Freesurfer August 2018

freesurfer@nmr.mgh.harvard.edu

104 participants
167 discussions

ERROR: dimension mismatch between y and X.
by Renew Andrade 06 Aug '18

06 Aug '18

External Email - Use Caution Hello Community! I have an issue while running dt_recon because as can be seen in the output terminal there is some error in matrix dimensions. Renes-MacBook-Air-2:~ andraderenew$ dt_recon --b /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/IXI_DATASET/15_HH/DTI/bval/bvals.txt /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/IXI_DATASET/15_HH/DTI/bvec/bvecs.txt --i /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/IXI_DATASET/15_HH/DTI/NIfTI/IXI015-HH-1258-DTI-00.nii.gz --s /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_15_HH_DTI_recon --o /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_15_HH_DTI_dtrecon -rwxrwxrwx 1 andraderenew staff 660396 Feb 23 2015 /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/IXI_DATASET/15_HH/DTI/NIfTI/IXI015-HH-1258-DTI-00.nii.gz INFO: SUBJECTS_DIR is /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir dt_recon logfile Mon Aug 6 15:24:20 -05 2018 VERSION $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $ setenv SUBJECTS_DIR /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir cd /Users/andraderenew /Applications/freesurfer/bin/dt_recon --b /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/IXI_DATASET/15_HH/DTI/bval/bvals.txt /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/IXI_DATASET/15_HH/DTI/bvec/bvecs.txt --i /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/IXI_DATASET/15_HH/DTI/NIfTI/IXI015-HH-1258-DTI-00.nii.gz --s /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_15_HH_DTI_recon --o /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_15_HH_DTI_dtrecon Renes-MacBook-Air-2.local andraderenew /usr/local/fsl/bin/eddy_correct ECRefTP 0 #@#------------------------------- Converting input Mon Aug 6 15:24:20 -05 2018 cd /Users/andraderenew mri_convert /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/IXI_DATASET/15_HH/DTI/NIfTI/IXI015-HH-1258-DTI-00.nii.gz /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_15_HH_DTI_dtrecon/dwi.nii mri_convert.bin /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/IXI_DATASET/15_HH/DTI/NIfTI/IXI015-HH-1258-DTI-00.nii.gz /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_15_HH_DTI_dtrecon/dwi.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/IXI_DATASET/15_HH/DTI/NIfTI/IXI015-HH-1258-DTI-00.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998806, -0.048201, -0.00797414) j_ras = (-0.0487688, 0.993409, 0.10373) k_ras = (-0.00292168, -0.103995, 0.994574) writing to /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_15_HH_DTI_dtrecon/dwi.nii... #@#------------------------------- Eddy/Motion Correct Mon Aug 6 15:24:20 -05 2018 cd /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_15_HH_DTI_dtrecon/ectmp eddy_correct /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_15_HH_DTI_dtrecon/dwi.nii /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_15_HH_DTI_dtrecon/dwi-ec.nii 0 processing /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_15_HH_DTI_dtrecon/dwi-ec_tmp0000 #@#------------------------------- Fitting Tensors Mon Aug 6 15:24:39 -05 2018 gzip /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_15_HH_DTI_dtrecon/dwi.nii gzip /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_15_HH_DTI_dtrecon/dwi-ec.nii cd /Users/andraderenew mri_glmfit --y /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_15_HH_DTI_dtrecon/dwi-ec.nii.gz --glmdir /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_15_HH_DTI_dtrecon --dti /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/IXI_DATASET/15_HH/DTI/bval/bvals.txt /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/IXI_DATASET/15_HH/DTI/bvec/bvecs.txt $Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $ cwd /Users/andraderenew cmdline mri_glmfit.bin --y /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_15_HH_DTI_dtrecon/dwi-ec.nii.gz --glmdir /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_15_HH_DTI_dtrecon --dti /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/IXI_DATASET/15_HH/DTI/bval/bvals.txt /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/IXI_DATASET/15_HH/DTI/bvec/bvecs.txt sysname Darwin hostname Renes-MacBook-Air-2.local machine x86_64 user andraderenew FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_15_HH_DTI_dtrecon/dwi-ec.nii.gz logyflag 1 usedti 1 glmdir /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_15_HH_DTI_dtrecon IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_15_HH_DTI_dtrecon Loading y from /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_15_HH_DTI_dtrecon/dwi-ec.nii.gz ... done reading. Using DTI Loading BValues from /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/IXI_DATASET/15_HH/DTI/bval/bvals.txt Found 16 bvalues Loading BVectors from /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/IXI_DATASET/15_HH/DTI/bvec/bvecs.txt Found 16 bvectorss Detected BVec file as FSL formatted Saving design matrix to /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_15_HH_DTI_dtrecon/Xg.dat Computing normalized matrix Normalized matrix condition is 63.8107 Matrix condition is 4.98981e+06 Pruning voxels by thr: 1.175494e-38 Found 253458 voxels in mask Saving mask to /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/IXI_15_HH_DTI_dtrecon/mask.nii.gz search space = 1552430.250000 ERROR: dimension mismatch between y and X. y has 1 inputs, X has 16 rows.

