Re: [Freesurfer] How to automate recon-all command for multiple subjects

External Email - Use Caution Hi The following code worked. for asubject in /home/vivek/Downloads/freesurfer/subjects/*.nii; do recon-all -s ${asubject%.nii} -i $asubject -all -qcache; done Thank you. On Tue, Nov 20, 2018 at 12:19 PM Vivek Sharma wrote: > I have a folder, lets n

[Freesurfer] Combining voxel-wise and vertex-wise data

External Email - Use Caution Hello Freesurfer Developers, I have a general question about how to analyse a certain combination of data. I have an independent variable that contains voxel-wise data and I have a dependent variable that contains vertex-wise cortical thickness value

Re: [Freesurfer] Bonferroni correction of 2spaces or 3spaces

External Email - Use Caution Dear Douglas, When doing --3spaces, is there a default subcortical mask in MNI space provided by freesurfer? Where is it stored? Thanks, Chao-Gan On Tue, Nov 20, 2018 at 10:12 AM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > > > On 11/

Re: [Freesurfer] mri_glmfit-sim MRISread(?????): could not open file

External Email - Use Caution Thanks Douglas, I've attached here the output from mri_glmfit-sim --glmdir lh.5.lgi_MAN_new.glmdir --cache 1.3 pos --cwp 0.05 --2spaces --debug Could you clarify how to use permutation to correct for MC for LGI? (as in what to enter for command line

Re: [Freesurfer] How to automate recon-all command for multiple subjects

oh, that was from your example. -i should be the full path to the input volume *or* one file in the correct dicom series. -s is something you choose to uniquely identify that subject's recon-all outputs cheers Bruce On Tue, 20 Nov 2018, Vivek Sharma wrote: External Email - Use C

Re: [Freesurfer] How to automate recon-all command for multiple subjects

in csh it would be something like setenv SUBJECTS_DIR foreach fname ($dir/*.nii) set fonly=${f:t} set fnoext=${f:r} recon-all -i $fname -s $fnoext -all end On Tue, 20 Nov 2018, Vivek Sharma wrote: External Email - Use Caution I have a folder, lets name x

[Freesurfer] Conversion of surface files to nibabel-readable files

External Email - Use Caution Dear FreeSurfer developers, I am trying to segment the cortex of my subjects into multiple layers and am trying several approaches. I have tried the command "mris_expand -thickness lh.white 0.5 lh.graymid" and it works perfectly. I am also interested

Re: [Freesurfer] Bonferroni correction of 2spaces or 3spaces

The masking is not done as part of the correction for mult comp but when you run mri_glmfit. When you run it on a volume, you have to specify the mask, so the mask depends upon your application. For fsfast, the mask in $FREESURFER_HOME/subjects/fsaverage/mri.2mm is used. On 11/20/18 4:57 AM, YA

Re: [Freesurfer] mri_glmfit-sim MRISread(?????): could not open file

can you verify that /home/cper2/BeneMin/Freesurfer/fsaverage/surf/lh.white exists and that you have read permission to it? Eg, can you load it with freeview -f /home/cper2/BeneMin/Freesurfer/fsaverage/surf/lh.white On 11/20/18 8:25 AM, C.P.E. Rollins wrote: External Email - Use Caution

Re: [Freesurfer] Recon-all - mghRead could not read rawavg.mgz

wow, I have no idea. Can you send us the .nii file and we will try? What machine is it failing on and does it print any error messages during conversion? Can you send us the full command line and terminal output of the mri_convert command that fails? cheers Bruce On Tue, 20 Nov 2018, Batuhan E

Re: [Freesurfer] Conversion of surface files to nibabel-readable files

Hi Inês nibabel should be able to read freesurfer images directly (thanks to Satra! I think): http://nipy.org/nibabel/reference/nibabel.freesurfer.html cheers Bruce On Tue, 20 Nov 2018, Borges Pereira Ines Isabel wrote: External Email - Use Caution Dear FreeSurfer deve

Re: [Freesurfer] Conversion of surface files to nibabel-readable files

External Email - Use Caution As you said, you can load FreeSurfer data (both the surface files and volume data) with the respective nibabel functions, i.e., read_geometry and read_morph_data. The ?h.pial and ?h.white files are surface meshes, so read_geometry would apply. I'm n

Re: [Freesurfer] Conversion of surface files to nibabel-readable files

Yes, I agree. Going to the volume irreversibly reduces the resolution and would have to be very highres to have a hope of representing more than two compartments. cheers Bruce On Tue, 20 Nov 2018, ts...@rcmd.org wrote: External Email - Use Caution As you said, you can load FreeSurfe

[Freesurfer] aseg.stats calculations

External Email - Use Caution Hello, I had a question regarding the aseg.stats and was hoping to get some help. 1. How is the TotalGray calculated? On the wiki page it mentioned that it is the sum of lhCortex + rhCortex + SubCortGray + CerebellumGM. I tried calculating th

Re: [Freesurfer] aseg.stats calculations

On 11/20/18 1:37 PM, Song, Da-Yea wrote: External Email - Use Caution Hello, I had a question regarding the aseg.stats and was hoping to get some help. 1. How is the TotalGray calculated? On the wiki page it mentioned that it is the sum of lhCortex + rhCortex + SubCortGray + Ce

