Freesurfer

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30132 discussions

How to run freesurfer on steps 1 to 12
by Francisco Ferreira 03 Jul '18

03 Jul '18

External Email - Use Caution Hello Freesurfer Developers, I would like to run steps 1 to 12 (included) with default parameters freesurfer on an MRI, as described here ( https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all) I didn't find any information on how to do it. Could you please help me? I'm only interested in the segmentation of cortical regions, specifically the hippocampus. So if there is another method to do this alone and all its pre-requisites, that would be great as it would greatly accelerate the segmentation. Thank you in advance, best regards, Francisco Ferreira

2 3

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

03 Jul '18

External Email - Use Caution Dear Sir, I have reviewed your journal which detailed about hippocampus parcellation ( https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAm… ) of subfields ( HBT - Head/body/Tail) , could you please let me know how to partition the atlas along the lines of Anterior CA1,CA3,CA4 and posterior CA1,CA3,CA4. Thanks Vasdudev

2 8

NeuroStars - a modern platform for providing user support
by Chris Gorgolewski 02 Jul '18

02 Jul '18

External Email - Use Caution Dear experts, I would like to introduce you to a (relatively) new platform (supported by INCF) for providing user support and letting users exchange and discuss ideas - http://NeuroStars.org. I know what you think - yet another website? what's wrong with email? NeuroStars has some nice features that makes everyone's life easier. For example: - When you start typing a question it automatically searchers all existing ones looking for similarities. Users can easily find answers without having to ask questions and the same question does not need to be asked twice: [image: Screenshot_9.png] - It's well indexed by google making it even easier for users to find answers [image: Screenshot_10.png] - It's not just for one project. Currently many projects (nipype, nilearn, mindboggle, fmriprep, mriqc, dhcp etc.) use it for user support. Each question has tags corresponding to its projects allowing for questions spanning multiple domains. You can choose which tags you will receive notifications about [image: Screenshot_11.png] All projects, experts and users are welcome at NeuroStars.org. All contributors are striving to provide friendly atmosphere and polite discussions. NeuroStars has potential to be the place where SPM, FSL, FreeSurfer, and AFNI come together! Best, Chris

1 0

Volumetric Group Analysis
by Mr. Tass 02 Jul '18

02 Jul '18

External Email - Use Caution Good morning I hope everyone had a gr8 weekend. im new here so i hope someone can help me understand a little about the right way to use freesurfer in order to calculate the gray matter volume for different areas of the brain and compare the volume between left and right hemisphere. so far i have freesurfer installed and recon-all a couple of test subjects. and everything seems to be working fine. i have several subjects with the axial cut MRI. is the axial cut enough to output accurate results? im little concerned as the T1 representation Outputted in FREEVIEW seems a bit fuzzy im following the below link for my group analysis. https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/VolumetricGroupAnalysis please if possible to sheld some light on this kind of analysis and if i am on the right track. thanks alot to you all best regards Sarah Get Outlook for Android<https://aka.ms/ghei36>

2 1

Poor anterior temporal lobe surfaces
by Meaghan Perdue 02 Jul '18

02 Jul '18

External Email - Use Caution Hello Freesurfer experts, I have tried several times to send this out, but I haven't received a response. Please let me know if there is a way to solve this issue. I have come across a problem with several subjects in which the pial surface fails to adequately capture the anterior temporal lobes. This occurs despite accurate brainmask and wm volumes. I have included a screen shot below, in this case, the wm surface is also affected, but this is not always the case. This is pediatric data that was acquired on a 1.5T scanner and processed in Freesurfer v 5.3. The following expert options have been employed to try to improve surface rendering: mris_make_surfaces -max_gray_at_csf_border 80 -max_csf 30 -min_gray_at_csf_border 35 Please let me know how I can solve this issue. As a second question, I've heard that segmentation and surface rendering is improved with v 6.0, and I'm wondering if subjects that have been initially run through v. 5.3 and had manual edits made can then have autorecon run through v 6.0 for improvement of surfaces? Please let me know if this would be a reliable/recommended approach to improving surfaces. Thank you, Meaghan Perdue -- Meaghan Perdue PhD Student Developmental Psychology Neurobiology of Language University of Connecticut Bousfield A302

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Compute cortical thickness within VOI
by Alshikho, Mohamad J. 02 Jul '18

