To avoid the overwriting of the talairach.xfm file, I tried using >>> (separately) the -notalairach and -notal-check flags. For both, the >>> talairach.xfm file stayed as the fixed talairach, but I got different >>> aseg and aparc results. >>> >>> I?d like to know more about how these to flags differ and if you have >>> a recommendation on which process is best.? The plan is to eventually >>> use this data in TRACULA. >>> >>> Thanks for your help, >>> >>> *Bryna Goeckner*?(she/her) >>> >>> Graduate Student >>> >>> Medical College of Wisconsin >>> >>> Neuroscience Doctoral Program

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Freesurfer February 2022