Freesurfer

freesurfer@nmr.mgh.harvard.edu

4 participants
30090 discussions

SPMPainting
by Geng Shuang 17 Jul '17

17 Jul '17

I am confused that how to align the brain.img with my functional data in spm... https://surfer.nmr.mgh.harvard.edu/fswiki/SpmPainting Best wishes! 1. Convert the brain.mgz volume to analyze: mri_convert $SUBJECTS_DIR/subjectname/mri/brain.mgz brain.img 2. Align brain.img with your functional data in spm (eg, func.img) ____________________________________________________________________________ Irene Geng Institute of Cognitive Neuroscience East China Normal University

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Re: [Freesurfer] Freesurfer pipeline for infant
by Lilla Zollei 17 Jul '17

17 Jul '17

Hi Gianluca, For your younger ages, this is the wiki that I would check: https://surfer.nmr.mgh.harvard.edu/fswiki/ChildBrainManualEdits We will look into the stats file. Best, Lilla On Tue, 11 Jul 2017, Gianluca Sforza wrote: > Hi Lilla,is there a range of age I should possibly take more care of with the FS outputs? > Should I refer to the advices on this page http://freesurfer.net/fswiki/FsTutorial/TroubleshootingData > > I take the opportunity to report a small issue in the format of the stat files rh.aparc.stats & lh.aparc.stats > While parsing those files, I found that a comma is missing after the field `CortexVol’ on the Measure Cortex row. > Please double check it; I am using last ver. 6 of FS. > > > sincerely > gianluca >

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Pediatric Atlas/Template
by Jessica Reynolds 17 Jul '17

17 Jul '17

I am wondering whether there are still plans to implement a pediatric atlas/template? I’m working with children aged 3-6 years. Thanks in advance, Jess.

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vertex-wise contra-lateral mapping on an ico surface
by Burke Rosen 14 Jul '17

14 Jul '17

Hello, I've created single subject surfaces sampled in ico7 space with make_average_subject --ico with a single input subject. Because of the ico7 sampling, both hemispheres have the same number of vertices. I am interested in the index-to-index mapping between equivalent contra-lateral vertices. How do I compute this mapping? Thank you, -Burke Rosen

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mri_concat to perform average cortical thickness & pial surface
by Dev vasu 14 Jul '17

14 Jul '17

Dear all, I have 115 subjects , and I would like to perform average cortical thickness ,pial surface . I have used mri_concat for this and i am getting dimension mismatch *" mri_concat k***/surf/lh.thickness --mean --o /media/vasudev/vkirsch4/Data_Driven/Thickness_Pial/lh_thickness/lh.thickness.fsaverage.mean.mgh ninputs = 115Checking inputsERROR: dimension mismatch between k100/surf/lh.thickness and k102/surf/lh.thickness "* I have checked the dimensions of the subjects and following is the output , it seems there is a problem with dimensions of all the thickness files, could some one please let me know how i could perform group average thickness in this case ? " mri_info k102/surf/lh.thickness Volume information for k102/surf/lh.thickness type: curv dimensions: 109303 x 1 x 1 voxel sizes: 1.0000, 1.0000, 1.0000 type: FLOAT (3) fov: 109303.000 dof: 0 xstart: -54651.5, xend: 54651.5 ystart: -0.5, yend: 0.5 zstart: -0.5, zend: 0.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform not present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.0000 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 0.0000 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 0.0000 Orientation : ??? Primary Slice Direction: unknown voxel to ras transform: -1.0000 0.0000 0.0000 54651.5000 0.0000 0.0000 1.0000 -0.5000 0.0000 -1.0000 0.0000 0.5000 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: -1.0000 0.0000 0.0000 54651.5000 -0.0000 -0.0000 -1.0000 0.5000 -0.0000 1.0000 -0.0000 0.5000 0.0000 0.0000 0.0000 1.0000 " mri_info k100/surf/lh.thickness Volume information for k100/surf/lh.thickness type: curv dimensions: 116434 x 1 x 1 voxel sizes: 1.0000, 1.0000, 1.0000 type: FLOAT (3) fov: 116434.000 dof: 0 xstart: -58217.0, xend: 58217.0 ystart: -0.5, yend: 0.5 zstart: -0.5, zend: 0.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform not present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.0000 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 0.0000 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 0.0000 Orientation : ??? Primary Slice Direction: unknown voxel to ras transform: -1.0000 0.0000 0.0000 58217.0000 0.0000 0.0000 1.0000 -0.5000 0.0000 -1.0000 0.0000 0.5000 0.0000 0.0000 0.0000 1.0000 " Thanks, Vasudev