Re: [Freesurfer] aseg.stats calculations {Disarmed}

External Email - Use Caution Thank you for pointing that out! I took another look and was able to get the following; TotalGray (from the aseg.stats) = 751765.612392 298534.487540 (lhCortex) + 287682.124852 (rhCortex) + 58860.00 (SubCortGray) + 52358.1 (L_cerebellum-cortex)

[Freesurfer] License issue

External Email - Use Caution Hello Freesurfers, Can anyone help with a licensing issue I have? I downloaded Freesurfer the other day with a brand new license and got the following message: “ERROR: Invalid FreeSurfer license key was found in license file”. I tried getting a new

Re: [Freesurfer] License issue

did you put it in $FREESURFER_HOME/.license ? Is it world-readable? On 11/20/18 2:38 PM, Sarah Haigh wrote: > External Email - Use Caution > > Hello Freesurfers, > > Can anyone help with a licensing issue I have? I downloaded Freesurfer the > other day with a brand new license and got th

[Freesurfer] CerebralWhiteMatterVol

External Email - Use Caution Hello, Does the CerebralWhiteMatterVol (from the aseg.stats) include the cerebellum? Thank you so much in advance for your help! Best, Da-yea -- Disclaimer: The materials in this

Re: [Freesurfer] License issue

External Email - Use Caution Yes, I set the FreeSurfer home environment and added the license file to that folder. It is Word readable. Sarah > On Nov 20, 2018, at 12:03 PM, Greve, Douglas N.,Ph.D. > wrote: > > did you put it in $FREESURFER_HOME/.license ? Is it world-readabl

Re: [Freesurfer] License issue

External Email - Use Caution Hello Sarah, If you can bring up a terminal with your freesurfer environment set, then please try the following commands, i.e., $ cd $FREESURFER_HOME $ cat $FS_LICENSE

Without posting the contents of your license, I think the

Re: [Freesurfer] CerebralWhiteMatterVol

No, it does not. On 11/20/18 3:54 PM, Song, Da-Yea wrote: External Email - Use Caution Hello, Does the CerebralWhiteMatterVol (from the aseg.stats) include the cerebellum? Thank you so much in advance for your help! Best, Da-yea Disclaimer: The materi

Re: [Freesurfer] mri_glmfit-sim MRISread(?????): could not open file

External Email - Use Caution Hi Douglas, Thanks for the response. Yes, I confirm that the file /home/cper2/BeneMin/Freesurfer/fsaverage/surf/lh.white exists and I can view it in freeview. Any other possible errors? Also, would you mind elaborating how to use permutation to correc

Re: [Freesurfer] License issue

External Email - Use Caution Hi, I ran the code and the license appeared, but no email address or numbers. These were the first few lines: FreeSurfer Software License Agreement ("Agreement") Version 1.0 (February 2011) Is this wrong? The rwx settings look cor

[Freesurfer] Surface based paired t test

External Email - Use Caution Dear Freesurfer experts, I would like to run surface based paired t test of PET data on surface. For every subject I have visit pre treatment and post treatment. I tried to follow the instructions here https://surfer.nmr.mgh.harvard.edu/fswiki/Paired

Re: [Freesurfer] License issue

External Email - Use Caution Hi Sarah, I would just move that file aside (rename it to something that is not license.txt) and follow the instructions on the wiki to generate another license.txt file.  Then you could check it again with the previous commands. https://surfer.nmr.

Re: [Freesurfer] License issue {Disarmed}

External Email - Use Caution Thank you! This seemed to work. I got my email address and the numbers this time in the license. Not sure what happened there. Good check. Sarah On Nov 20, 2018, at 3:46 PM, fsbuild mailto:fsbu...@contbay.com>> wrote: External Email - Use

Re: [Freesurfer] Bonferroni correction of 2spaces or 3spaces

External Email - Use Caution Thanks, Douglas! I found subcort.mask.mgz there, that should work (subcortical mask in MNI space)! Best, Chao-Gan On Wed, Nov 21, 2018 at 12:45 AM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > The masking is not done as part of the cor

[Freesurfer] differences between 'lh_G_front_middle_thickness' and 'lh_S_front_middle_thickness'

External Email - Use Caution Hi FS experts and users I found two middle frontal cortex in thickness, with different prefix. So what is the difference? Another question: Can I get the thickness of hippocampus and amygdala? Thanks. Rujing 2018-11-21 charujing123 _

[Freesurfer] nu_correct ERROR (FreeSurfer v6)

External Email - Use Caution Dear FreeSurfer Developers, I have the most recent version of FreeSurfer installed on a MacOS Mojave (10.14) and as I was running recon-all, I received the following error message: "Assertion failed at line 742 in file templates/CachedArray.cc nu_esti

[Freesurfer] 'lh_G_Ins_lg&S_cent_ins_volume' and 'lh_G_insular_short_volume'

External Email - Use Caution Hi, what is difference between 'lh_G_Ins_lg&S_cent_ins_volume' and 'lh_G_insular_short_volume'. Are these both insula? Thanks. Rujing 2018-11-21 charujing123 ___ Freesurfer mailing list Freesurfer@nmr.mgh.