Freesurfer

freesurfer@nmr.mgh.harvard.edu

14 participants
30083 discussions

Tracula 7.2 using older structural outputs
by Alexopoulos, Dimitrios 21 Nov '21

21 Nov '21

External Email - Use Caution HI, Can you run Tracula 7.2 using older structural outputs generated with FS 6.0 and 7.1.1? Jim ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

3 2

TRACULA configuration file for bash
by Alvarado,Luis R 21 Nov '21

21 Nov '21

External Email - Use Caution Hi FS and TRACULA experts, I have a simple question. Do I need to replace: setenv SUBJECTS_DIR $TUTORIAL_DATA/diffusion_tutorial/fs with: export SUBJECTS_DIR $TUTORIAL_DATA/diffusion_tutorial/fs inside the TRACULA configuration file, if my shell is bash? or should I leave that alone? Best, Luis R. Alvarado Graduate Student Fellow Department of Anatomical Sciences and Neurobiology University of Louisville Kentucky Spinal Cord Injury Research Center 220 Abraham Flexner Way, Suite 1500 Louisville, KY 40202

2 1

Tracula -- Segmentation Fault
by Kaplan, Elizabeth 19 Nov '21

19 Nov '21

External Email - Use Caution I ran recon-all on a group of three subjects, followed by trac-all -prep This process exited with errors: Segmentation fault Original DWI and T1 images appear normal, with no large distortions or missing voxels. My configuration file and trac-all.log are attached below. Any guidance is appreciated! -- [image: Brown logo] *Elizabeth Kaplan '22* *She / Her / Hers* Sc.B. Candidate Cognitive Neuroscience B.A. Candidate Contemplative Studies 69 Brown St Mail #4391 Providence, RI 02912

2 1

recon-all reconbatchjobs Segmentation fault
by Peled, Noam 19 Nov '21

19 Nov '21

Dear Freesurfer group, I was running recon-all (Freesurfer 7.2 on Ubuntu) and received the following error: " mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 UC07 rh Waiting for PID 6337 of (6337 6340) to complete... Waiting for PID 6340 of (6337 6340) to complete... /home/basuia/Documents/mmvt_root/freesurfer/bin/reconbatchjobs: line 77: 6340 Segmentation fault (core dumped) exec $JOB >> $LOG 2>&1 PIDs (6337 6340) completed and logs appended. " Please find the log file attached. Any idea what is the problem? Thanks, Noam

3 5

recon-all error with T1 dcm images
by Wei Shao 19 Nov '21

19 Nov '21

External Email - Use Caution Hi, Dear Freesurfer experts I'm have met a recon-all errors with data collected recently like this ADNI_002_S_6652_MR_Accelerated_Sagittal_MPRAGE__br_raw_20190122095958285_147_S786989_I1118713.dcm The attachments are the recon-all script and the output log. Can you help me with this? Thanks Best, Wei

2 1

"Vertex Talairach" in tksurfer?...
by Gonzalo Rojas Costa 19 Nov '21

19 Nov '21

External Email - Use Caution Hi: "Vertex Talairach" in tksurfer: how does it relate to MNI coordinates? Sincerely, Gonzalo Rojas Costa Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 https://secure-web.cisco.com/1jo94BTSUPIktp_eQAT5GZbTfpsA5KIpUTdHrT-g0xQG4-… https://secure-web.cisco.com/13i-ZsZNcbWZqtgw0IQqpdq0G6AvtrIwdfNJ8UTQmrf8Eh… https://secure-web.cisco.com/1nQ-nK1zgqFE9FeklGRmkE8GyAOu5VBkwnRcdrdjH0AT19… http://secure-web.cisco.com/16_Ws70db2hTLXeCVLoJofARkDDcVXKV7r9SqYHL1F22JaH… https://secure-web.cisco.com/1Q9jZG4ZNnNMXhDtADVtnz_v3JI4jUseEVnhR7Yv-c6tC1…