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Re: [Freesurfer] Help for dmri_pathstats error
by Yuwen Hung 14 Jul '17

14 Jul '17

Dear DTI Experts: I wonder if there is anyone that might know a direction to look into this error? I just need to know what program generates this "path.map.txt" for the tracula script dmri_pathstats to run through. dmri_pathstats --intrc START_610/dpath/lh.cst_AS_avg33_mni_bbr --dtbase START_610/dmri/dtifit --path lh.cst --subj START_610 --out START_610/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.overall.txt --outvox START_610/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.byvoxel.txt --debug cwd /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610 cmdline dmri_pathstats --intrc START_610/dpath/lh.cst_AS_avg33_mni_bbr --dtbase START_610/dmri/dtifit --path lh.cst --subj START_610 --out START_610/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.overall.txt --outvox START_610/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.byvoxel.txt --debug sysname Linux hostname node031 machine x86_64 user yuwenh Input tracula directory: /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610/START_610/dpath/lh.cst_AS_avg33_mni_bbr Input DTI fit base: /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610/START_610/dmri/dtifit Pathway name: lh.cst Subject name: START_610 Output file for overall measures: /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610/START_610/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.overall.txt Output file for voxel-by-voxel measures: /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610/START_610/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.byvoxel.txt Lower threshold for probability: 0.200000 Computing statistics on /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610/START_610/dpath/lh.cst_AS_avg33_mni_bbr... ERROR: Could not open /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610/START_610/dpath/lh.cst_AS_avg33_mni_bbr/path.map.txt for reading Any thought would be greatly appreciated. Thank you - Yuwen

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Re: [Freesurfer] ERROR: dimension mismatch between input volume and seg - VolumeROICorticalThickness
by M Janani 14 Jul '17

14 Jul '17

Hi Douglas Greve<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from…>, Thanks for your support. I tried with the --reshape-factor 6. But it didn't work for me. The segmentation was created using the below mentioned data 1. SPM standard ROI 2. .dat file generated using the T1.nii(available in SPM8 template) and fsaverage. Please help us to proceed further. Regards, Janani ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- How did you create the segmentation? You can change the shape of the seg with mri_surf2surf --reshape 6 --s fsaverage --hemi lh --sval seg.mgh --tval seg.reshape.mgh On 7/7/17 10:15 AM, M Janani wrote: Hi Team, I'm attempting to extract cortical thickness values for a region-of-interest (ROI) defined in volume spacesubject for PiB MRI. I got the below mentioned error while computing the stats value cwd cmdline mri_segstats --seg freesurfer/subjects/fsaverage/surf/lh.fsaverage.CBLROI.mgh --in lh.thickness.fsaverage.mgh --sum segstats-CBLROI.txt sysname Linux hostname teslak80 machine x86_64 user lakshman UseRobust 0 Loading /freesurfer/subjects/fsaverage/surf/lh.fsaverage.CBLROI.mgh Loading lh.thickness.fsaverage.mgh ERROR: dimension mismatch between input volume and seg input 27307 1 6 seg 23406 1 7 I tried with the solution provided in the below mail, but it didn't work for me https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-January/027405.…<https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-January/027405.h…> <https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-January/027405.h…> Any help would be really helpful. Regards, Janani ::DISCLAIMER:: ---------------------------------------------------------------------------------------------------------------------------------------------------- The contents of this e-mail and any attachment(s) are confidential and intended for the named recipient(s) only. E-mail transmission is not guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or may contain viruses in transmission. The e mail and its contents (with or without referred errors) shall therefore not attach any liability on the originator or HCL or its affiliates. Views or opinions, if any, presented in this email are solely those of the author and may not necessarily reflect the views or opinions of HCL or its affiliates. Any form of reproduction, dissemination, copying, disclosure, modification, distribution and / or publication of this message without the prior written consent of authorized representative of HCL is strictly prohibited. If you have received this email in error please delete it and notify the sender immediately. Before opening any email and/or attachments, please check them for viruses and other defects. ---------------------------------------------------------------------------------------------------------------------------------------------------- _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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Switch FreeSurfer Desikan-Killiany atlas to Civet
by 沙志强 14 Jul '17

