Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

Sulc maps
by Reza Rajimehr 13 Nov '20

13 Nov '20

External Email - Use Caution Hi, In the .sulc files, the range of sulcal depth values are very different (about 10 times higher) in Freesurfer v6 compared to Freesurfer v5.3. Is there just a simple scaling factor here, or the procedure for calculating sulcal depth has been changed? Thanks, Reza

2 3

AAL Segmentation with Freesurfer
by Stephan Wunderlich 13 Nov '20

13 Nov '20

External Email - Use Caution Dear all, Is there a possibility to segment a brain with freesurfer to an AAL Atlas. So that I get the volume and amount of voxel for all the ROIs of the AAL Atlas? Best, Steph

2 1

(no subject)
by 福田京佑 13 Nov '20

13 Nov '20

External Email - Use Caution Windows 10 版のメール<https://secure-web.cisco.com/1CT7pzF-C5ssyuoMHeVvfiMj6xt7XXosJhSiYcA59aK8ex…>から送信

1 0

Help with MRI labels
by Alberto Del Cerro Leon 12 Nov '20

12 Nov '20

External Email - Use Caution Good afternoon, my name is Alberto del Cerro and I am a PhD student in the cognitive and computational neuroscience laboratory (LNCyC) at the biomedical technology center (CTB) of the Polytechnic University of Madrid (UPM). I am currently extracting the structural data from the T1 images of my project and I would like to extract the volume, thickness and curvature data in the regions of interest where I obtained results in electrophysiology (MEG). The point is that for this data I used the AAL atlas and I would like to use these regions to obtain structural data in FreeSurfer. Researching on the internet I have read that this is possible with the mri_label2vol command but I would like to know how I can proceed to obtain this data. Can you guide me in this process?

2 2

Re: [Freesurfer] Support: Password Request for Ubuntu_710 to download Freesurfer on Windows 10 {Disarmed} {Disarmed}
by fsbuild 12 Nov '20

12 Nov '20

External Email - Use Caution Hello James, I will send the password directly to your email shortly.. -R. On Nov 12, 2020, at 09:56, Park, James <james.kunwoo.park(a)emory.edu> wrote:        External Email - Use Caution        Dear Freesurfer Team, Hello, my name is James Park and I have recently been trying to utilize Freesurfer on a new Windows Computer. I was able follow the instructions provided on : MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/14p-Zxk74tVoTu8QrA0S0_iUpBL5mkrv-GBxx2… unfortunately was unable to log into the desktop of the virtual machine because it requires a password for the “developer” account. I noticed in previous mailing archives this password was sent privately – could I also receive this password by chance? Thank you for your help in advance. Sincerely,James Parkemail: james.kunwoo.park@emory.edu This e-mail message (including any attachments) is for the sole use ofthe intended recipient(s) and may contain confidential and privilegedinformation. If the reader of this message is not the intendedrecipient, you are hereby notified that any dissemination, distributionor copying of this message (including any attachments) is strictlyprohibited.If you have received this message in error, please contactthe sender by reply e-mail message and destroy all copies of theoriginal message (including attachments)._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

Support: Password Request for Ubuntu_710 to download Freesurfer on Windows 10 {Disarmed}
by Park, James 12 Nov '20

12 Nov '20

External Email - Use Caution Dear Freesurfer Team, Hello, my name is James Park and I have recently been trying to utilize Freesurfer on a new Windows Computer. I was able follow the instructions provided on : https://secure-web.cisco.com/1eXouftPDgg37AuJADlljMENUWBEUfGROCh_5ifJ-wvqNh…<https://secure-web.cisco.com/1EEXroSruFwS_tEl0TiiJP0980pQWotjNew0Aa2WayNcN9…> but unfortunately was unable to log into the desktop of the virtual machine because it requires a password for the “developer” account. I noticed in previous mailing archives this password was sent privately – could I also receive this password by chance? Thank you for your help in advance. Sincerely, James Park email: james.kunwoo.park(a)emory.edu<mailto:james.kunwoo.park@emory.edu> ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).

