Freesurfer February 2019

freesurfer@nmr.mgh.harvard.edu

114 participants
196 discussions

Different aseg and aparc stats with Freesurfer 5.3 and 6.0
by Ranila Bhoyroo 13 Feb '19

13 Feb '19

External Email - Use Caution Hello Experts, I was working with some data pre-processed using freesurfer v5.3 - i think this was done on linux. Recently I pre-processed the dataset using v6.0 on an imac. I extracted cortical thickness and surface area from both hemispheres. The data is different for each version. What worries me is that I am correlating the neural metrics with some behavioral data and this gives me different results. My sample size is only 20. Some advice would be very helpful. Thanks. Cheers, *Ranila *

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Postdoctoral position (EEG-MRI) available at NORMENT (Oslo, Norway)
by Kjetil Nordbø Jørgensen 13 Feb '19

13 Feb '19

External Email - Use Caution Dear FreeSurfer users! A three-year position as postdoctoral fellow is now available at the Norwegian Centre for Mental Disorders Research (NORMENT) in Oslo, Norway. NORMENT is a Center of Excellence (CoE) funded by the Research Council of Norway. The main purpose of the research is to disentangle and characterize the neurobiological, genetic, psychological and environmental factors contributing to the development of severe mental disorders. Within this context, the postdoctoral fellow is expected to focus on the relationships between MRI-derived measures of brain myelination and EEG-derived electrophysiological measures in connection to psychotic symptomatology. More information about the position can be found here: https://www.jobbnorge.no/ledige-stillinger/stilling/163184/postdoctoral-res… We welcome applicants! Please note the short deadline, February 17th. Kind regards, Kjetil Nordbø Jørgensen, PhD Postdoctoral fellow and clinical psychologist Diakonhjemmet Hospital and the Norwegian Centre for Mental Disorders Research (NORMENT) Oslo, Norway

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Re: [Freesurfer] problem using recon-all
by Shachar Gal 13 Feb '19

13 Feb '19

External Email - Use Caution Hey Douglas, A couple of question about the patch In order to use it, I need to download the regular Freesurfer version-6, and replace only the scripts that are in the patch? (i.e Make_average_surface, recon_all, conf2hires, longmc) Which recon-all to use? The one under the hcp sub folder? Thanks! Shachar

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Makefile for Tracula
by Kirstie Whitaker 12 Feb '19

12 Feb '19

External Email - Use Caution Hi everyone! Firstly - and most importantly - thank you for the awesome tool, and for all your help in using it! I'm re-processing (and re-quality controll-ing) data that was formatted in v5.3 into v6 and I've come to re-running trac-all. I've been using v6 with the updated Makefile (if anyone's googling this question, see the note at this page about the fact that v6 doesn't ship with the correct make file https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingDataV6.… ). I wonder if a) there is a makefile for trac-all (that would be amazing) or b) you could tell me which files I need to delete so I re-process them now that the surfaces are updated? I assume the DTI processing hasn't changed, so I shouldn't need to change the bedpostx folder for example, but I'm not 100% sure on which other files have dependences on the reconstructions :) (The surfaces got pretty messed up in this update so I'd like to go back to basics....without having to rerun things we KNOW aren't related to the surface reconstructions.) Thank you! Kirstie -- Kirstie Whitaker, PhD Research Fellow, Alan Turing Institute Research Associate, University of Cambridge *Mailing Address* Brain Mapping Unit Department of Psychiatry Sir William Hardy Building Downing Street Cambridge CB2 3EB *Phone: *+44 7583 535 307 *Website:* https://whitakerlab.github.io *Twitter:* @kirstie_j <https://twitter.com/kirstie_j>

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segmentHA_T2.sh hippo stream fails and doesn't recon both side, using 2019-02-03 dev version, centos6
by ROBERT CARY WELSH 12 Feb '19

12 Feb '19

External Email - Use Caution Hi Freesurfer, I’m running the dev version of freesurfer (cent06 from website, dated 2019-02-03) after seeing the (volumesAmygdala.txt error) message thread of https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg59610.html But it still fails. Previously, I ran the recon-all using stable cent06, and then tried the new hippo pipeline with the command: export SUBJECTS_DIR=/erato/data/WelshData/MHD19/Freesurfer/SubjectsDerivedUCLA segmentHA_T2.sh -s AD_CS_8_23_04 mri/hippo.mgz hippo 1 I’m attaching the log file from the stream. Robert ------------------------------ Robert Welsh, PhD Associate Professor Department of Psychiatry University of Utah robert.c.welsh(a)utah.edu

