Freesurfer December 2018

freesurfer@nmr.mgh.harvard.edu

109 participants
175 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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Freesurfer December 2018