Freesurfer January 2018

freesurfer@nmr.mgh.harvard.edu

124 participants
195 discussions

Errors while compiling FreeSurfer
by zuxfoucault Wong 11 Jan '18

11 Jan '18

Hi Freesurfers, Referring to https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-October/054329.…, I still got errors as following after compiling tcltktixblt via build_tcltktixblt.csh as the instruction in https://archive.fo/sNCX#selection-971.5-971.26 on ubuntu 16.04. /usr/bin/ld: IconLoaderTest.o: undefined reference to symbol 'Tcl_GetStringResult' /home/bc/software/environment/freesurfer_src/centos6-x86_64-packages/tcltktixblt/current/lib/ libtcl8.4.so: error adding symbols: DSO missing from command line collect2: error: ld returned 1 exit status Makefile:947: recipe for target 'IconLoaderTest' failed make[2]: *** [IconLoaderTest] Error 1 make[2]: Leaving directory '/home/bc/software/environment/freesurfer_src/freesurfer/vtkutils' Makefile:1256: recipe for target 'check-am' failed make[1]: *** [check-am] Error 2 make[1]: Leaving directory '/home/bc/software/environment/freesurfer_src/freesurfer/vtkutils' Makefile:1060: recipe for target 'check-recursive' failed make: *** [check-recursive] Error 1 Any suggestions? Thank you for your time! Best, Foucault

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Errors on compiling FreeSurfer
by zuxfoucault Wong 11 Jan '18

11 Jan '18

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Nonlinear CVS registration into average brain for coordinates
by Zhou, David Wei 10 Jan '18

10 Jan '18

Hi all, I have a data set of 14 subjects with intracranial (both cortical and subcortical) electrode implants, already recon'ed in Freesurfer, with an average brain + surface computed of these subjects. I would like to map each subject's electrode coordinates (a set of RAS points) into the average brain using a nonlinear transformation to account for individual deviations in surface topology. I'm trying to figure out the steps that must be taken to achieve this. With my average brain as a template, it seems like I would use mri_cvs_register to produce each subject warped onto the template. After generating those warps, how does one apply the same warp to a set of coordinates, for example to find out where my electrodes end up in the template brain? Which output file in .../cvs contains the data necessary to compute the coordinates in the template? I'd appreciate any instruction, thanks! David

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Re: [Freesurfer] hippocampal subfields in younger populations
by Iglesias Gonzalez, Eugenio 10 Jan '18

10 Jan '18

Dear Christian, They atlas is built using subfield segmentations on scans of older adult brains, but: 1. it’s also built with whole hippocampus segmentations of scans of subjects of a wider age range. 2. the deformation model should be able to account for large parts of the anatomical differences between subjects of different ages. > I would think this would be an issue for young kids that have markedly different brain volumes, but not for older kids and young adults that differ less dramatically from older adults. I agree with this statement. I hope this helps! /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Christian Krog Tamnes <c.k.tamnes(a)psykologi.uio.no> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Wednesday, 10 January 2018 at 11:33 To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] hippocampal subfields in younger populations Dear FreeSurfer and hippocampal subfield segmentation developers, I have noted that the FS6.0 hippocampal subfield segmentation procedure was developed using scans of older adult brains. Has the application of this method to kids, adolescents and/or young adults in any way been validated? Or do you have any thoughts regarding such use of the method? I would think this would be an issue for young kids that have markedly different brain volumes, but not for older kids and young adults that differ less dramatically from older adults. But I would greatly appreciate any input regarding this. Best regards, Christian

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reconstruction for very significant atrophy
by Rockers, Elijah D. 10 Jan '18

10 Jan '18

Hello, We have some images that reflect severe atrophy in some subjects, in which gray matter is virtually undetectable on the MRI in some regions. However, upon checking the segmentations visually, the white/pial surfaces are reflecting a significant cortical thickness in these areas. Is there perhaps any recon-all setting that might extend the white matter area out a little more aggressively than it does with the default settings? Thanks, - Eli Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S. News & World Report as the No. 1 hospital in Texas for patient care. Houston Methodist is nationally ranked in 8 specialties and is designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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Error using chol - FS-FAST selxavg3-sess
by stdp82＠virgilio.it 10 Jan '18

10 Jan '18

Running the "selxavg3-sess -s" command line in FS-FAST for seed-based functional connectivity analysis the following errors occurred: -------------------------- Temporally filtering Error using chol Matrix must be positive definite. Error in fast_selxavg3b (line 947) Wseg = inv(chol(toeplitz(acfrun))'); -------------------------- Thanks Stefano

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combining masks
by John Anderson 10 Jan '18

10 Jan '18

Dear Freesurfer experts, I want to create mask for the midbrain and the precentral gyrus. I used FSV6 to do the reconstruction. Then I used the flag -brainstem-structures in recon-all to segment the brain stem. How can I create one mask that include structures from wmpac.mgz and brainstemSsLabels.v10.mgz for instance I want to use mri_binarize to create one mask contains the following labels 1024 2024 3024 4024 from wmpar.mgz and 173 from brainstemSsLabels.v10.mgz Any advice you provide is highly appreciated. Thanks John

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surfstat maps using freesurfer outputs on skull-stripped data
by Duran, Tugce 10 Jan '18

10 Jan '18

Hi FS experts, I’m running SurfStat on my freesurfer skullstriped data (recon-all with –noskullstrip flag) and getting pecan shaped brain images as shown in the attached file. Do you know what freesurfer process (make_average_subject or glm or other) is causing this issue? Thanks! Tugce Duran, B.S. Research Technologist II [cid:image001.png@01D3861A.789F16C0]<https://medicine.iu.edu/departments/neurology/research/> Indiana Alzheimer Disease Center (iADC) Office: 317-278-7015 durant(a)iupui.edu<mailto:durant@iupui.edu>

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Using MRS voxel mask in freesurfer surface space
by Poortata Shirish Lalwani 10 Jan '18

10 Jan '18

Hi, We are obtaining MRS data and functional MRI data on two separate days for each subject. We use structural scan obtained during both these sessions for the freesurfer segmentation. MRS scan gives us a binary mask (nii format) in the same space as the structural image obtained during that particular scan. We want to use this binary mask during the surface based functional MRI analysis. I am not sure how to transform this binary mask to the surface space. Is there a way to do this? Best, Pia

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Is it poosible to redistribute a part of buckner_data for group work?
by Kiyotaka Nemoto 10 Jan '18

10 Jan '18

Dear FreeSurfer experts, We are planning to have a one-day neuroimaging workshop in Japan. One topic of the workshop is "FreeSurfer troubleshooting", in which we go through the online tutorial you provide ( https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData) in Japanese language. So we would like to use the buckner_data for the workshop. However, the problem is that some have difficulties downloading the data (It takes more than 2 days to download...) So I'm wondering if we can share the part of buckner_data with attendees for the workshop in a closed network (via a site with login requirements). I read through the FreeSurfer license, and README in the buckner_data, but it doesn't mention about redistributing the data. We would like to respect the license, so could you let me know if we can redistribute the part of buckner_data? Best regards, Kiyotaka -- Kiyotaka Nemoto, M.D., Ph.D. Associate Professor Department of Neuropsychiatry Division of Clinical Medicine, Faculty of Medicine University of Tsukuba 1-1-1Tennodai Tsukuba, Ibaraki 305-8575, Japan E-mail: kiyotaka(a)nemotos.net

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Freesurfer January 2018