Freesurfer

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30132 discussions

Custom Annotation: 1st Annot Visible in TKSurfer but not Freeview
by Ursula Tooley 17 Jul '17

17 Jul '17

Hi FreeSurfer Experts, I’ve created a custom annotation file in MATLAB, using read_annotation.m and write_annotation.m, relabeling the Glasser parcellation regions. It seems to display as expected in tksurfer and tkmedit, but in freeview the first annotation is completely transparent (see images below), although if I hover my mouse over the area, it’s labeled with the correct struct_name. I’ve changed the alpha value in the annotation file and see no difference in freeview, and also given some previous listserv posts tried changing the RGB values for that first annotation in colortable.table. View in tksurfer: tksurfer fsaverage lh inflated -annotation my_annotation.annot View in freeview: freeview $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=my_annotation.annot Any help would be greatly appreciated. I’m running FS 6.0, Freeview V2, this occurs both locally on my OSX El Capitan and on an HPC running Linux Centos. Thanks in advance, Ursula --- Ursula Tooley Ph.D. Student Neuroscience Graduate Group University of Pennsylvania utooley(a)gmail.com 202.413.5627

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Re: [Freesurfer] FS Version 6 Long Processing
by Allison Rainford 17 Jul '17

17 Jul '17

Hi FreeSurfer Team, My lab has recently begun editing longitudinal data in version 6 and have found that we cannot use the same flags for -autorecon2 as we did when running longs in version 5.1. Typically, after making any necessary edits to a long, we run -autorecon2-pial -autorecon3. This flag hasn't been successful in version 6, producing an error message that the flag is unrecognized. Because we still only require some brainmask edits on the longs, we would like to know how we can continue to run these to process only pial. All help is greatly appreciated! Allison

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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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