2 1

Get error while performing cortical and sub cortical segmentation for PET images
by Yubraj Gupta 06 Aug '18

06 Aug '18

External Email - Use Caution Hello Freesurfer Developers, I'm attempting to compute RECON-all for PET images, for some image I am getting the stats folder with no error, but for some of my subjects I get the following error when recon-all is processing ERROR: mrisAddEdge: too many edges (254) XL defect detected... Large defect found - not a problem, but a curiosity No such file or directory I've searched the list and no similar errors have been reported. Does anyone have any thought on how to troubleshoot this one? Also, I've attached the recon-all.log with ADNI file in case it's of any use. 1) Freesurfer version: freesurfer-linux-centos7_x86_64-dev- 20180725-1793f7a 2) platform: centos-release 7centos 3) unmae -a: Linux tars 3.10.0-693.11.1.el7.x86_64 #1 SMP Mon Dec 4 23:52:40 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached 5) subject attached: see attached

2 1

Freesurfer dev version not available on the server
by Scheffler, F, Mev [fredas＠sun.ac.za] 06 Aug '18

06 Aug '18

External Email - Use Caution Dear Freesurfer Developers I’ve been trying to download the development version but I keep getting an error message. Error: The share does not exist on the server. Please check the share name, and then try again. Any suggestions or alternatives? Thanks very much for your help. Kind regards, FREDA SCHEFFLER Researcher / PhD Candidate [email.jpg] MA Research Psychology Faculty of Medicine and Health Sciences Fakulteit Geneeskunde en Gesondheidswetenskappe Universiteit Stellenbosch University PO Box | Posbus 241, Cape Town | Kaapstad, 8000 Francie van Zijl Drive | -rylaan, Tygerberg, 7505 South Africa | Suid-Afrika Tel: +27 21 938 9771 Email | E-pos: fredas(a)sun.ac.za [http://cdn.sun.ac.za/100/ProductionFooter.jpg]<http://www.sun.ac.za/english/about-us/strategic-documents> The integrity and confidentiality of this email are governed by these terms. Disclaimer<http://www.sun.ac.za/emaildisclaimer> Die integriteit en vertroulikheid van hierdie e-pos word deur die volgende bepalings bereël. Vrywaringsklousule<http://www.sun.ac.za/emaildisclaimer>

1 0

ERROR: input(s) cannot have multiple frames!
by Renew Andrade 05 Aug '18

05 Aug '18

External Email - Use Caution Hello community! I have an issue while running recon-all -all in a dpi file. What do you suggest as a solution? Thank you! Renes-MacBook-Air-2:~ andraderenew$ recon-all -all -i /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/parkinson/p06316/dwi_2500/NIfTI/p06316_bmatrix_2500.nii.gz -s Parkinson_p06316_dwi_2500 Subject Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c INFO: SUBJECTS_DIR is /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir Actual FREESURFER_HOME /Applications/freesurfer Darwin Renes-MacBook-Air-2.local 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar 5 22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64 /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_dwi_2500 \n mri_convert /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/parkinson/p06316/dwi_2500/NIfTI/p06316_bmatrix_2500.nii.gz /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_dwi_2500/mri/orig/001.mgz \n mri_convert.bin /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/parkinson/p06316/dwi_2500/NIfTI/p06316_bmatrix_2500.nii.gz /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_dwi_2500/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-repositories/parkinson/p06316/dwi_2500/NIfTI/p06316_bmatrix_2500.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0.973179, 0.23005) k_ras = (0, -0.23005, 0.973179) writing to /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_dwi_2500/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Sun Aug 5 21:11:50 -05 2018 Found 1 runs /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_dwi_2500/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... ERROR: input(s) cannot have multiple frames! /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_dwi_2500/mri/orig/001.mgz has 121 frames Darwin Renes-MacBook-Air-2.local 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar 5 22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64 recon-all -s Parkinson_p06316_dwi_2500 exited with ERRORS at Sun Aug 5 21:11:50 -05 2018 For more details, see the log file /Volumes/TOSHIBA_EXT/freesurfer_subjects_dir/Parkinson_p06316_dwi_2500/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

2 1

Question about run FreeSurfer
by Alexandra Trujillo 05 Aug '18

05 Aug '18

External Email - Use Caution Hello, I'm Alexandra, postgraduate student in Argentina. I would like install and run FreeSurfer in Linux, I'm following the instructions of ' https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall' and I obtained this output (correctly): Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni FSL_DIR /usr/local/fsl But, when I test have this output: bash: /usr/local/freesurfer/bin/freeview: /bin/tcsh: intérprete erróneo: No existe el archivo o el directorio and, No se ha encontrado la orden «freeview» I need to know how open the freeview GUI to view a .mgz or .nii.gz file. Thanks for your answers. Cordialy, Alexandra T.