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mri_segstat: same output with two different label
by Francesca Strappini 12 Feb '19

12 Feb '19

External Email - Use Caution Dear Freesurfer's experts, I'm trying to run a ROIs mean intensity analysis using mri_segstat. I'm using as an input contrast maps created with mkcontrast-sess and selxavg3-sess (block-design experiment) and as masks, some labels created on the surface with a retinotopic analysis. I noticed that all my outputs with the same label have the same values, regardless of the contrast map that I'm giving as an input. However, if I plot the contrast maps on the surface I can clearly see that there are differences, so also the mean signal should be different. Maybe I'm not running the command correctly: mri_segstats --i z.nii.gz --slabel sub1 lh lh.V2dorsal_sub1.label --sfavg lh.V2dorsal_sub1_condition1_avg --snr --sum lh.V2dorsal_sub1_condition1_sum These are two outputs from the same regions but with two different z maps as inputs. I can also see that are indicated two different values as mean intensity, -0.95028 and 1.31525, what's the difference between them? # Title Segmentation Statistics # # generating_program mri_segstats # cvs_version $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ # cmdline mri_segstats --i disorder/z.nii.gz --slabel AB lh /home/labs/malach/frastra/freesurfer/subjects/AB/label/lh.V2dorsal_AB.label --sfavg lh.V2dorsal_AB_disorder_avg --snr --sum lh.V2dorsal_AB_disorder_sum # sysname Linux # hostname access4.wexac.weizmann.ac.il # machine x86_64 # user frastra # anatomy_type surface # # SUBJECTS_DIR /home/labs/malach/frastra/freesurfer/subjects # subjectname AB # Label AB lh /home/labs/malach/frastra/freesurfer/subjects/AB/label/lh.V2dorsal_AB.label # InVolFile disorder/z.nii.gz # InVolFileTimeStamp 2018/12/08 20:12:18 # InVolFrame 0 # ExcludeSegId # Only reporting non-empty segmentations # VertexArea_mm2 0.657815 # TableCol 1 ColHeader Index # TableCol 1 FieldName Index # TableCol 1 Units NA # TableCol 2 ColHeader SegId # TableCol 2 FieldName Segmentation Id # TableCol 2 Units NA # TableCol 3 ColHeader NVertices # TableCol 3 FieldName Number of Vertices # TableCol 3 Units unitless # TableCol 4 ColHeader Area_mm2 # TableCol 4 FieldName Area # TableCol 4 Units mm^2 # TableCol 5 ColHeader Mean # TableCol 5 FieldName Intensity Mean # TableCol 5 Units unknown # TableCol 6 ColHeader StdDev # TableCol 6 FieldName Itensity StdDev # TableCol 6 Units unknown # TableCol 7 ColHeader Min # TableCol 7 FieldName Intensity Min # TableCol 7 Units unknown # TableCol 8 ColHeader Max # TableCol 8 FieldName Intensity Max # TableCol 8 Units unknown # TableCol 9 ColHeader Range # TableCol 9 FieldName Intensity Range # TableCol 9 Units unknown # NRows 2 # NTableCols 9 # ColHeaders Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max Range SNR 1 0 161272 106116.2 Seg0000 -0.9503 2.4005 -13.2314 11.4302 24.6617 -0.3959 2 1 1369 871.1 Seg0001 1.3153 3.8989 -8.2296 10.3666 18.5962 0.3373 # Title Segmentation Statistics # # generating_program mri_segstats # cvs_version $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ # cmdline mri_segstats --i order/z.nii.gz --slabel AB lh /home/labs/malach/frastra/freesurfer/subjects/AB/label/lh.V2dorsal_AB.label --sfavg lh.V2dorsal_AB_order_avg --snr --sum lh.V2dorsal_AB_order_sum # sysname Linux # hostname access4.wexac.weizmann.ac.il # machine x86_64 # user frastra # anatomy_type surface # # SUBJECTS_DIR /home/labs/malach/frastra/freesurfer/subjects # subjectname AB # Label AB lh /home/labs/malach/frastra/freesurfer/subjects/AB/label/lh.V2dorsal_AB.label # InVolFile order/z.nii.gz # InVolFileTimeStamp 2018/12/08 20:12:49 # InVolFrame 0 # ExcludeSegId # Only reporting non-empty segmentations # VertexArea_mm2 0.657815 # TableCol 1 ColHeader Index # TableCol 1 FieldName Index # TableCol 1 Units NA # TableCol 2 ColHeader SegId # TableCol 2 FieldName Segmentation Id # TableCol 2 Units NA # TableCol 3 ColHeader NVertices # TableCol 3 FieldName Number of Vertices # TableCol 3 Units unitless # TableCol 4 ColHeader Area_mm2 # TableCol 4 FieldName Area # TableCol 4 Units mm^2 # TableCol 5 ColHeader Mean # TableCol 5 FieldName Intensity Mean # TableCol 5 Units unknown # TableCol 6 ColHeader StdDev # TableCol 6 FieldName Itensity StdDev # TableCol 6 Units unknown # TableCol 7 ColHeader Min # TableCol 7 FieldName Intensity Min # TableCol 7 Units unknown # TableCol 8 ColHeader Max # TableCol 8 FieldName Intensity Max # TableCol 8 Units unknown # TableCol 9 ColHeader Range # TableCol 9 FieldName Intensity Range # TableCol 9 Units unknown # NRows 2 # NTableCols 9 # ColHeaders Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max Range SNR 1 0 161272 106116.2 Seg0000 -0.9503 2.4005 -13.2314 11.4302 24.6617 -0.3959 2 1 1369 871.1 Seg0001 1.3153 3.8989 -8.2296 10.3666 18.5962 0.3373 Thanks a lot for the help Best Francesca -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strappini(a)weizmann.ac.il