1 0

tkregister issue with reg-feat2anat {Disarmed}
by Walsh, Erin 12 Nov '20

12 Nov '20

External Email - Use Caution Greetings, I am experiencing a similar tkregister2 issue described in this thread when attempting to run reg-feat2anat: https://secure-web.cisco.com/1H9mU-9s00zN3P3mT0enoWLpI-9zwcO9lCds21sBQW9qoS… I am using FSL version 5.0.10 and Freesurfer version 7. I have pasted the --debug output after my signature. I am wondering if there should be a call for tkregister2_cmdl_cmdl (as opposed to tkregister2_cmdl)? set TKR = tkregister2_cmdl set TKR = tkregister2_cmdl if ( $usedev ) set TKR = $DEV/$TKR/$TKR if ( 0 ) set TKR = /tkregister2_cmdl/tkregister2_cmdl if ( ! $manual ) set TKR = $TKR"_cmdl" if ( ! 0 ) set TKR = tkregister2_cmdl_cmdl set TKR = tkregister2_cmdl_cmdl Thank you for any help you can provide! Erin -- Erin Walsh, Ph.D. Assistant Professor University of North Carolina-Chapel Hill Department of Psychiatry Chapel Hill, NC 27599-3367 erin_walsh(a)med.unc.edu pronouns: she/her set echo = 1 ; set debug = 1 ; set debug = 1 breaksw breaksw end end while ( $#argv != 0 ) while ( 4 != 0 ) set flag = $argv[1] ; shift ; set flag = --feat shift switch ( $flag ) switch ( --feat ) case "--featdir": case --featdir: if ( $#argv == 0 ) goto arg1err ; if ( 3 == 0 ) goto arg1err set FeatDir = $argv[1] ; shift ; set FeatDir = /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat shift breaksw breaksw end end while ( $#argv != 0 ) while ( 2 != 0 ) set flag = $argv[1] ; shift ; set flag = --subject shift switch ( $flag ) switch ( --subject ) if ( $#argv == 0 ) goto arg1err ; if ( 1 == 0 ) goto arg1err set subject = $argv[1] ; shift ; set subject = BA0023_V1 shift breaksw breaksw end end while ( $#argv != 0 ) while ( 0 != 0 ) goto parse_args_return ; goto parse_args_return goto check_params ; goto check_params if ( $DoBBR ) then if ( 1 ) then which bbregister > /dev/null which bbregister if ( $status ) then if ( 0 ) then endif endif if ( $#FeatDir == 0 ) then if ( 1 == 0 ) then if ( ! -e $FeatDir ) then if ( ! -e /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat ) then if ( ! $manual ) then if ( ! 0 ) then if ( $#subject == 0 ) then if ( 1 == 0 ) then else else if ( $?SUBJECTS_DIR == 0 ) then if ( 1 == 0 ) then if ( ! -e $SUBJECTS_DIR ) then if ( ! -e /proj/dichterlab/BATA/Analysis/FreeSurfer_7 ) then if ( ! -e $SUBJECTS_DIR/$subject ) then if ( ! -e /proj/dichterlab/BATA/Analysis/FreeSurfer_7/BA0023_V1 ) then if ( $manxfm != "func2anat" && $manxfm != "std2anat" && $manxfm != "func2std" ) then if ( func2anat != func2anat && func2anat != std2anat && func2anat != func2std ) then goto check_params_return ; goto check_params_return if ( $?DEV == 0 ) set DEV = "" ; if ( 0 == 0 ) set DEV = set DEV = set TKR = tkregister2_cmdl set TKR = tkregister2_cmdl if ( $usedev ) set TKR = $DEV/$TKR/$TKR if ( 0 ) set TKR = /tkregister2_cmdl/tkregister2_cmdl if ( ! $manual ) set TKR = $TKR"_cmdl" if ( ! 0 ) set TKR = tkregister2_cmdl_cmdl set TKR = tkregister2_cmdl_cmdl set MM = mri_matrix_multiply set MM = mri_matrix_multiply if ( $usedev ) set MM = $DEV/$MM/$MM if ( 0 ) set MM = /mri_matrix_multiply/mri_matrix_multiply echo FeatDir is $FeatDir echo FeatDir is /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat FeatDir is /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat mkdir -p $FeatDir/reg/freesurfer/tmp mkdir -p /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/tmp set exf2std_fslmat = $FeatDir/reg/example_func2standard.mat set exf2std_fslmat = /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/example_func2standard.mat if ( ! -e $exf2std_fslmat ) then if ( ! -e /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/example_func2standard.mat ) then set exfbase = $FeatDir/example_func set exfbase = /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/example_func if ( -e $exfbase.nii.gz ) then if ( -e /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/example_func.nii.gz ) then setenv FSLOUTPUTTYPE NIFTI_GZ setenv FSLOUTPUTTYPE NIFTI_GZ set fslext = nii.gz ; set fslext = nii.gz endif endif if ( -e $exfbase.nii ) then if ( -e /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/example_func.nii ) then if ( -e $exfbase.img ) then if ( -e /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/example_func.img ) then if ( $#fslext == 0 ) then if ( 1 == 0 ) then set tempvol = $FeatDir/example_func.