Re: [Freesurfer] Recon-all issue with decompressing in mri_convert step

There might be some issues with jpeg compressed dicom files in 7.2 and before. Can you try using 7.3 to do the conversion with mri_convert or dcmunpack (add -dcm2niix to either one to get the new, better code). On 9/5/2022 10:53 PM, Beatrice Everall wrote: External Email - Use Caution

[Freesurfer] Recon-all issue with decompressing in mri_convert step

External Email - Use Caution - Hi there :) - I am trying to run recon-all on MRI data; I have multiple sequences including T1 maps and MAGiC. I have tried to run recon-all on these sequences but get the same error each time: - - ERROR: 512, see /tmp/tmp.H88WWu.dcmdjpeg.out for more

Re: [Freesurfer] recon-all issue in vmPFC with high-res T1/T2 data {Disarmed}

External Email - Use Caution Yes, the lh.orig is changing, but not lh.white. (I responded to this on the 23rd, but the reply didn't show up in the archive and I'm not sure it went through, so I'm trying again.) Thanks, Ben On Wed, Dec 23, 2020 at 12:37 PM Greve, Douglas N.,Ph.D.

Re: [Freesurfer] recon-all issue in vmPFC with high-res T1/T2 data {Disarmed}

Is the lh.orig surface changing? On 12/17/2020 5:53 PM, Ben Deen wrote: External Email - Use Caution Hi all, I'm encountering an issue with surface reconstruction quality in ventromedial prefrontal cortex, using relatively high resolution (.8mm) T1- and T2-weighted input data to recon

[Freesurfer] recon-all issue in vmPFC with high-res T1/T2 data {Disarmed}

External Email - Use Caution Hi all, I'm encountering an issue with surface reconstruction quality in ventromedial prefrontal cortex, using relatively high resolution (.8mm) T1- and T2-weighted input data to recon-all. I'm using the following command, with Freesurfer 7.1.1 running

Re: [Freesurfer] FreeSurfer recon-all issue

: MIKHAEL Shadia Sent: 31 December 2017 11:18 To: 'freesurfer@nmr.mgh.harvard.edu' Subject: RE: FreeSurfer recon-all issue Dear Antonin, Thank you for your suggestions at https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2017-December/055319.html . I've tried both, but th

Re: [Freesurfer] FreeSurfer recon-all issue

freesurfer@nmr.mgh.harvard.edu' Subject: FreeSurfer recon-all issue Hello all, I'm having trouble with recon-all on a Linux server, I'm running into the following error for all of my subjects: . mris_curvature -w lh.white.preaparc total integrated curvature = 6.657*4pi (83

Re: [Freesurfer] FreeSurfer recon-all issue

Dear Shadia, There are 2 spots in recon-all where symbolic link is created. The first you can overcome by: find following line in your recon-all: set cmd2 = (ln -s $hemi.white.preaparc.$suffix $hemi.white.$suffix) and replace it by set cmd2 = (cp $hemi.white.preaparc.$suffix $hemi.white.$suffix

Re: [Freesurfer] recon-all issue {Disarmed}

regler for taushetsplikt Fra: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] På vegne av Taylor Hilton Sendt: 8. februar 2017 15:45 Til: Freesurfer support list Emne: Re: [Freesurfer] recon-all issue {Disarmed} Apologies, that was an old log, attaching the re

Re: [Freesurfer] recon-all issue {Disarmed}

This error suggests to me that you are mounting some external drive, or docker container, or some mix of file systems incompatible with symlinks? Try moving the subject to a local directory On 02/08/2017 10:41 AM, Taylor Hilton wrote: > This is the output: ln: failed to create symbolic link 'lh

Re: [Freesurfer] recon-all issue {Disarmed}

This is the output: ln: failed to create symbolic link 'lh.white.H': Operation not supported > On Feb 8, 2017, at 10:38 AM, Douglas N Greve > wrote: > > can you run the commands below and tell me what happens? > > cd /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10007/surf > ln -s lh.