02 Jul '18

Dear FreeSurfer experts, I have MRS volume of interest (VOI) was placed in the motor cortex during MRS data acquisition. In order to compute the gray and white matter volume within the VOI, I synthesized this VOI using "mri_volsynth". Then I registered it to T1 Freesurfer space using "spmregister". Finally, I used "mri_segstats" to compute the gray and white matter volume for all the structures within this VOI. My question is how can I compute cortical thickness for the cortical structures within this VOI. By looking into "recon-all.log" I found that the command "mris_anatomical_stats" was used to compute cortical thickness from the surfaces. Is it a correct procedure to map this VOI onto surface using "mri_vol2surf" then feed the output into "mris_anatomical_stats" as an annotation file? Thank you for any guidance. Mohamad

2 2

degrees of freedom
by John Absher 01 Jul '18

01 Jul '18

External Email - Use Caution In group analysis, is it better to have matched controls (1:1) or to use age, education and other characteristics as confounds in the glm? In the latter situation, we would control for these demographic variables in the glm and the control group n could be smaller, the same or larger than the test group. We are looking at TBI+ and TBI- subjects across a broad age range to look at patterns of cortical thinning. Thanks. John R. Absher, MD, FAAN GHS Neurosciences jabsher(a)ghs.org<mailto:jabsher@ghs.org> 864-350-6655 (mobile)

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Proposed addition for Freesurfer - automated control points
by Chris Adamson 30 Jun '18

30 Jun '18

External Email - Use Caution Freesurfer devs, I presented an automated control point adding tool at HBM and a few freesurfer lab people came over and had a look. I was wondering if someone would like to review it for either inclusion or to perhaps reference from the wiki as a tool for people to use if they choose? Thanks in advance, Chris. Dr Chris Adamson Senior Research Officer Developmental Imaging, Clinical Sciences Murdoch Childrens Research Institute The Royal Children's Hospital Flemington Road, Parkville, VIC 3052 Australia E chris.adamson(a)mcri.edu.au<mailto:chris.adamson@mcri.edu.au> www.mcri.edu.au<http://www.mcri.edu.au/> This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise deal with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated to be those of Murdoch Childrens Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from or in respect of the Communication. P Please consider the environment before printing this email

2 2

TIV should be considered as a covariant for thickness, volume and area analyses
by Ting Li 29 Jun '18

29 Jun '18

External Email - Use Caution Hi FreeSurfer Experts, I would like to do the surface analysis among two groups, like the thickness, volume and area. When I run the GLM, do I have to consider the eTIV as a covariant or not? Thanks a lot! Best wishes, Ting