$fslext set tempvol = /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/example_func.nii.gz echo "template volume is $tempvol" echo template volume is /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/example_func.nii.gz template volume is /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/example_func.nii.gz set anat2exf_regdat = $FeatDir/reg/freesurfer/anat2exf.register.dat set anat2exf_regdat = /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/anat2exf.register.dat set anat2std_regdat = $FeatDir/reg/freesurfer/anat2std.register.dat set anat2std_regdat = /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/anat2std.register.dat set std2anat_fslmat = $FeatDir/reg/freesurfer/std2anat.fsl.mat set std2anat_fslmat = /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/std2anat.fsl.mat set exf2anat_init_fslmat = $FeatDir/reg/freesurfer/exf2anat.init.fsl.mat set exf2anat_init_fslmat = /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/exf2anat.init.fsl.mat set exf2anat_fslmat = $FeatDir/reg/freesurfer/exf2anat.fsl.mat set exf2anat_fslmat = /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/exf2anat.fsl.mat set std2exf_regdat = $FeatDir/reg/freesurfer/std2exf.register.dat set std2exf_regdat = /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/std2exf.register.dat set exf2std_regdat = $FeatDir/reg/freesurfer/exf2std.register.dat set exf2std_regdat = /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/exf2std.register.dat set segregdat = $FeatDir/reg/freesurfer/reg.bbr.dat set segregdat = /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/reg.bbr.dat set stdbrain = $FeatDir/reg/standard.$fslext set stdbrain = /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/standard.nii.gz set refvolcor = $SUBJECTS_DIR/$subject/mri/$anatvol.mgz set refvolcor = /proj/dichterlab/BATA/Analysis/FreeSurfer_7/BA0023_V1/mri/brainmask.mgz if ( ! -e $refvolcor ) then if ( ! -e /proj/dichterlab/BATA/Analysis/FreeSurfer_7/BA0023_V1/mri/brainmask.mgz ) then if ( $manual && $manxfm == func2anat ) then if ( 0 && func2anat == func2anat ) then if ( $manual && $manxfm == std2anat ) then if ( 0 && func2anat == std2anat ) then if ( $manual && $manxfm == func2std ) then if ( 0 && func2anat == func2std ) then set LF = $FeatDir/reg/freesurfer/reg-feat2anat.log set LF = /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/reg-feat2anat.log if ( -e $LF ) mv $LF $LF.bak if ( -e /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/reg-feat2anat.log ) mv /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/reg-feat2anat.log /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/reg-feat2anat.log.bak echo log file is $LF echo log file is /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/reg-feat2anat.log log file is /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/reg-feat2anat.log date | tee -a $LF tee -a /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/reg-feat2anat.log date Wed Nov 11 18:22:53 EST 2020 pwd | tee -a $LF tee -a /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/reg-feat2anat.log pwd /proj/dichterlab/BATA/Scripts/Hammer/Hammer_Activation/Censoring_Pipeline/Freesurfer echo $0 | tee -a $LF tee -a /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/reg-feat2anat.log echo /nas/longleaf/apps/freesurfer/7.1.0/freesurfer/bin/reg-feat2anat /nas/longleaf/apps/freesurfer/7.1.0/freesurfer/bin/reg-feat2anat echo $cmdargs | tee -a $LF tee -a /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/reg-feat2anat.log echo --debug --feat /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat --subject BA0023_V1 --debug --feat /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat --subject BA0023_V1 uname -a | tee -a $LF tee -a /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/reg-feat2anat.log uname -a Linux c1125.ll.unc.edu 3.10.0-1127.19.1.el7.x86_64 #1 SMP Tue Aug 11 19:12:04 EDT 2020 x86_64 x86_64 x86_64 GNU/Linux set refvolcor = $SUBJECTS_DIR/$subject/mri/$anatvol.mgz set refvolcor = /proj/dichterlab/BATA/Analysis/FreeSurfer_7/BA0023_V1/mri/brainmask.mgz if ( ! -e $refvolcor ) then if ( ! -e /proj/dichterlab/BATA/Analysis/FreeSurfer_7/BA0023_V1/mri/brainmask.mgz ) then if ( $fslext == img ) then if ( nii.gz == img ) then mri_info --o /tmp/reg-feat2anat.rasgood.