[Freesurfer] myelination and freesurfer segmentation...

External Email - Use Caution Hi: Could you please tell me if Is there is a paper on myelination and segmentation? Sincerely, Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes,

[Freesurfer] GLM

External Email - Use Caution Hi experts, I am using FS 6.0 for analyzing the cortical thickness difference between 3 groups: patient1, patient2 and control. In DODS model, I need to creat 2 files, FSDG and mtx file. And we have 3 variables: age, gender and cortical

Re: [Freesurfer] automating custom color map

I think there is no option to set custom color code for overlay from command-line. I’ll add that option and let you know when it’s ready. Best, Ruopeng > On Nov 1, 2018, at 4:51 PM, Nillo, Ryan Michael R > wrote: > > External Email - Use Caution > Hi Freesurfer Users, > > I

Re: [Freesurfer] Tracula Question-How the threshold in final merged tracts are defined?

They are not random, they are 20% of the maximum value. If you want to generate stats at a different threshold, you can find the dmri_pathstats command line in trac-all.log and add the --pthr option (the default 20% would be --pthr .2). On Nov 1, 2018 9:01 PM, June Kang wrote: External

Re: [Freesurfer] Third party dependencies directory not found when building from source

External Email - Use Caution Thank you for information of build parameter at CentOS6 packages archive. I also remember. Ubuntu 18.04 Default gcc/g++/gfortran compiler is now version 7.3.0-27. Therefore, at the compilation of freesurfer in Ubuntu 18.04, I have installed

[Freesurfer] Tracula Question-How the threshold in final merged tracts are defined?

External Email - Use Caution In the visualization step of Tracula processing, freeview -tv merged_avg33_mni_bbr shows some tracts with very high threshold (i.e. 171), which make them look like the reconstruction-failed ones. The tracts failed to reconstruction usually show

[Freesurfer] aparcstats2table --parcs-from-file trouble

Hi, I extracted some volumes using mri_annotation2lable --> mri_aparc2aseg --> mri_segstats . Now I am trying to extract the summary table using aparcstats2table --parcs-from-file , but every time an error message pops up: ERROR: cannot read The stats files generated by the mri_segstats

[Freesurfer] ICV normalization (longitudinal pipeline)

External Email - Use Caution Hello FS experts, I am using longitudinal processing pipeline ( https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing) to calculate the cortical volume (CV) over a course of treatment (two conditions: pre condition and post condition). In

Re: [Freesurfer] Third party dependencies directory not found when building from source

External Email - Use Caution ​Hello Kazuhiro, With the old configure/automake tools, I used the following configure command on a CentOS7 machine (release 7.4.17-8) to build with the 5.0.35 Cuda distribution with the CentOS6 packages archive. (My cuda 5 distribution was

Re: [Freesurfer] Third party dependencies directory not found when building from source

External Email - Use Caution ​Hello Christian, To build Freesurfer e.g., on CentOS7, we use rev 4.8.5 of gcc, g++ and gfortran. You can tell cmake what compilers to use on the command line with CC=path/gcc CXX=path/g++ FC=path/gfortran If you need to specify the gfortran

Re: [Freesurfer] Export stats

External Email - Use Caution Hi Bruce, No, I would want to export all measures in a xls or sav file in order todo perform external analysis. The question is if it's possible to export jointly the mean area, volume...measures in an unique file. I have tried It using the

Re: [Freesurfer] Export stats

Hi Miguel the stats are already stored in a text file in the stats dir. Do you need something not in those files? cheers Bruce On Thu, 1 Nov 2018, Miguel Ángel Rivas Fernández wrote: External Email - Use Caution Hi Freesurfer devs, Is there any way to export all the

Re: [Freesurfer] Third party dependencies directory not found when building from source

External Email - Use Caution Hi, I'm Kazuhiro. I also met trouble for compilation of freesurfer stable6 repository under my Ubuntu 18.04 LTS machine. Even the binary package of freesurfer6.0(freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz) can work under Ubuntu 18.04,

[Freesurfer] Export stats

External Email - Use Caution Hi Freesurfer devs, Is there any way to export all the stats using an unique command? For example, export the mean area, volume, thickness, thicknessstd, meancurv values of the Desikian-Killiany atlas using an unique command or is only possible export