2 2

Eddy correct command not found
by Renew Andrade 29 Jun '18

29 Jun '18

External Email - Use Caution Dear community: I have a problem with trac-all processing with the tutorial data. sh-3.2# trac-all -prep -c $TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial INFO: SUBJECTS_DIR is /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_recons INFO: Diffusion root is /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial Actual FREESURFER_HOME /Applications/freesurfer INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos6_x86_64-dev-20130423 Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c flirt: Command not found. INFO: current FREESURFER_HOME does not match that of previous processing. Current: /Applications/freesurfer Previous: /usr/local/freesurfer/dev trac-preproc -c /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/scripts/dmrirc.local -log /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/scripts/trac-all.log -cmd /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/scripts/trac-all.cmd #------------------------------------- /Applications/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Fri Jun 29 21:19:12 CEST 2018 mri_convert --bvec-voxel /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz mri_convert.bin --bvec-voxel /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz $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/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm... Getting Series No INFO: Found 75 files in /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/orig INFO: Scanning for Series Number 11 Scanning Directory INFO: found 70 files in series INFO: loading series header info. RunNo = 10 WARNING: Run 1 appears to be truncated Files Found: 70, Files Expected (lRep+1): 120 FileName /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm Identification NumarisVer syngo MR 2004A 4VA25A ScannerModel Trio PatientName Trio_calib_002_run2 Date and time StudyDate 20050905 StudyTime 100821.656000 SeriesTime 104226.748000 AcqTime 104209.522496 Acquisition parameters PulseSeq ep_b0#0 Protocol DIFFUSION_HighRes PhEncDir COL EchoNo 0 FlipAngle 90 EchoTime 100 InversionTime -1 RepetitionTime 10100 PhEncFOV 256 ReadoutFOV 256 Image information RunNo 10 SeriesNo 11 ImageNo 1 NImageRows 1024 NImageCols 1024 NFrames 70 SliceArraylSize 60 IsMosaic 1 ImgPos 1048.1801 1002.6923 -265.4914 VolRes 2.0000 2.0000 2.0000 VolDim 128 128 60 Vc -0.9997 0.0244 0.0005 Vr -0.0238 -0.9764 0.2147 Vs 0.0057 0.2147 0.9767 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID unknown INFO: sorting. INFO: (128 128 60), nframes = 70, ismosaic=1 sdfi->UseSliceScaleFactor 0 datatype = 4, short=4, float=3 Numaris Version: syngo MR 2004A 4VA25A Maj = 4, Min=2, MinMin = 5 Repetition Time = 10100, TR = 10100 ms PE Dir COL COL AutoAlign matrix detected AutoAlign Matrix --------------------- 0.99970 0.02376 -0.00570 -0.49480; -0.02443 0.97638 -0.21466 -40.55519; 0.00047 0.21474 0.97667 12.50291; 0.00000 0.00000 0.00000 1.00000; FileName /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm Identification NumarisVer syngo MR 2004A 4VA25A ScannerModel Trio PatientName Trio_calib_002_run2 Date and time StudyDate 20050905 StudyTime 100821.656000 SeriesTime 104226.748000 AcqTime 104209.522496 Acquisition parameters PulseSeq ep_b0#0 Protocol DIFFUSION_HighRes PhEncDir COL EchoNo 0 FlipAngle 90 EchoTime 100 InversionTime -1 RepetitionTime 10100 PhEncFOV 256 ReadoutFOV 256 Image information RunNo 10 SeriesNo 11 ImageNo 1 NImageRows 1024 NImageCols 1024 NFrames 70 SliceArraylSize 60 IsMosaic 1 ImgPos 131.1612 149.7402 -72.6670 VolRes 2.0000 2.0000 2.0000 VolDim 128 128 60 Vc -0.9997 0.0244 0.0005 Vr -0.0238 -0.9764 0.2147 Vs 0.0057 0.2147 0.9767 VolCenter 0.5005 40.7699 13.4796 TransferSyntaxUID unknown UseSliceScaleFactor 0 (slice 0: 1) IsDWI = 0 sagrev = 1, correv =1, trarev = 0 Vs = 0.0057 0.214665 0.976671 INFO: no Siemens slice order reversal detected (good!). TR=10100.00, TE=100.00, TI=-1.00, flip angle=90.00 i_ras = (-0.999702, 0.0244268, 0.000465598) j_ras = (-0.023757, -0.976382, 0.21474) k_ras = (0.0057, 0.214665, 0.976671) writing to /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz... mri_probedicom --i /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm > /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dcminfo.dat cp /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/orig/gradients.txt /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig.bvecs cp /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/orig/bvalues.txt /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig.bvals mv -f /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/bvecs.tmp /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig.bvecs mv -f /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/bvals.tmp /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig.bvals orientLAS /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig_las.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 8 mri_convert -oni 128 -onj 128 -onk 60 -oid -0.999701 0.0244268 0.000465598 -ojd 0.023757 0.976382 -0.21474 -okd 0.0057 0.214665 0.976671 -oc 0.548018 42.7227 13.0501 -rt nearest /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig_las.nii.gz mri_convert.bin -oni 128 -onj 128 -onk 60 -oid -0.999701 0.0244268 0.000465598 -ojd 0.023757 0.976382 -0.21474 -okd 0.0057 0.214665 0.976671 -oc 0.548018 42.7227 13.0501 -rt nearest /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig_las.nii.gz normalizing out_i_direction: (-0.999701, 0.0244268, 0.000465598) -> (-0.999702, 0.0244268, 0.000465598) normalizing out_j_direction: (0.023757, 0.976382, -0.21474) -> (0.023757, 0.976382, -0.21474) normalizing out_k_direction: (0.0057, 0.214665, 0.976671) -> (0.0057, 0.214665, 0.976671) $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/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz... TR=10100.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999701, 0.0244268, 0.000465598) j_ras = (-0.023757, -0.976382, 0.21474) k_ras = (0.0057, 0.214665, 0.976671) Reslicing using nearest writing to /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig_las.nii.gz... INFO: found /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig.bvals, copying INFO: found /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig.bvecs, converting to LAS mv -f /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig_las.bvecs /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/bvecs mv -f /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig_las.bvals /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/bvals eddy_correct /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig_las.nii.gz /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi.nii.gz 0 eddy_correct: Command not found. 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 trac-preproc exited with ERRORS at Fri Jun 29 21:20:22 CEST 2018 What should be the problem? Sincerely, Andrade.

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