$$ --ras_good $FeatDir/example_func.$fslext > & /dev/null mri_info --o /tmp/reg-feat2anat.rasgood.36869 --ras_good /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/example_func.nii.gz set exf_ras_good = `cat /tmp/reg-feat2anat.rasgood.$$` ; set exf_ras_good = `cat /tmp/reg-feat2anat.rasgood.$$` cat /tmp/reg-feat2anat.rasgood.36869 endif endif echo "example_func ras_good_flag $exf_ras_good" | tee -a $LF tee -a /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/reg-feat2anat.log echo example_func ras_good_flag 1 example_func ras_good_flag 1 if ( $exf_ras_good ) then if ( 1 ) then echo "-------------------------------------------------------" | tee -a $LF tee -a /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/reg-feat2anat.log echo ------------------------------------------------------- ------------------------------------------------------- echo "Initializing exf2anat with header" | tee -a $LF tee -a /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/reg-feat2anat.log echo Initializing exf2anat with header Initializing exf2anat with header set cmd = ( $TKR --targ $refvolcor --mov $FeatDir/example_func.$fslext --reg $anat2exf_regdat.init --fslregout $exf2anat_init_fslmat --regheader ) set cmd = ( tkregister2_cmdl_cmdl --targ /proj/dichterlab/BATA/Analysis/FreeSurfer_7/BA0023_V1/mri/brainmask.mgz --mov /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/example_func.nii.gz --reg /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/anat2exf.register.dat.init --fslregout /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/exf2anat.init.fsl.mat --regheader ) if ( ! $debug ) set cmd = ( $cmd --noedit ) if ( ! 1 ) set cmd = ( tkregister2_cmdl_cmdl --targ /proj/dichterlab/BATA/Analysis/FreeSurfer_7/BA0023_V1/mri/brainmask.mgz --mov /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/example_func.nii.gz --reg /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/anat2exf.register.dat.init --fslregout /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/exf2anat.init.fsl.mat --regheader --noedit ) echo $cmd | tee -a $LF tee -a /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/reg-feat2anat.log echo tkregister2_cmdl_cmdl --targ /proj/dichterlab/BATA/Analysis/FreeSurfer_7/BA0023_V1/mri/brainmask.mgz --mov /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/example_func.nii.gz --reg /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/anat2exf.register.dat.init --fslregout /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/exf2anat.init.fsl.mat --regheader tkregister2_cmdl_cmdl --targ /proj/dichterlab/BATA/Analysis/FreeSurfer_7/BA0023_V1/mri/brainmask.mgz --mov /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/example_func.nii.gz --reg /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/anat2exf.register.dat.init --fslregout /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/exf2anat.init.fsl.mat --regheader $cmd | tee -a $LF tee -a /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/reg-feat2anat.log tkregister2_cmdl_cmdl --targ /proj/dichterlab/BATA/Analysis/FreeSurfer_7/BA0023_V1/mri/brainmask.mgz --mov /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/example_func.nii.gz --reg /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/anat2exf.register.dat.init --fslregout /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/exf2anat.init.fsl.mat --regheader tkregister2_cmdl_cmdl: Command not found. if ( $status ) exit 1 ; if ( 1 ) exit 1 exit 1

