Freesurfer

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30076 discussions

(no subject)
by Sara Jafakesh 02 Dec '18

02 Dec '18

External Email - Use Caution Dear freesurfer experts, I want to calculate functional connectivity between two seeds with freesurfer-linux-centos6_x86_64_stable_pub-v6 . after using fcseed-config and fseed-sess commands, I use fcseedcor command. the command that I trying to run is as follow: fcseedcor -s subj1 -fsd rest -seed lh-seed2.dat -seed lh-seed3.dat -xreg wm.dat 5 -xreg vcsf.dat 5 -xreg mcprextreg 6 -hpf .001 -lpf .1 -nskip 6 -o seedcor2.dat but the output of fcseedcor is not .dat file ( the connectivity matrix for my result 2*2 matrix) as it has been explained in the fcssedcor help. the output is just the .log file named seedcor2.dat.log. although it has been done without error: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c $Id: fcseedcor,v 1.3 2015/12/10 22:51:29 zkaufman Exp $ Linux localhost.localdomain 2.6.32-642.el6.x86_64 #1 SMP Tue May 10 17:27:01 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux ------- matlab output -------------------- matlab: Command not found. Started at Sat Dec 1 18:05:11 IRST 2018 Ended at Sat Dec 1 18:05:12 IRST 2018 Fcseedcor-Run-Time-Sec 1 Fcseedcor-Run-Time-Hours 0.00 fcseedcor Done I really dont know what is the problem. I would be grateful if you could help me. best regards , sara

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mris_preproc paired diff outputs 0 values
by Sims, Sara A 02 Dec '18

02 Dec '18

External Email - Use Caution Hello, I am trying to do a paired difference analysis of two runs of probtrackx (I have already put them on the surface). The two conditions are “central” and “far” for each subject. I have already checked the individual subjects data and it does indeed have values. Here is a sample of my subject list: 100206.central 100206.far 100307.central 100307.far 100408.central 100408.far …etc. Here is my mris_preproc script: mris_preproc --target fsaverage --hemi lh --isp $in/FP/100206.central/lhsurf.mgh --isp $in/FP/100206.far/lhsurf.mgh --isp $in/FP/100307.central/lhsurf.mgh --isp $in/FP/100307.far/lhsurf.mgh --isp $in/FP/100408.central/lhsurf.mgh --isp $in/FP/100408.far/lhsurf.mgh … --out $out/preproc_FP_cf_lh/lh.paired-diff.FP_cf.mgh --f $sublist --paired-diff The output log shows no errors, the number of inputs equals the number in the subject list and it creates a file but it’s all zeros. I just have no idea as to why this would happen? Thanks, Sara Sims

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Triangular mesh sampling problem
by 1013364183 01 Dec '18

01 Dec '18

External Email - Use Caution Dear FS We now have high and low resolution images, we want to resample each triangular surface mesh generated from low-resolution data onto the corresponding triangular surface mesh generated from high-resolution data and vice versa as follows: For every vertex in a low-resolution surface mesh we found the closest point on the high-resolution surface mesh (which typically fell within a triangle face of the mesh), and defined a point at that location on the high-resolution surface mesh (subsequently referred to as “sparse” meshes).What should we do to use freesurfer to do the above? Thanks in advance yours yujunjie

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Exited with errors-No such file or directory
by Renew Andrade 01 Dec '18

01 Dec '18

External Email - Use Caution Dear FreeSurfer community: I have a subject from IXI dataset that ends with errors. I don´t know what to do to prevent it from happening and to have succesful run. Sincerely, Andrade.

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回复： ?????? ?????? Triangular mesh sampling problem
by 1013364183 01 Dec '18