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Converting MNI152 coorindates to fsaverage space
by ts+ml＠rcmd.org 11 Feb '19

11 Feb '19

External Email - Use Caution Dear list, I have some points of interest (volume coordinates, e.g. '5.9, -27.7, 49.7') in MNI152 space. I would like to transform them to fsaverage space. How should I do that? I noticed that FreeSurfer comes with the file $FREESURFER_HOME/average/mni152.register.dat that contains a matrix. Is all I have to do read that matrix and apply it to each coordinate? And if so, for which direction is the matrix (do I have to invert it)? Best, -- Tim

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Why in the aseg.stats file the nvoxel value doesn't equal to the volume or follow a arithmetic correlation?
by 赵永翔 11 Feb '19

11 Feb '19

External Email - Use Caution Hi all. I was puzzled when I checked the the aseg.stats in the fs_output_folder after I run the routuine recon-all cmd.(fs6.0_linux) In this stat file I found that the nvoxel value doesn't equal to the volumes of each subcortical segmentation. They even doesn't follow a arithmetic correlation. But the header reads that the voxel is equal to 1 mm^3 in volume. So why? I wiil be greatly appreciated if somebody could tell me if there is anything wrong with my ideas. the sample of my aseg.stat file(some lines) is appended here. # Title Segmentation Statistics # # generating_program mri_segstats # cvs_version $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ # VoxelVolume_mm3 1 # ColHeaders Index SegId NVoxels Volume_mm3 StructName normMean normStdDev normMin normMax normRange 1 4 18001 18343.9 Left-Lateral-Ventricle 37.8841 9.3238 24.0000 90.0000 66.0000 2 5 1641 1672.0 Left-Inf-Lat-Vent 45.0488 11.6523 23.0000 82.0000 59.0000 3 7 16241 16825.4 Left-Cerebellum-White-Matter 84.3527 5.6642 29.0000 98.0000 69.0000 4 8 52760 52711.2 Left-Cerebellum-Cortex 66.2411 9.4589 25.0000 91.0000 66.0000 5 10 7246 6891.5 Left-Thalamus-Proper 91.3607 9.1942 41.0000 107.0000 66.0000 6 11 3246 3140.1 Left-Caudate 85.8783 7.9460 53.0000 107.0000 54.0000 7 12 4285 4264.4 Left-Putamen 91.0488 4.3328 63.0000 104.0000 41.0000 8 13 2022 2006.2 Left-Pallidum 100.0514 4.3088 75.0000 118.0000 43.0000 9 14 2969 3048.2 3rd-Ventricle 39.8787 8.2650 26.0000 81.0000 55.0000 10 15 1552 1705.4 4th-Ventricle 40.3808 9.6486 23.0000 79.0000 56.0000 11 16 19144 18890.9 Brain-Stem 83.6324 10.1835 34.0000 108.0000 74.0000 12 17 3738 3442.8 Left-Hippocampus 74.7269 8.1358 40.0000 97.0000 57.0000 13 18 1100 1054.6 Left-Amygdala 76.2536 7.1347 43.0000 95.0000 52.0000 14 24 1791 1694.4 CSF 51.9894 11.2187 32.0000 94.0000 62.0000 15 26 278 249.5 Left-Accumbens-area 85.4928 6.2711 54.0000 93.0000 39.0000 16 28 4171 3992.6 Left-VentralDC 92.5809 11.1675 41.0000 116.0000 75.0000 17 30 0 0.0 Left-vessel 0.0000 0.0000 0.0000 0.0000 0.0000 18 31 928 888.8 Left-choroid-plexus 52.3438 10.8472 31.0000 78.0000 47.0000 19 43 20737 20900.1 Right-Lateral-Ventricle 37.1717 8.9953 25.0000 92.0000 67.0000 20 44 5481 5495.9 Right-Inf-Lat-Vent 37.8816 9.1653 26.0000 79.0000 53.0000 21 46 16633 17143.0 Right-Cerebellum-White-Matter 83.6901 5.3551 40.0000 99.0000 