Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30071 discussions

Start a nNew thread

mri_robust_template - MyMatrix::RotationMean Error
by Andrew Beaudin 10 Jul '22

10 Jul '22

2 1

recon-all error: mri_cc
by cooperr1＠student.unimelb.edu.au 10 Jul '22

10 Jul '22

External Email - Use Caution Dear FreeSurfer developers, I'm attempting to run recon-all with the longitudinal stream, but one subject (out of >500) fails recon-all (I've re-started many times). The cross-sectional and base (i.e. steps 1 and 2 of the longitudinal processing) have completed successfully; it's this final step that has the error. It appears that the error lies in mri_cc. The final lines of the recon-all.log are below: #-------------------------------------- #@# CC Seg Wed Jun 29 14:56:47 AEST 2022 mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /data/scratch/projects/punim0822/subjdir_matched/sub-NDARINVL8EJK2VY_ses-bas elineYear1Arm1_run-01_T1w.long.sub-NDARINVL8EJK2VY/mri/transforms/cc_up.lta sub-NDARINVL8EJK2VY_ses-baselineYear1Arm1_run-01_T1w.long.sub-NDARINVL8EJK2V Y will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /data/scratch/projects/punim0822/subjdir_matched/sub-NDARINVL8EJK2VY_ses-bas elineYear1Arm1_run-01_T1w.long.sub-NDARINVL8EJK2VY/mri/transforms/cc_up.lta reading aseg from /data/scratch/projects/punim0822/subjdir_matched/sub-NDARINVL8EJK2VY_ses-bas elineYear1Arm1_run-01_T1w.long.sub-NDARINVL8EJK2VY/mri/aseg.auto_noCCseg.mgz error: No such file or directory error: mri_cc: volume /data/scratch/projects/punim0822/subjdir_matched/sub-NDARINVL8EJK2VY_ses-bas elineYear1Arm1_run-01_T1w.long.sub-NDARINVL8EJK2VY/mri/aseg.auto_noCCseg.mgz already has CC in it. Run with -force to reprocess (not recommended) @#@FSTIME 2022:06:29:14:56:47 mri_cc N 7 e 0.39 S 0.00 U 0.38 P 99% M 21240 F 0 R 1813 W 0 c 6 w 5 I 0 O 0 L 64.77 63.93 63.78 @#@FSLOADPOST 2022:06:29:14:56:47 mri_cc N 7 64.77 63.93 63.78 Linux spartan-bm112.hpc.unimelb.edu.au 3.10.0-1160.36.2.el7.x86_64 #1 SMP Thu Jul 8 02:53:40 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub-NDARINVL8EJK2VY_ses-baselineYear1Arm1_run-01_T1w.long.sub-NDARINVL8EJK2V Y exited with ERRORS at Wed Jun 29 14:56:47 AEST 2022 Freesurfer version: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b (I have also attempted with version 7.1.0 with identical results) Platform: centos7_x86_64 Recon-all.log: attached. With thanks, Rebecca

2 1

Cohen's D from selxavg3-sess output
by Caspar M. Schwiedrzik 10 Jul '22

10 Jul '22

External Email - Use Caution Hi! I would like to compute Cohen's D for individual subjects. I was wondering whether I can use the output from selxavg3-sess for this: ces./rstd Or does this only work with gamma and rstd after mri_glmfit? Thank you, Caspar