Re: [Freesurfer] recon-all issue {Disarmed}

can you run the commands below and tell me what happens? cd /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10007/surf ln -s lh.white.preaparc.H lh.white.H On 02/08/2017 09:44 AM, Taylor Hilton wrote: > Apologies, that was an old log, attaching the relevant one here. > > > > >> On Feb 7, 2

Re: [Freesurfer] recon-all issue {Disarmed}

According to the log file, the error is that you need a new license: GNU libc version: 2.23 ERROR: Systems running GNU glibc version greater than 2.15 require a newly formatted license file (it's free). Please download a new one from the following page: http://surfer.nmr.mgh.harvard.edu/registrat

Re: [Freesurfer] recon-all issue {Disarmed}

Yes I’ll attach it here.  I’m using a linux server(Ubuntu). recon-all.log Description: Binary data On Feb 7, 2017, at 12:32 PM, Douglas Greve wrote: Can you send the full recon-all.log? What platform are you running on? On 2/7/17 11:19 AM, Tay

Re: [Freesurfer] recon-all issue

Can you send the full recon-all.log? What platform are you running on? On 2/7/17 11:19 AM, Taylor Hilton wrote: Hi all, Having trouble with an error running "recon-all -subjid ${i} -autorecon2” across all subjects. Below is where it has the error in recon-all.log. We also tried running th

[Freesurfer] recon-all issue

Hi all, Having trouble with an error running "recon-all -subjid ${i} -autorecon2” across all subjects. Below is where it has the error in recon-all.log. We also tried running the last command (“ln -s …”) manually and got the error “ln: failed to create symbolic link ‘lh.white.H’: Operation

Re: [Freesurfer] recon-all issue

souldnt be there, or am I mistaken? > > Thanks very much in advance > Susanne > > > Today's Topics: > > 1. Re: recon-all issue (Bruce Fischl) > > > ---------- > > Message: 1 > Date: Wed, 13 J

Re: [Freesurfer] recon-all issue

t: Re: [Freesurfer] recon-all issue To: Freesurfer support list Message-ID: Content-Type: text/plain; charset="utf-8" Hi Susanne can you include prior correspondance so we have some context for your emails. Certainly 2 vs. 1 and 3 will give different results since you have changed

Re: [Freesurfer] recon-all issue

Hi Susanne can you include prior correspondance so we have some context for your emails. Certainly 2 vs. 1 and 3 will give different results since you have changed the input file. I would think think 1 and 3 would be the same, but we need to know how you did the conversion. Look at the 001.mg

Re: [Freesurfer] recon-all issue

Hi Susanne can you just send us the recon-all command lines that are issued by your script? And tell us what is different? Bruce On Tue, 12 Jan 2016, Schell, Susanne wrote: Dear colleagues,   as I posted before, we are recently using the freesurfer recon-all command. Here are three diff

Re: [Freesurfer] recon-all issue

Dear colleagues, as I posted before, we are recently using the freesurfer recon-all command. Here are three different commands we used: 1)# Version 1: Import as DICOM #!/bin/sh -e # Segmentierung mit FreeSurfer. # Die Ergebnisse werden in dem Verzeichnis gespeichert, in dem sich # dieses Script

Re: [Freesurfer] recon-all issue

how different? Eg, what is the size of hippocampus in each? On 12/23/15 9:28 AM, Bruce Fischl wrote: Hi Susanne we will need the full command lines you used and screen output in order to help you cheers Bruce On Wed, 23 Dec 2015, Schell, Susanne wrote: Dear colleagues, We are recently

Re: [Freesurfer] recon-all issue

Hi Susanne we will need the full command lines you used and screen output in order to help you cheers Bruce On Wed, 23 Dec 2015, Schell, Susanne wrote: Dear colleagues,   We are recently using the freesurfer recon-all command   recon-all –s –I .nii.gz recon-all –s –all

Re: [Freesurfer] recon-all issue

Dear colleagues, We are recently using the freesurfer recon-all command recon-all -s -I .nii.gz recon-all -s -all where stands for the subject ID. I have been trying to execute this command with the different input files: 1) original dicom-files 2) nii-file where

Re: [Freesurfer] recon-all issue (CSF seg as gray matter)

Hi Alex that's pretty bad! You could start by specifying some expert options about the ranges of gray and white matter intensities to mri_segment and mris_make_surfaces. Hopefully someone will chime in with the syntax, as I don't remember it. You can also check the recon-all.log to see what ran

[Freesurfer] recon-all issue (CSF seg as gray matter)

Hi, after running recon-all on many datasets without any manual intervention, it looks like I finally have to. As you can see in : https://dl.dropboxusercontent.com/u/2140486/Screen%20Shot%202013-08-28%20at%2013.16.52.png the CSF is segmented as gray matter while white+gray matters are merged.

[Freesurfer] recon-all issue

First, I am a newcomer to the FreeSurfer community so bear with me. I have installed a snapshot of FreeSurfer for OSX: freesurfer-Darwin- tiger-full.dmg I seem to have everything working fine in terms of environment settings etc. I created a subject directory and populated it with some T1