Freesurfer December 2018

freesurfer@nmr.mgh.harvard.edu

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Re: [Freesurfer] Problem in Installing FreeSurfer on Mint19
by Maedeh Khalilian 04 Dec '18

04 Dec '18

External Email - Use Caution Dear Tim, I did it successfully, Thanks more... Best Maedeh

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Set annotation cluster color
by Ting Li 03 Dec '18

03 Dec '18

External Email - Use Caution Dear Freesurfer Expert, Can I change the color of loading from the annot file in Freeview? Thanks a lot! Best regards, Ting

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When no control points are needed...
by Rosalia Dacosta Aguayo 03 Dec '18

03 Dec '18

External Email - Use Caution Dear Bruce and Bram, After improving the pial surface for my participants, I have seen that some of them do not need control points. My question is: for those ones, should I run -autorecon2 and -autorecon3 or only -autorecon3. Hi Bruce and Bram, I will try to upload two problematic files. When I told you that I have been editing all my participants I was referring that some of them need more editing than others, and the ones that needed the less I just tried to improve the pial surface not too much, but now the results are better than before. Thank you in advance for your help. Yours sincerely, Rosalia

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mris_preproc paired diff outputs 0 values
by Sims, Sara A 03 Dec '18

03 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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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

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. I really dont know what is the problem. I would be grateful if you could help me. best regards , sara

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Freesurfer December 2018