2 1

Problem with sxconcat-sess
by Shapiro, Noah Lorenz 10 Jul '22

10 Jul '22

Hello, I am trying to concatenate my functional data with the following command (Ps: I am relatively new to FreeSurfer): sxconcat-sess -sf functional_ID_jun22_allSubjects -analysis PCC_Bold_R -contrast bilateral_isthmuscingulate_bold_config -o DMN_Right. I get an error that says the dof file cannot be found for my 26 scans in $SUBJECTS_DIR. However, running: find . -name "dof" The dof file was created for 12 scans. I used the same analysis pipeline for all the scans. I searched the mailing list, and haven't found anything that could help my problem. Any idea why the dof was not created for all scans? How can I create the dof for the remaining scans? Please let me know if you need further details. I am using Freesurfer version 6.0.0. Any help is very much appreciated. Please find the terminal output below. Best wishes, Noah actrumri[0]:RECONS$ echo $SUBJECTS_DIR /autofs/space/arnold_001/users/Noah/ACTRU_pipeline/ACTRU/Niagen/RECONS actrumri[0]:RECONS$ isxconcat-sess -sf functional_ID_jun22_allSubjects -analysis PCC_Bold_R -contrast bilateral_isthmuscingulate_bold_config -o DMN_Right DMN_Right/PCC_Bold_R/log/isxconcat.log ERROR: cannot find /autofs/space/arnold_001/users/Noah/ACTRU_pipeline/ACTRU/Niagen/RECONS/RIB_668_018_3_recon.long.RIB_668_018/bold/PCC_Bold_R/dof actrumri[0]:RECONS$ find . -name "dof" ./RIB_668_021_1_recon.long.RIB_668_021/bold/PCC_Bold_L/dof ./RIB_668_021_1_recon.long.RIB_668_021/bold/PCC_Bold_V/dof ./RIB_668_021_1_recon.long.RIB_668_021/bold/PCC_Bold_R/dof ./RIB_668_019_1_recon.long.RIB_668_019/bold/PCC_Bold_L/dof ./RIB_668_019_1_recon.long.RIB_668_019/bold/PCC_Bold_V/dof ./RIB_668_019_1_recon.long.RIB_668_019/bold/PCC_Bold_R/dof ./RIB_668_035_3_recon.long.RIB_668_035/bold/PCC_Bold_L/dof ./RIB_668_035_3_recon.long.RIB_668_035/bold/PCC_Bold_V/dof ./RIB_668_035_3_recon.long.RIB_668_035/bold/PCC_Bold_R/dof ./RIB_668_026_1_recon.long.RIB_668_026/bold/PCC_Bold_L/dof ./RIB_668_026_1_recon.long.RIB_668_026/bold/PCC_Bold_V/dof ./RIB_668_026_1_recon.long.RIB_668_026/bold/PCC_Bold_R/dof actrumri[0]:RECONS$ isxconcat-sess -sf functional_ID_jun22_allSubjects -analysis PCC_Bold_L -contrast bilateral_isthmuscingulate_bold_config -o DMN_Left DMN_Left/PCC_Bold_L/log/isxconcat.log ERROR: cannot find /autofs/space/arnold_001/users/Noah/ACTRU_pipeline/ACTRU/Niagen/RECONS/RIB_668_018_3_recon.long.RIB_668_018/bold/PCC_Bold_L/dof actrumri[0]:RECONS$ find . -name "dof" ./RIB_668_021_1_recon.long.RIB_668_021/bold/PCC_Bold_L/dof ./RIB_668_021_1_recon.long.RIB_668_021/bold/PCC_Bold_V/dof ./RIB_668_021_1_recon.long.RIB_668_021/bold/PCC_Bold_R/dof ./RIB_668_019_1_recon.long.RIB_668_019/bold/PCC_Bold_L/dof ./RIB_668_019_1_recon.long.RIB_668_019/bold/PCC_Bold_V/dof ./RIB_668_019_1_recon.long.RIB_668_019/bold/PCC_Bold_R/dof ./RIB_668_035_3_recon.long.RIB_668_035/bold/PCC_Bold_L/dof ./RIB_668_035_3_recon.long.RIB_668_035/bold/PCC_Bold_V/dof ./RIB_668_035_3_recon.long.RIB_668_035/bold/PCC_Bold_R/dof ./RIB_668_026_1_recon.long.RIB_668_026/bold/PCC_Bold_L/dof ./RIB_668_026_1_recon.long.RIB_668_026/bold/PCC_Bold_V/dof ./RIB_668_026_1_recon.long.RIB_668_026/bold/PCC_Bold_R/dof actrumri[0]:RECONS$

3 6

Tksurfer Error
by Rachel Wagner 10 Jul '22

10 Jul '22

External Email - Use Caution Hello, I am attempting to paint my spm functional data onto freesurfer’s anatomical image. I ran this code: tksurfer bert lh inflated -overlay updated.img -overlay-reg register.dat And got this error: Tcl_Init failed: Can't find a usable init.tcl in the following directories: /usr/pubsw/packages/tcltktixblt/current/lib/tcl8.4 This probably means that Tcl wasn't installed properly. Tk_Init failed: invalid command name "tcl_findLibrary" Tix_Init failed: Can't find a usable Tix Init.tcl in the following directories: ./library ./tix8.1 ./library ./tix8.1 /usr/pubsw/packages/tcltktixblt/current/lib/tix8.1 How can I fix this error? Thanks, Rachel

