Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

reproducing sig.mgh
by Eric Cunningham 03 Nov '15

03 Nov '15

Hello Freesurfer Experts, I am trying to reproduce the values in sig.mgh using matlab, just to confirm that I know what is going on. My numbers do not match exactly, and I am hoping someone can explain my error, or point me in the right direction. With Qdec, I built a model with one discrete factor (A) with groups (A1) and (A2), one continuous covariate (B), and one nuisance factor (C). I extracted the values from sig.mgh from the folder: lh-Diff-A1-A2-Cor-area-B at a specific vertex. I also extracted the values from y.mgh at the same vertex. I then ran an anova with contrast matrix, and expected the -log10(p-value) of the A*B term to match that of sig.mgh. [1 0 0;... (A) 0 1 0;... (B) 0 0 1;... (C) 1 1 0]; (A*B) Thank you for your time, -E

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FreeSurfer and OpenMP
by Linda BOUMGHAR 03 Nov '15

03 Nov '15

I would like to use freesurfer with OpenMP, with 4 processors. I wrote this : recon-all -all -i /mnt/linuxwin/lboumgha/data/CENTER_TBI/tro/suj1/T1.nii.gz -subjid subj1 -openmp <8> and I got this error message : bash: syntax error near unexpected token `8' What is the good syntax if I want tu use OpenMP, please? Great regards, Linda Boumghar ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

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Voxel based vs surface based
by John Anderson 03 Nov '15

03 Nov '15

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Differences in the asc and FreeSurfer format of the surface data
by Razlighi, Qolamreza R. 03 Nov '15

03 Nov '15

Hi Guys, Why converting a surface to .asc format changes its spatial orientation? Specifically, I have converted lh.while to lh.white.asc (using: mris_convert lh.white lh.white.asc) and plot both of them using freeview but they are not corresponding. In fact, lh.white corresponds to the volume image (e.g orig.mgz) but the lh.white.asc doesn't. See the attached screenshot. The red curve is the lh.white.asc. Any explanation would be greatly appreciated. Best -- Ray Razlighi, Ph.D. Assistant Professor Quantitative Neuroimaging Laboratory Division of Cognitive Neuroscience Department of Neurology Columbia University Alt: razlighi(a)gmail.com Office Phone: 212-342-1352 Office Fax: 212-342-1838 Website: http://www.columbia.edu/cu/qnl/

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using ADNI preprocessed files in FS
by Riphagen Joost (NP) 03 Nov '15

03 Nov '15

Hi, Sorry for the very basic question but I have not been able to find the answer in the archives, nor anywhere else. I want to use ADNI data in FS ADNI data is available in either original DICOM or has been preprocessed in the following manner: Phillips Systems: unpreprocessed DICOM N3 corrected GE and Siemens systems with transmit-receive head RF coils: unpreprocessed DICOM gradwarped gradwarp plus N3 GE and Siemens systems with receive-only head RF coils: unpreprocessed DICOM gradwarped gradwarp plus B1 plus N3 I reality there are quite a few more options available. Question is which one to use best for FS (plan is to rerun in a newer FS version) I suppose that using the files that are gradwarped and B-1 corrected is sensible for using in FS. However the "best" files after quality control have been N3 corrected which makes it a lot easier for me to extract these files from the database (I need a few hundred, meaning I have many thousands of files to extract from). Would running recon all, but omitting the N3 step be correct ? Thanks a lot, JM Joost Riphagen, MD Phd candidate Maastricht University.

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comparison of subcortical volume with 1.5 T and 3T...
by Gonzalo Rojas Costa 03 Nov '15

03 Nov '15

Hi: I have some longitudinal study of a patient with 1.5 T images... now, we have 3T mprage images of the same patient... how can I do the comparison of the subcortical volume of the patient ?... Sincerely, Gonzalo Rojas Costa -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

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subfields segmentation FS v6.0
by Daniele Orlandi 03 Nov '15

03 Nov '15

Dear all I'm running the new pipleline for hippocampal subfields segmentation with FreeSurfer v6.0 on a T13D image. As results i can extract values for the Whole hippocampus and the following subfields: Hippocampal_tail, subiculum, CA1, hippocampal-fissure, presubiculum, parasubiculum, molecular_layer_HP, GC-ML-DG, CA3, CA4, fimbria, HATA but not for Alveus as reported in the paper of Iglesias, JE. et al. 2015. Was my computation wrong? Best, Daniele

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recon-all crashing
by Biekman, Brian Darnell 02 Nov '15

02 Nov '15

To Whom It May Concern: I am conducting FreeSurfer analysis for a multi-site project and I'm unable to run recon-all on the T1 data for all but one of the sites. The problem I'm dealing with is identical for all of the subjects for which recon-all crashes. I do not want to speculate as to why recon-all works for one of the sites but it's worth mentioning that that site has a slightly different T1 protocol and that these images were uploaded via a physical backup disk while for the other sites, I downloaded the T1 data for the other sites from a database shared by all of the project investigators. I would like to upload the images for one the T1-weighted sequences that crashes recon-all. If somebody could let me know how to go about that, I would really appreciate it. Thank you. Here is the requested information for anyone reporting a bug: FREESURFER_HOME: /Applications/freesurfer Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Kernel info: Darwin 15.0.0 x86_64 Subject Name: 14-140-0052 Command Line Executed: recon-all -all -i /users/brianbiekman/Desktop/Brain_Scope/14-140-0052/00001.dcm -s 14-140-0052 Error message generated: Screenshot of error message attached recon-all log: Attached

