[Freesurfer] FS_7_2_0_Ubuntu_18_04_06.ova.7z password

2022-08-12 Thread Anne-Claire Binter
External Email - Use Caution Hi, I would like to use the freesurfer image in a virtual machine. Can you send me the password for opening the archive? Best regards, Anne-Claire Binter -- Postdoctoral researcher ISGlobal Barcelona Institute for Global Health - Campus MAR Barcel

[Freesurfer] Algorithm of automatic range for heatmap in freeview

2022-08-12 Thread Urs Kleinholdermann
External Email - Use Caution Dear list, I'm using freeview to overlay Z values on the MNI Brain with the "heat" colormap. The maximum value of the colored range is smaller than the largest Z value and obviously is determined automatically when I check "Autoset Mid" and let the

[Freesurfer] running mri_glmfit with atlas

2022-08-12 Thread Hye Min Shin
External Email - Use Caution Hello experts, While going through GroupAnalysis tutorial for freesurfer ( https://secure-web.cisco.com/1vsiSpzodxBizvnBXlCu7-xP4XPwjzJ4w3O_H2Phnc0vsqMpZRz0rEKqiMW5Puygi_PzEgPwghoVAArMbdCwTTAjPfNMV3G8hIql8WKQ0Ny8pZEX2gqmZM6LwVFupm6M7RsvtHspD-NgRplh0jHl

[Freesurfer] SAMSEG

2022-08-12 Thread Alberto Del Cerro Leon
External Email - Use Caution Hello, I am reading the paper "A contrast-adaptive method for simultaneous whole-brain and lesion segmentation in multiple sclerosis" relative to SAMSEG method and I would like to ask you a question. Due to the use of a training set in the lesion shape

Re: [Freesurfer] SAMSEG

2022-08-12 Thread Koen Van Leemput
External Email - Use Caution Hi Alberto, As you already indicated, it's really a combination of an unsupervised clustering method with a supervised shape model, so the dichotomy between the two doesn't neatly apply. When I think about this type of method, I consider it an unsuperv

[Freesurfer] Shift in cortical parcellation, issues with previously suggested solution

2022-08-12 Thread Trolle, Carl
Ok. I'm trying to attach a copy of the output I get in the terminal-window. The commands I've been running for the mris_register and mris_ca_label are "mris_register -L subject/label/?h.central_sulcus.label FREESURFER_HOME/average/?h.destrieux.simple.2009-07-29.gcs S_central subject/surf/?h.sph

Re: [Freesurfer] SAMSEG

2022-08-12 Thread Alberto Del Cerro Leon
External Email - Use Caution Thanks for the explanation!! El vie, 12 ago 2022 a las 17:04, Koen Van Leemput () escribió: > External Email - Use Caution > > Hi Alberto, > > As you already indicated, it's really a combination of an unsupervised > clustering method with a su

Re: [Freesurfer] Tracula - Preproc

2022-08-12 Thread Alan Francis
External Email - Use Caution Hi Anastasia and King wei - I checked the directory /usr/local/freesurfer/7.2.0-1. It shows that FSL is part of that installation. Do you recommend a second installation of FSL separately? Thanks so much for your help and comments! Alan On Thu, Aug

[Freesurfer] Virtual Box Passcode

2022-08-12 Thread Watkins, Scott
External Email - Use Caution Good morning, Please send the Virtual Box passcode to unlock the .ova archive file. Thanks, Scott Watkins Systems Analyst Radiology - PACS IT School of Medicine University of Missouri Health (573) 884-9822 _

Re: [Freesurfer] Tracula - Preproc

2022-08-12 Thread Yendiki, Anastasia
The error message that you got says that the bet command isn't in your Unix path. You need to fix that, so that you don't get that error. If bet and all the other FSL executables are already installed somewhere on your computer, you need to add that directory to your Unix path. I'm not sure what

Re: [Freesurfer] Tracula - Preproc

2022-08-12 Thread King-Wai Chu
External Email - Use Caution Hi Alan, If you really have FSL installed inside Freesurfer, it is not the way to do it. If you type echo $FSLDIR does it return anything? If FSL is installed the way you said it is, echo $FSLDIR should give something like /usr/local/freesurfer/7.2.0-1

Re: [Freesurfer] Tracula - Preproc

2022-08-12 Thread Alan Francis
External Email - Use Caution Hi Anastasia and King_Wei : Thank you for your suggestions. I have fixed the bet issue by reinstalling FSL. But I have one more error: ERROR: must set ANTSPATH environment variable to use ANTs I tried setting set ANTSPATH = 0 but that did not work.

Re: [Freesurfer] Tracula - Preproc

2022-08-12 Thread Yendiki, Anastasia
If you want to use ANTs for registration, you have to have ANTs installed and set ANTSPATH to its location. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Alan Francis Sent: Friday, August 12, 2022 4:35 PM To: Freesurfer support list Subject: Re: [F

Re: [Freesurfer] Tracula - Preproc

2022-08-12 Thread King-Wai Chu
External Email - Use Caution Hi Alan, You need to install Advanced Normalization Tools(ANTS) https://secure-web.cisco.com/1xl8ADqLGMhYjn7TbMOsRonEy_R5C4feN8mMJ-Q7bddD3E_kk_PzT6LUVVJPXi70pbS8fDlYVtT5FZrovy4oO8F6esYTNDGGmBMZIcnfJjKjqysycppupQwOtlATRsVGkxuOe_hdaI5TbjfjkBv6w3Sy0DIhpR6

Re: [Freesurfer] Tracula - Preproc

2022-08-12 Thread Alan Francis
External Email - Use Caution Hi Anastasia : I installed ANTS and tried this set ANTSPATH = /home/afrancis/Imaging/ANTs but it did not work. Is there a different set path? Thanks, Alan On Fri, Aug 12, 2022 at 3:39 PM Yendiki, Anastasia wrote: > If you want to use ANTs for re

Re: [Freesurfer] Tracula - Preproc

2022-08-12 Thread King-Wai Chu
External Email - Use Caution For bash shell ANTSPATH=/home/afrancis/Imaging/ANTs For tcsh setenv ANTSPATH /home/afrancis/Imaging/ANTs On Fri, Aug 12, 2022 at 5:54 PM Alan Francis wrote: > External Email - Use Caution > > Hi Anastasia : > > I installed ANTS and tried thi

[Freesurfer] FreeSurfer 7Zip archive passcode

2022-08-12 Thread 王馨霈
External Email - Use Caution Hello, I would like to ask for the passcode for the VM file (FS_7_2_0_Ubuntu_18_04_06.ova.7z). Thank you in advance, Hsin Pei Wang ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nm