1 0

Re: [Freesurfer] SNR covariate in cortical thickness & volumetrics between groups analyses
by John Anderson 05 Aug '18

05 Aug '18

External Email - Use Caution > Dear FS experts, > I would like to inquire about including SNR as a covariate for the between groups comparison in cortical thickness. Is this procedure valid? I have some T1 images of low quality and the majority are high in quality. I reviewed the segmentation and the cortical surfaces and fixed manually as possible. I don't want to exclude images from the data sets, so I am thinking of regressing out SNR. > It seems that the command "mri_segstats" can report SNR for every ROI in the brain. Is it correct to include whole brain SNR covariate for between group comparisons (cortical thickness and volumetric analyses). > If yes, do I need to include actual SNR values in the FSGD file or the demeaned values ? > > We appreciate your guidance! > John

3 3

Resting-State and Brain Connectivity 2018: abstract submission remains open until August 11
by Kelvin Mok 03 Aug '18

03 Aug '18

External Email - Use Caution ------------------------------ *From:* Amir Shmuel, Dr. *Sent:* 03 August 2018 15:55 *Subject:* Resting-State and Brain Connectivity 2018: abstract submission remains open until August 11 *Resting-State and Brain Connectivity 2018: abstract submission remains open accepted until August 11* We have received over 270 submissions! Abstract submission will remain open for late submissions until 11:59 PM on August 11, 2018. Early registration fee applies until 11:59 PM on August 15, 2018. We have added a *RECEPTION* to the evening schedule of September 26, 2018. This will include a “*SCIENTIFIC MATCHING and DATING*” event. Meet a scientist that can advise/give feedback on your paradigm design, modeling, analysis, machine-learning etc. We have added a satellite workshop on *HOW TO INCORPORATE MACHINE LEARNING AND/OR DEEP LEARNING IN YOUR DATA ANALYSIS*, scheduled for Saturday, 29th of September 2018. We will host a *SCI-ART EXHIBIT*, “The Lines that Connect”, organized by Dr. Amanpreet Badhwar. *Amir Shmuel* *Chair of the organizing committee* *Resting-State and Brain Connectivity 2018* *Montreal, QC, Canada* *http://restingstate.com/2018/ <http://restingstate.com/2018/>* *[image: http://restingstate.com/2018/wp-content/uploads/2017/06/resting-state-logo-…

1 0

ICV bias in CV measures
by Sahil Bajaj 03 Aug '18

03 Aug '18

External Email - Use Caution Dear FS experts, This paper was published in 2013: https://www.sciencedirect.com/science/article/pii/S1053811913007064?via%3Di… I was just wondering if the current version of FreeSurfer can still introduce bias in cortical volume measures if ICV is used as an covariate or this has been fixed in the latest FS version. Specific to this issue, if nothing has been updated in FS (since 2013), would you still recommend to *ALWAYS* use ICV as a covariate while comparing CV? Thanks, Sahil

1 0

SNA covariate in cortical thickness between groups analysis
by John Anderson 03 Aug '18

03 Aug '18

External Email - Use Caution Daer FS experts, I would like to inquire about including SNR as a covariate for the between groups cpmparison in cortical thickness. Is this procedure correct mathematically? Do I need to demean the SNA values before including it covariates? Finally, do you recommend any quality parameters other than SNR to be included covariate? I look forward to learn from your expertise, Thanks, John

2 1

Anterior / Posterior Partition in Hippocampus parcellation atlas
by Dev vasu 03 Aug '18

03 Aug '18

External Email - Use Caution Dear All, I have a problem with the Freesurfer hippocampal longitudinal segmentation results , when i have done segmentation using following algorithm ( https://github.com/CobraLab/antsRegistration-MAGeT) with no anterior/posterior partitioning ( Head/body/tail ) , on my subject pool the volumes that i have obtained for each subfield is very different from the volumes of corresponding subfields that i am getting when i have done subfield segmentation using freesurfer. I think algorithm does influence the segmentation procedure, if this is the case then i am getting different results for histology based segmentation using https://github.com/CobraLab/antsRegistration-MAGeT and freesurfer. When i compare the subfield volumes between healthy and disease patients that i have obtained using first segmentation procedure using ANTS-MAGeT , i notice statistical significance in subfields like CA1,CA2-CA3 but when i do the same using freesurfer based algorithm i notice no statistical significance in these subfields. Do you think the algorithm has any influence on segmentation to such a level that we get completely different results on two occasions. Thanks Vasudev

2 1

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 August 2018