2 1

MNI coordinates to vertex...
by Gonzalo Rojas Costa 19 Nov '21

19 Nov '21

External Email - Use Caution Hi: I have MNI 152 coordinates equivalent to 10-10 and 10-20 EEG electrodes (see Supplementary Tables 1 and 2 in paper https://secure-web.cisco.com/1h63DivIA2LKRlpONd2jZm_aVQOA0BCPi_yLJr4IOlwxEn… How to convert that MNI coordinates to vertex in the pial surface ? Sincerely Gonzalo Rojas Costa Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 http://secure-web.cisco.com/15G7UB7H3xj-A5kT53KhLNPISazwoqZ-keP4CKddUdONSza… https://secure-web.cisco.com/12viTch2L-4x6NKy94c7WpcDwZ3HTM2I3oGRkhAsSGTmNz… https://secure-web.cisco.com/1j6d3d9sra7KYe340OH3hwmLgVbtcqgErcrjhSz4FftpTg… https://secure-web.cisco.com/1U5osbupkYDzRTSQetIvNibKkd020KxYF82vGNYJMRCBn6… http://secure-web.cisco.com/14Rn0C97f3SuE-gY9gJeCiBXYhQ9pvBuNH5M-itIL_uLqiI… https://secure-web.cisco.com/1DJcTJuO0lQGWBymluz9_ARIefxo929bzOP041a22SpnJK…

2 1

V5 / v7
by Brusaferri, Ludovica 19 Nov '21

19 Nov '21

Hi! I am using a pipeline that was implemented and validated using fs 5.3 , which does the following: * compute transformation matrix for linear registration of SUV with T1-2mm, with spm * use tkergister to transform the matrix into .mat, and then invert the matrix * use flirt to move T1 images into PET space The last step gives me different results if I enable FS vs 7, and the registration seems to be off. Do you know why this would be the case? Thank you! Ludovica

2 1

permutation simulation errror
by Brown, Alexander 19 Nov '21

19 Nov '21

External Email - Use Caution Hello, I am attempting to run a permutation simulation to correct for multiple comparisons and am getting the following error: < mri_glmfit-sim --glmdir /home/cns_2/Desktop/SC_PF_analysis/qdec/Untitled --perm 1000 1.3 neg --perm-resid ERROR: cannot find residual /home/cns_2/Desktop/SC_PF_analysis/qdec/Untitled/eres needed with --perm-resid when running mri_glmfit, make sure to include --eres-save > Attached is the mri glmfit log. I ran the command with the --eres-save flag, and the eres.mgh file is generated in the glm directory. I have downloaded the patch and have run this style of analysis multiple times without issue until today. I appreciate any help! Please let me know if you need any additional information. Thanks, Alex Alex Brown CNS Core Facility Department of Psychological Sciences 115 Melvin H. Marx Building 1416 Carrie Francke Drive Columbia, MO 65211 Contact: 573-884-8779

2 23

Hippocampal Subfield segmentation problem - Matlab exits due to fatal error
by Georgia Kapizioni 19 Nov '21

19 Nov '21

External Email - Use Caution Dear Freesurfer experts, I am trying to run hippocampal subfields segmentation, using the command: segmentHA_T1.sh subject The analysis is running for approximately 20 mins and then the following error appears: f this problem is reproducible, please submit a Service Request via: http://secure-web.cisco.com/1BR3I-eWJj4WoMclKofhZEhxAL0gJoDY1byinZeM2eZlrhY… A technical support engineer might contact you with further information. Thank you for your help.** This crash report has been saved to disk as /Users/theodore/matlab_crash_dump.4118-1 ** MATLAB is exiting because of fatal error /Applications/freesurfer/7.1.1/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 33: 4118 Killed: 9 /Applications/freesurfer/7.1.1/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML 6529 /Users/xxx/Downloads/xxx/qcache 0.333333333333333333333333333333333333 /Applications/freesurfer/7.1.1/average/HippoSF/atlas/AtlasMesh.gz /Applications/freesurfer/7.1.1/average/HippoSF/atlas/AtlasDump.mgz /Applications/freesurfer/7.1.1/average/HippoSF/atlas/compressionLookupTable.txt 0.05 left L-BFGS v21 '/Applications/freesurfer/7.1.1/bin/fs_run_from_mcr /Applications/freesurfer/7.1.1/bin/' 0 Darwin MacBook-Pro-Theodore.local 20.3.0 Darwin Kernel Version 20.3.0: Thu Jan 21 00:07:06 PST 2021; root:xnu-7195.81.3~1/RELEASE_X86_64 x86_64 T1 hippocampal subfields exited with ERRORS at Πεμ 18 Νοε 2021 15:34:58 EET Attached please also find the script output. I am using the 7. 1. version of FS. Could you please help me resolve this issue? Thank you in advance, Georgia

2 4

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