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Mac Version and Output differs
by Kasper Jessen 02 Nov '15

02 Nov '15

Dear FreeSurfer group, I have tested the data output on the same subjects using the same FreeSurfer version but on different machines, a MacPro and a iMac. The output are different, which argues that it is important to run freesurfer on the same computer on all your subjects. Is it due to a randomisation in freesurfer (maybe because of seed points)? Is it possible to get the same results even though you run in on different computers? *MacPro:* build-stamp.txt: freesurfer-Darwin-lion-stable-pub-v5.3.0 Darwin mac-pro-2014.regionh.top.local 13.4.0 Darwin Kernel Version 13.4.0: Wed Mar 18 16:20:14 PDT 2015; root:xnu-2422.115.14~1/RELEASE_X86_64 x86_64 *iMac: * build-stamp.txt: freesurfer-Darwin-lion-stable-pub-v5.3.0 Darwin Nikolajs-iMac.local 11.4.2 Darwin Kernel Version 11.4.2: Thu Aug 23 16:25:48 PDT 2012; root:xnu-1699.32.7~1/RELEASE_X86_64 x86_64 Best regards, Kasper Jessen

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Tracula ends with errors
by denizzgursel 02 Nov '15

02 Nov '15

Dear all, I am very new to using TRACULA and Freesurfer. I am trying to apply tracula on the provided tutorial data. When I ran the command trac-all -prep -c dmrirc.tutorial, after eddy current correction, I get this error: mv -f /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/bvecs /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/bvecs.norot xfmrot /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/dwi.ecclog /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/bvecs.norot /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/bvecs R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. n -sf /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/dwi.nii.gz /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/data.nii.gz mri_convert --frame 0 /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/dwi.nii.gz /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/dwi_frame0.nii.gz mri_convert --frame 0 /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/dwi.nii.gz /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/dwi_frame0.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/dwi.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999278, -0.0375823, -0.00564044) j_ras = (-0.0367492, 0.917788, 0.395367) k_ras = (0.00968205, -0.395289, 0.918506) keeping frame 0 writing to /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/dwi_frame0.nii.gz... mri_concat --i /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/dwi_frame0.nii.gz --mean --o /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/lowb.nii.gz ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Computing mean across frames Writing to /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/lowb.nii.gz bet /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/lowb.nii.gz /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/lowb_brain.nii.gz -m -f 0.3 mv -f /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/lowb_brain_mask.nii.gz /data_augus t/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dlabel/diff #------------------------------------- #@# Inter-subject registration Mon Nov 2 15:39:02 CET 2015 flirt -in /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/lowb_brain.nii.gz -ref /data_RAID/Kathrin/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/lowb_brain_mni.nii.gz -omat /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/xfms/diff2mni.mat -cost corratio convert_xfm -omat /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/xfms/mni2diff.mat -inverse /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/xfms/diff2mni.mat #------------------------------------- #@# Masks Mon Nov 2 15:39:20 CET 2015 flirt -in /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dlabel/diff/lowb_brain_mask.nii.gz -ref /data_RAID/Kathrin/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dlabel/mni/lowb_brain_mask.bbr.nii.gz -applyxfm -init /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/xfms/diff2mni.bbr.mat -interp nearestneighbour flirt -in /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dlabel/diff/lowb_brain_mask.nii.gz -ref /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/brain_anat_orig.nii.gz -out /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dlabel/anatorig/lowb_brain_mask.bbr.nii.gz -applyxfm -init /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/xfms/diff2anatorig.bbr.mat -interp nearestneighbour ln -sf /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dlabel/diff/aparc+aseg_mask.bbr.nii.gz /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/nodif_brain_mask.nii.gz #------------------------------------- #@# Tensor fit Mon Nov 2 15:39:23 CET 2015 dtifit -k /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/dwi.nii.gz -m /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -r /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/bvecs -b /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/bvals -o /data_august/Deniz/tutorial/tutorial_data/diffusion_tutorial//elmo.2012/dmri/dtifit 0 128 0 128 0 64 terminate called after throwing an instance of 'NEWMAT::IndexException' Abort Linux slow.mri.tu-muenchen.de 3.7.10-1.40-desktop #1 SMP PREEMPT Thu Jul 10 11:22:12 UTC 2014 (9b06319) x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Mon Nov 2 15:39:23 CET 2015 My config file is as simple as possible. I only defined the data path, output path, subject list and dcmlist. The problem seems to be related to bvecs file, I looked at it, and it seems to have 0.0000 in the beginning. Could this create a problem? Thank you. Best, -- D.

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