2 1

mri_vol2vol usage
by RENXI LI 11 Nov '20

11 Nov '20

External Email - Use Caution Hi FreeSurfer Experts: I am trying to register the subject’s functional image processed by SPM12 to the Freesurfer subject anatomical space using mri_vol2vol, what would be the required arguments in this case? Best, Renxi

2 5

Flywheel is Hiring
by Andy Worth 11 Nov '20

11 Nov '20

External Email - Use Caution Hello Freesurfer and Neuroinformatics Experts, At Flywheel <https://secure-web.cisco.com/11jOUe69pAmrkatJBPAWf3tKPRB9iRsFQ1T1VU_vkte1Jm…>, we are developing a data sharing and distributed computing platform serving biomedical imaging and life sciences research. We are hiring <https://secure-web.cisco.com/1fl-xuQEhMmhR5ixf6wZmLmzBbB3uWIuQ-GPTt40NoYIdz…> to grow our Scientific Solutions Engineering team of PhDs and Engineers. Specifically, we are looking for coders with mad skills in reproducible scientific cloud computing (python, Docker), workflow / pipeline implementation (NiPype, CWL, Toil, Cromwell, Snakemake, Nextflow, Galaxy, SevenBridges, Arvados, COINSTAC, etc.), Machine Learning workflows (Kubeflow, Airflow, SKLearn, MLflow, etc.), and a research background in medical imaging or bioinformatics. Knowledge of the Brain Imaging Data Structure (BIDS) standard is a huge plus. Compensation is competitive, company is inclusive, and we are open to hire remotely (half of us are). If you are interested, please have a look at our job ad here <https://secure-web.cisco.com/1fl-xuQEhMmhR5ixf6wZmLmzBbB3uWIuQ-GPTt40NoYIdz…>. If you know someone who might be interested, please pass along the link. We really do cool things. Cheers, Andy Worth Scientific Solutions Engineer he, him, his <http://secure-web.cisco.com/1p9cujki7p3fAOSgSS0m9jUN6Ox0zw7VzFNuhwyeKuHQM59…>

1 0

mris_anatomical_stats error: stating file
by Chan, Shi Yu 11 Nov '20

11 Nov '20

Hi FreeSurfer Developers, I'm trying to calculate cortical thickness statistics from the Yeo 17 Network cortical parcellation and have used mri_surf2surf to get the .annot files for each subject. However, when I run mris_anatomical_stats, I get an error: ERROR: stating file subjects_dir/sub-001/label/sub-001/label/rh.Yeo2011_17Networks_N1000.annot It seems like the "sub-001/label" portion is repeated. The command I use for mris_anatomical_stats is: mris_anatomical_stats -th3 -mgz -cortex sub-001/label/lh.cortex.label -f sub-001/stats/lh.Yeo_17Networks.stats -b -a sub-001/label/lh.Yeo2011_17Networks_N1000.annot sub-001 lh white The command still runs despite the error, and outputs the stats files accordingly, so I'm not sure how important this error is, but I can't figure out how to fix it. This is a similar issue to: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg67595.html but I've checked $SUBJECTS_DIR, and it is correct. If I run ls $SUBJECTS_DIR/sub-001 I'll see all the different sub-folders in sub-001 (mri stats labels etc) Any help would be much appreciated! Thank you!

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