14 Jul '17

Hello FreeSurfer Developers, I am attempting to switch the Desikan-Killiany atlas of FreeSurfer to Civet. But I have no idea to solve the problem. Would you like to give me some suggestions or some detailed steps to help me accomplish the tasks ? Best wishes, Zhiqiang Sha

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problems with recon-all in 6.0
by Lars M. Rimol 14 Jul '17

14 Jul '17

Hi, I'm trying to run recon-all in FreeSurfer 6.0 but I keep getting error messages and some strange behavior: ls 01001/0/2/ 100.dcm 106.dcm 111.dcm 117.dcm 122.dcm 128.dcm 133.dcm 139.dcm 144.dcm 14.dcm 155.dcm 160.dcm 166.dcm 171.dcm 17.dcm 22.dcm 28.dcm 33.dcm 39.dcm 44.dcm 4.dcm 55.dcm 60.dcm 66.dcm 71.dcm 77.dcm 82.dcm 88.dcm 93.dcm 99.dcm 101.dcm 107.dcm 112.dcm 118.dcm 123.dcm 129.dcm 134.dcm 13.dcm 145.dcm 150.dcm 156.dcm 161.dcm 167.dcm 172.dcm 18.dcm 23.dcm 29.dcm 34.dcm 3.dcm 45.dcm 50.dcm 56.dcm 61.dcm 67.dcm 72.dcm 78.dcm 83.dcm 89.dcm 94.dcm 9.dcm 102.dcm 108.dcm 113.dcm 119.dcm 124.dcm 12.dcm 135.dcm 140.dcm 146.dcm 151.dcm 157.dcm 162.dcm 168.dcm 173.dcm 19.dcm 24.dcm 2.dcm 35.dcm 40.dcm 46.dcm 51.dcm 57.dcm 62.dcm 68.dcm 73.dcm 79.dcm 84.dcm 8.dcm 95.dcm 103.dcm 109.dcm 114.dcm 11.dcm 125.dcm 130.dcm 136.dcm 141.dcm 147.dcm 152.dcm 158.dcm 163.dcm 169.dcm 174.dcm 1.dcm 25.dcm 30.dcm 36.dcm 41.dcm 47.dcm 52.dcm 58.dcm 63.dcm 69.dcm 74.dcm 7.dcm 85.dcm 90.dcm 96.dcm 104.dcm 10.dcm 115.dcm 120.dcm 126.dcm 131.dcm 137.dcm 142.dcm 148.dcm 153.dcm 159.dcm 164.dcm 16.dcm 175.dcm 20.dcm 26.dcm 31.dcm 37.dcm 42.dcm 48.dcm 53.dcm 59.dcm 64.dcm 6.dcm 75.dcm 80.dcm 86.dcm 91.dcm 97.dcm 105.dcm 110.dcm 116.dcm 121.dcm 127.dcm 132.dcm 138.dcm 143.dcm 149.dcm 154.dcm 15.dcm 165.dcm 170.dcm 176.dcm 21.dcm 27.dcm 32.dcm 38.dcm 43.dcm 49.dcm 54.dcm 5.dcm 65.dcm 70.dcm 76.dcm 81.dcm 87.dcm 92.dcm 98.dcm recon-all -subject 1001_c1 -i 01001/0/2/1.dcm -all ................................ writing to /work/projects/nn9208k/tbi/morfometri_test/�1001_c1/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor fr. 14. juli 10:04:21 +0200 2017 ERROR: no run data found in /work/projects/nn9208k/tbi/morfometri_test/�1001_c1/mri. Make sure to have a volume called 001.mgz in /work/projects/nn9208k/tbi/morfometri_test/�1001_c1/mri/orig. If you have a second run of data call it 002.mgz, etc. See also: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion Linux compute-16-36.local 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s �1001_c1 exited with ERRORS at fr. 14. juli 10:04:21 +0200 2017 Not sure why it crashes, and why does it add "?" to the subject name? Thank you! sincerely yours, Lars M. Rimol, PhD Senior researcher, Norwegian Advisory Unit for functional MRI Department of Radiology, St. Olav's University hospital, 7006 Trondheim, Norway

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Mid point on Freeview
by Trisanna Sprung-Much 14 Jul '17

14 Jul '17

Hi there I have a question concerning viewing a surface in Freeview (FS 6.0): *What does the "mid point" variable refer to?* I can change it and it seems to change the shading within the sulci when I am looking at a white matter surface. Many thanks Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology

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