01 Dec '18

External Email - Use Caution Dear Bruce， We are studying your paper "Advantages of cortical surface reconstruction using submillimeter 7 T MEMPRAGE". I don't know how the process in Figure 2 is implemented.I use mri_surf2surf to map lh.thickness from high resolution to low resolution, can this statement implement the operation of Figure 2(a)? yours yujunjie ------------------ 原始邮件 ------------------ 发件人: "Bruce Fischl"<fischl(a)nmr.mgh.harvard.edu>; 发送时间: 2018年12月1日(星期六) 晚上11:51 收件人: "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu>; 主题: Re: [Freesurfer] ?????? ?????? Triangular mesh sampling problem Hi yujunjie can you explain what your goal is? I'm not really sure that I understand. cheers Bruce On Sat, 1 Dec 2018, 1013364183 wrote: > > External Email - Use Caution > > Dear Bruce, > I use mri_surf2surf to map lh.thickness from high resolution to low resolution, and vice versa, > can this statement implement the operation of Figure 2(a)? > > yours yujunjie > > ------------------ ???????? ------------------ > ??????: "Bruce Fischl"<fischl(a)nmr.mgh.harvard.edu>; > ????????: 2018??11??29??(??????) ????11:46 > ??????: "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu>; > ????: Re: [Freesurfer] ?????? Triangular mesh sampling problem > > Hi yujunjie > > there is source code in mrishash.c and mrisurf.c for this kind of thing, > e.g. MHTfindClosestVertex. We don't have any complete code that will do > exactly what you want though, so you will have to poke around in the source > yourself I'm afraid. > > cheers > Bruce > > > On > Thu, 29 Nov 2018, 1013364183 wrote: > > > > > External Email - Use Caution > > > > Dear Bruce, > > I want to do the following, which source code should we use, and if so, can you send me a > > connection? > > We now have high and low resolution images, we want to resample each triangular surface mesh > > generated from low-resolution data onto the corresponding triangular surface mesh generated from > > high-resolution data and vice versa as follows: For every vertex in a low-resolution surface mesh > we > > found the closest point on the high-resolution surface mesh (which typically fell within a > triangle > > face of the mesh), and defined a point at that location on the high-resolution surface mesh > > (subsequently referred to as ??sparse?? meshes).What should we do to use freesurfer to do the > above? > > > > Thank you in advance > > look forward to your reply > > yours yujunjie > > ------------------ ???????? ------------------ > > ??????: "Bruce Fischl"<fischl(a)nmr.mgh.harvard.edu>; > > ????????: 2018??11??7??(??????) ????2:42 > > ??????: "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu>; > > ????: Re: [Freesurfer] Triangular mesh sampling problem > > > > Hi yujunjie > > > > we have code interenally that will do what you are asking, but no binary, > > sorry. You could download our source code and try to write your own, > > although it will be a bit of a project. > > > > cheers > > Bruce > > On Tue, 6 Nov 2018, 1013364183 > > wrote: > > > > > > > > External Email - Use Caution > > > > > > Dear FS > > > We now have high and low resolution images, we want to resample each triangular surface mesh > > > generated from low-resolution data onto the corresponding triangular surface mesh generated from > > > high-resolution data and vice versa as follows: For every vertex in a low-resolution surface > mesh > > we > > > found the closest point on the high-resolution surface mesh (which typically fell within a > > triangle > > > face of the mesh), and defined a point at that location on the high-resolution surface mesh > > > (subsequently referred to as ??sparse?? meshes).What should we do to use freesurfer to do the > > above? > > > > > > Thanks in advance > > > > > > yours yujunjie > > > > > > > > _______________________________________________ > > 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 > > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Segmentation of hippocampal subfields on FS v6 stable data?
by ts+ml＠rcmd.org 30 Nov '18

30 Nov '18

External Email - Use Caution Dear FreeSurfer experts, we would like to use the 'Segmentation of hippocampal subfields and nuclei of the amygdala' feature [1] that is available in the development version of FreeSurfer. However, we already pre-processed all subjects from the study using recon-all from FreeSurfer v6.0 stable. Can we apply the hippocampal subfields methods to the data pre-processed with the stable version, or should we run recon-all again using the dev version before we proceed? Thanks, Tim [1] https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAm… -- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

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Using the SUIT atlas
by Nillo, Ryan Michael R 30 Nov '18

30 Nov '18

External Email - Use Caution Hi FreeSurfer users, I am using the SUIT atlas (http://www.diedrichsenlab.org/imaging/suit.htm) to parcellate the cerebellum.To ensure there are no problems with registration, the SUIT pipeline requires that the origin of the input images are centered at the anterior commissure. Does FreeSurfer have any tools to set this origin from the command line? Thank you for your help, Ryan Nillo Research Associate I UCSF Department of Radiology and Biomedical Imaging

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Two problematic participants -- unable to run recon-all
by Rosalia Dacosta Aguayo 30 Nov '18

30 Nov '18

External Email - Use Caution Dear Free Surfer experts, I have run recon-all for all my participants and I am editing the brainmask and making control points. I have seen that for two participants, Free Surfer were not run. I run those two participant again and I saw that they were stuck in the vertex correction, more than 30.000. I do not know how to cope with this problem and I would greatly appreciate any help with this. Would it be possible to upload these two subjects so you can inspect them and tell me what is happening with them? Best wishes, Rosalia

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Correspondence between regions of Harvard-Oxford & DKT atlases
by Tudor Popescu 30 Nov '18

30 Nov '18

External Email - Use Caution Dear FreeSurfer experts, I have a network of interest described in terms of regions from the Harvard-Oxford atlas. I would next need to describe this network in terms of regions from the DKT (Desikan–Killiany–Tourville) atlas. I have not found hints of any correspondence table or script among the files in the dataverse.harvard.edu repository, nor in the Klein&Tourville 2012 paper. How is this sort of correspondence best established, in a way that also quantifies the transformation's accuracy (amount of overlap) for each parcelated region? Many thanks! Best wishes, Tudor

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Re: [Freesurfer] hippocampal subfield question
by Iglesias Gonzalez, Eugenio 29 Nov '18

29 Nov '18

External Email - Use Caution Dear Arkadiy, Technically you should do it after, but the changes will be tiny, so it’s probably fine to do it before (as long as you’re consistent across subjects). Cheers, /E -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London, and Research Affiliate Computer Science and Artificial Intelligence Laboratory (CSAIL) Massachusetts Institute of Technology http://www.jeiglesias.com From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Maksimovskiy, Arkadiy" <AMAKSIMOVSKIY(a)mclean.harvard.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Thursday, 29 November 2018 at 17:13 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] hippocampal subfield question Dear Experts, I was wondering if it is important to wait for the manual edits to be done on a dataset before running hippocampal subfield analyses. I believe that recon-all processing is sufficient, and edits can be done in parallel. But wanted to make sure that they will not affect the nuclei/subfield segmentation. Thank you for your help, Arkadiy -- Arkadiy L. Maksimovskiy, Ph.D. Postdoctoral Research Fellow McLean Imaging Center, McLean Hospital Department of Psychiatry, Harvard Medical School

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Freesurfer