2 2

mri_concat killed
by Benjamin Deck 10 Jul '22

10 Jul '22

External Email - Use Caution Hi there, I am attempting to concat a number of volume files that are filled cortical ribbons from a series of label files. My workflow is to take the following steps: *Convert overlay file to label file* mri_vol2label --i ${inDir}/Indi_Matched_ROIs/${net}/${sub}/${hemi}.${netMaskName}_native.mgh \ --id 1 \ --l ${inDir}/Indi_Matched_ROIs/${net}/${sub}/${hemi}.${netMaskName}_native.label \ --surf ${sub} ${hemi} white \ --dilate 2 mri_label2label --srclabel ${inDir}/Indi_Matched_ROIs/${net}/${sub}/${hemi}.${netMaskName}_native.label \ --s ${sub} \ --hemi ${hemi} \ --trglabel /${subDir}/${sub}/label/li2019/${hemi}.${netMaskName}_native.label \ --regmethod surface *Convert label to volume * mri_label2vol --label /${subDir}/${sub}/label/li2019/${hemi}.${netMaskName}_native.label \ --identity \ --fill-ribbon \ --subject ${sub} \ --hemi ${hemi} \ --o /${subDir}/${sub}/mri/li2019_vols/${hemi}.${netMaskName}_native.mgz *Finally concatenate the vols together* mri_concat --f rois.txt --o yeo2011_nat.mgz --sum ninputs = 104 Checking inputs nframestot = 104 Allocing output Done allocing Killed Not sure why this is being killed. OS: WSL2 Ubuntu FS version: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b Thanks for your help! -- *Benjamin L. Deck* *Doctoral Student* *Applied Cognitive and Brain Sciences* *Department of Psychological and Brain Sciences* *Drexel University* <https://secure-web.cisco.com/1YhK4K5F2roM94PXj8RhOckUkCKJ0E3EcVeEJ8IfNRgJUQ…> Virus-free. http://secure-web.cisco.com/1YLbrDWxmBkdEGq0tv_IFuOJQDM7x0wCDq8h35ylt8kjv2A… <https://secure-web.cisco.com/1MZHAAPhLAJ8ofUmsU3lV3kCeJvwetaDxZd4U6AuxDlSyz…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

2 1

Segmentation Mistakes
by Wang, Yu 10 Jul '22

10 Jul '22

External Email - Use Caution Hello FreeSurfer Developers, I used the recon-all -s c1NT816 -i smwrc1NT816_screen_mpr.nii -no-ants-n4 -all command, and the script of recon-all did not shows any errors. But the segmentation of this shows very strange and the screenshot of FREEVIEW was attached in https://secure-web.cisco.com/1DiZCsT29ph0nxelagWzgxiK83DeI03n5r7jqcEK7snAAy… I have search for this mistake online, and I only find a similar one (https://secure-web.cisco.com/17rnPwV1D9noAjOEul8R2iNskGBej5a9MhpLH-Wq1n1UTw…) but it do not show the method about what would cause this problems and how to solve it. 1. FreeSurfer version: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b 2. Platform: ubantu 20.04.4 3. uname -a: Linux sulu 5.4.0-113-lowlatency #127-Ubuntu SMP PREEMPT Wed May 18 15:12:18 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux 4. recon-all.log: see attached I will be appreciated if you can give me a hand with these problems. And looking forward to your reply. Thanks in advance, Yu

2 1

Command Not Found
by Rachel Wagner 10 Jul '22

10 Jul '22

External Email - Use Caution Hello, Thank you for your help! I am trying to register my spm image and am getting the following error: developer@developer-VirtualBox:~$ kregister2 --s home --mov updated.mgz --regheader --reg register.dat --surf orig kregister2: command not found Is my path not set correctly? Thanks again, Rachel Wagner

3 4

Convert coordinates from FreeSurfer space to Native space
by Yi-Yu Chou 10 Jul '22

10 Jul '22

External Email - Use Caution Dear FreeSurfer experts: I wonder if there is a command to convert coordinates from FreeSurfer space to the native space. Thanks in advance ! Yiyu

4 3

(no subject)
by Alex Zhang 10 Jul '22

10 Jul '22

External Email - Use Caution Hi, The FreeSurfer VM image needs a pass code to unarchive. Would you please send me the pass code? Alex

1 0

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