Freesurfer

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30132 discussions

Warping fsaverage maps to MNI152 volume
by Alon Baram 03 Dec '18

03 Dec '18

External Email - Use Caution Hello, I have a significance map I obtained through some analysis I did in Matlab. It's currently in fsaverage space. I want to move it to MNI152 space to compare with other results. From exploring the archives, it seems there are two ways of doing this, and I'm not sure which is better - any advice or correction would be appreciated. *Method 1*: First move to fsaverage volume, then us volumetc registraion to move to MNI152: 1. mri_surf2vol --surfval sigMap.mgh --identity fsaverage --template ./fsaverage/mri/T1.mgz --hemi rh --o sigMap.fsspace.mgz 2. mri_vol2vol --inv --targ sigMap.fsspace.mgz --mov /$FSL_DIR/data/standard/MNI152_T1_2mm.nii.gz --o sigMap_MNI.nii --interp nearest --reg fsaverage/mri/transforms/reg.mni152.2mm.dat *Method 2*: Run recon-all on the MNI152 T1 image. Use mri_surf2surf to map to move sigMap to the MNI152 surface. Then use mri_surf2vol with the --identity flag to move from MIN152 surface to volume. I ran method 1 and it looks OK though in some place it seems the out put doesn't follow white matter super nicely (though generally quite good). See attached image. I haven't ran method 2 yet. Thanks very much! Alon [image: image.png]

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Surface displacement
by 1013364183 03 Dec '18

03 Dec '18

External Email - Use Caution Dear FS, We want to calculate the displacement of different surfaces, what should we do? yours yujunjie

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Recon-all - mghRead could not read rawavg.mgz
by Diamond, Bram Ryder 03 Dec '18

03 Dec '18

Hi Batuhan, Can you please upload the BE2 subject data using our ftp file exchange and let me know the exact command and terminal output when you ran mri_convert? Info on our ftp file exchange: https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange Thanks, Bram Bram R. Diamond, BSc Research Technician II Laboratory for Computational Neuroimaging Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street Charlestown, MA 02129 (p): 617-726-6598

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Problem in Installing FreeSurfer on Mint19
by Maedeh Khalilian 03 Dec '18

03 Dec '18

External Email - Use Caution Dear experts, Thank u very much for all the help so far I have mint19 on my system and I have installed FreeSurfer on it. when I run a command like "mri_convert" it is ok. But when I run "recon-all" and some other commands, I see the error below : bash: /usr/local/freesurfer/bin/recon-all: /bin/tcsh: bad interpreter: No such file or directory by the way my default setup file is .bashrc. I really dunno what the problem is.I would be grateful if u could help me. Cheers, Maedeh

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trouble in manual editing of pial surface
by 박경일 02 Dec '18

02 Dec '18

External Email - Use Caution Dear experts I met a problem during manual editing. My version is 5.3. Following FS tutorial, freeview process was run, which loaded T1, brainmask and apar+aseg images. Then, I clicked 'voxel edit', checked 'recon-edit' and clicked a part of image which had been excluded from cortex (outside the pial line). I saved it and also re-ran the recon-all process. The saved images were as follows. I compared the values before and after editing, but, the values of total cortical volume, e-TIV and the volume of temporal pole and sup temporal gyrus, were not changed. I have no idea whether some steps were skipped and why my editing did not reflect the numerical values of this areas. Thanks always. Sincerely yours Kyung

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fcseedcor output
by Sara Jafakesh 02 Dec '18

02 Dec '18

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(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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