59.0000 22 47 54353 54454.1 Right-Cerebellum-Cortex 66.2976 9.1862 20.0000 89.0000 69.0000 23 49 6416 6042.8 Right-Thalamus-Proper 89.1852 9.9130 37.0000 106.0000 69.0000 24 50 3294 3062.4 Right-Caudate 87.1703 8.2085 53.0000 107.0000 54.0000 25 51 3794 3796.8 Right-Putamen 92.5113 4.1020 62.0000 104.0000 42.0000 26 52 2124 2028.5 Right-Pallidum 102.1172 4.1392 75.0000 118.0000 43.0000 27 53 2980 2742.1 Right-Hippocampus 73.9638 9.4803 28.0000 96.0000 68.0000 28 54 1299 1132.8 Right-Amygdala 69.1655 14.6045 28.0000 98.0000 70.0000 29 58 273 223.8 Right-Accumbens-area 88.0403 5.5989 64.0000 99.0000 35.0000 30 60 3924 3713.0 Right-VentralDC 92.1210 12.3974 35.0000 117.0000 82.0000 31 62 13 24.5 Right-vessel 60.4615 6.2930 48.0000 71.0000 23.0000 32 63 1302 1224.4 Right-choroid-plexus 51.1751 10.0901 31.0000 79.0000 48.0000 33 72 0 0.0 5th-Ventricle 0.0000 0.0000 0.0000 0.0000 0.0000 34 77 1508 1452.2 WM-hypointensities 74.0351 13.0445 37.0000 107.0000 70.0000 35 78 0 0.0 Left-WM-hypointensities 0.0000 0.0000 0.0000 0.0000 0.0000 Thank you! -- Yongxiang Zhao Ph.D. student Radiology Department of Xuanwu Hospital, Capital Medical University 2014-2017 Xuanwu Hospital, Capital Medical University Postgraduate 2009-2014 Qingdao Medical College Undergraduate

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Re: [Freesurfer] zero values when run recon-all with T2pial flag (V6.0)
by Morgan Botdorf 11 Feb '19

11 Feb '19

External Email - Use Caution Yes, attached is the recon-all.log file for one subject. -Morgan -- Morgan Botdorf, M.S. Graduate Student Neurocognitive Development Lab University of Maryland, College Park mbotdorf(a)terpmail.umd.edu >Date: Thu, 7 Feb 2019 22:29:43 +0000 >From: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu> >Subject: Re: [Freesurfer] zero values when run recon-all with T2pial > flag (V6.0) >To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> >Message-ID: <6ea86bbf-6001-e95d-dcee-84cc8ba5d6e9(a)mgh.harvard.edu> >Content-Type: text/plain; charset="utf-8" > >I have not. Can you send the recon-all.log file? >On 2/1/19 6:01 PM, Morgan Botdorf wrote: > > ????????External Email - Use Caution > > Dear all, > > I recently ran recon-all on data using the T2pial flag to improve the > pial surface (using version 6.0). The T2 images seemed to improve the > pial surfaces; however, when I extract stats using the Destrieux > atlas, I get zero values for several regions and for > BrainSegVolNotVent and eTIV. If I run recon-all without the T2 image, > I get data for these regions,?BrainSegVolNotVent, and eTIV. Has anyone > run into similar issues using the T2pial flag or have an idea of what > may be causing this problem? > > Thank you in advance?for your help! > > Morgan

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Question
by alireza gazani 11 Feb '19

11 Feb '19

External Email - Use Caution Hello, I have a question and I couldn't find any answer in the archive. We have clinical T-1 (post-contrast) images, can we use them for subcortical analysis? I know they can't be used for cortical thickness analysis. Thank you!

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Freesurfer February 2019