Re: [Freesurfer] arguments to use after pial edits

External Email - Use Caution Thanks Matt! Should I also add the -autorecon3 flag, or does that get performed automatically if I put in "autorecon2"? Best, Darko > Message: 4 > Date: Mon, 30 Nov 2020 19:16:06 + > From: "Glasser, Matthew" > Subject: Re: [Freesurfer] arguments

[Freesurfer] arguments to use after pial edits {Disarmed}

External Email - Use Caution Dear Freesurfer experts, I am using Human Connectone Project pipelines to calculate cortical myelin levels. These pipelines use Freesurfer 6. Since certain subjects' brain surfaces had some chunks and spikes sticking out, I edited the brainmask.mgz

Re: [Freesurfer] Question about the input for longitudinal processing pipeline

External Email - Use Caution Thanks a lot for the reply and the suggestions, Douglas! These scans are at 3T. Best, Darko > -- > > Message: 4 > Date: Wed, 20 Nov 2019 22:45:18 + > From: "Greve, Douglas N.,Ph.D." > Subject: Re: [Freesurfer] Question

Re: [Freesurfer] Question about the input for longitudinal processing pipeline

External Email - Use Caution Hi Douglas, thanks for your reply. Indeed, in this particular data set they don't all have contrast, which is unfortunate. But my question was also general, if we assume that they all have contrast, would it be OK to use those images as inputs in the

[Freesurfer] Question about the input for longitudinal processing pipeline

External Email - Use Caution Dear Freesurfer experts, I wanted to run the Freesurfer's longitudinal processing pipeline (described here https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing) on a series of MRI scans from a single patient. However, after looking at the

Re: [Freesurfer] unable to open freeview

H” to make sure that the brew error is no longer > present > > Andrew > > > > *From: *Darko Komnenić <komnen...@gmail.com> > *Date: *Thursday, April 19, 2018 at 1:08 PM > > *To: *"Hoopes, Andrew" <ahoo...@mgh.harvard.edu> > *Cc: *FS Help <freesurfer

Re: [Freesurfer] unable to open freeview

[Freesurfer] unable to open freeview > > > > An update, > > in the .bash_profile file, there is a line about linuxbrew. Do you > recommend that I remove it? Sending the file attached. > > Best, > > Darko > > > > On Thu, Apr 19, 2018 at 11:59 AM, Darko

Re: [Freesurfer] unable to open freeview

An update, in the .bash_profile file, there is a line about linuxbrew. Do you recommend that I remove it? Sending the file attached. Best, Darko On Thu, Apr 19, 2018 at 11:59 AM, Darko Komnenić <komnen...@gmail.com> wrote: > Hi Andrew, > sorry for the delay. Attached is the hidden

Re: [Freesurfer] unable to open freeview

hoo...@mgh.harvard.edu> wrote: > Are you using a bash shell? If you are, there should be a file located at > ~/.bashrc (it’s a hidden file in your home folder) > > Andrew > > > > > > *From: *Darko Komnenić <komnen...@gmail.com> > *Date: *Tuesday, April 17, 201

Re: [Freesurfer] unable to open freeview

unmatched errors with > freesurfer tools? I can try to help you solve this, but I’m not quite sure > I understand the initial problem. > > > > PS: At some point in your .bashrc is linuxbrew called? You don’t want that > “Linuxbrew directory detected…” error in your PATH vari

Re: [Freesurfer] unable to open freeview

sourcing the > TCL package. Can you send me your tcl_setup file in $FREESURFER_HOME/bin? > > > > It would also be helpful if you add another “echo $PATH” line right below > the “#!/bin/tcsh -ef” in the freeview script > > > > best > > Andrew > > > > *

Re: [Freesurfer] unable to open freeview

at 6:36 PM, Darko Komnenić <komnen...@gmail.com> wrote: > Hi Andrew, > thanks for getting back so quickly. > Here are the outputs: > “tcsh --version” gives a "tcsh 6.18.01 (Astron) 2012-02-14 > (x86_64-unknown-linux) options wide,nls,dl,al,kan,rh,nd,color,filec" >

Re: [Freesurfer] unable to open freeview

the > following line right before the call to “freeview.bin $argv”: > > > > echo $PATH > > > > and send the output over. > > > > best > > Andrew > > > > > > *From: *Darko Komnenić <komnen...@gmail.com> > *Date: *Tuesday, Apr

Re: [Freesurfer] unable to open freeview

gt; > > *From: *<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Darko > Komnenić <komnen...@gmail.com> > *Reply-To: *FS Help <freesurfer@nmr.mgh.harvard.edu> > *Date: *Tuesday, April 17, 2018 at 11:17 AM > *To: *FS Help <freesurfer@nmr.mgh.harvard.edu> >

[Freesurfer] unable to open freeview

Dear experts, I encountered a problem when trying to open freeview. I am using FreeSurfer v.5.3.0-HCP, and after sourcing it, I tried typing simply freeview in the terminal, as described in this link: http://freesurfer.net/fswiki/FreeviewGuide/FreeviewGeneralUsage/FreeviewQuickStart but the

Re: [Freesurfer] Freesurfer Digest, Vol 169, Issue 41

Hi Bruce, I attached the recon-all.log! Thanks in advance for taking a look! Darko Message: 3 Date: Sat, 31 Mar 2018 06:47:12 -0400 From: Bruce Fischl Subject: Re: [Freesurfer] mri_watershed Error: indices out of bounds To: Freesurfer support list

[Freesurfer] mri_watershed Error: indices out of bounds

Dear experts, while running recon-all on FreeSurfer 5.1.0 I encountered the following error: mri_watershed Error: indices out of bounds I searched the email archive and found this thread:

Re: [Freesurfer] defining input images in a for-loop in recon-all

Hi Bruce, thanks for the reply. I only have one acquisition per subject. I guess I can make a separate text file with a list of paths to dicoms and then somehow try to pair the path and the subject name in the recon-all command. > From: Bruce Fischl > Subject: Re:

[Freesurfer] defining input images in a for-loop in recon-all

Dear experts, I would like to run a for-loop in FreeSurfer 5.1. so that I can have multiple subjects analyzed over the holiday, without having to come to the lab and start each of them myself. I searched the previous emails in this list and know that I can make a file with a subject list, and then

[Freesurfer] A question about FS6 hippocampal subfield segmentation output file

Dear FreeSurfer experts, in the txt files [lr]h.hippoSfVolumes-T1.v10.txt we can see the volumes of individual hippocampal subfields - I was wondering what are the units in which volume is given? Millimeters cubic, voxels, or something else? Thanks in advance! Best, Darko

[Freesurfer] [error] no installation candidates for curl

Dear FreeSurfer experts, I am trying to perform hippocampal subfield segmentation with FreeSurfer 6. I followed the instructions found on this page: https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields which said that I first need to download Matlab Runtime. Which brought me to this