Re: [Freesurfer] Problem running recon-all

External Email - Use Caution If you use a shared drive that is formatted in a way that is not compatible with the linux (ext3, ext4) file system, e.g., a shared windows drive, then running the linux software is not expected to work. A Windows file system does not support soft

Re: [Freesurfer] Problem running recon-all

External Email - Use Caution I did not see that message, which is why I posted again. Sorry about that! I will try using the package installer. We're using the .tar.gz method because it is located on a shared drive, but maybe we'll just need to install it locally if that works.

Re: [Freesurfer] Problem running recon-all

External Email - Use Caution Did you try the instructions you were sent yesterday to run the actual installer and not use the tar file (which is not an installer) ? - R. I would try downloading and running the actual package installer,

Re: [Freesurfer] Problem running recon-all

External Email - Use Caution I also see this error which is sent to stderr: /usr/bin/time: cannot run recon-all: No such file or directory It seems to be something related to the time command (or bash keyword) Is your Freesurfer Environment sourced correctly? Here is the wiki

Re: [Freesurfer] Problem running recon-all

, April 23, 2024 9:21 AM To: freesurfer Subject: [Freesurfer] Problem running recon-all External Email - Use Caution I recently installed freesurfer 7.4.1 on a Debian 12 system (using the Ubuntu 22 .tar.gz). When running recon-all, I get the following error: -bash: /opt/freesurfer

Re: [Freesurfer] Problem running recon-all

: [Freesurfer] Problem running recon-all External Email - Use Caution I recently installed freesurfer 7.4.1 on a Debian 12 system (using the Ubuntu 22 .tar.gz). When running recon-all, I get the following error: -bash: /opt/freesurfer/freesurfer-7.4.1/bin/recon-all: cannot execute: required

[Freesurfer] Problem running recon-all

External Email - Use Caution I recently installed freesurfer 7.4.1 on a Debian 12 system (using the Ubuntu 22 .tar.gz). When running recon-all, I get the following error: -bash: /opt/freesurfer/freesurfer-7.4.1/bin/recon-all: cannot execute: required file not found Paths are all

Re: [Freesurfer] Problem with recon-all --> nii.gz file not found

: Freitag, 13. Januar 2023 16:27:17 An: Freesurfer support list Betreff: Re: [Freesurfer] Problem with recon-all --> nii.gz file not found External Email - Use Caution -i needs to be followed by the input volume Move /home/lirh717c/Desktop/V5LGN/sub-08-ses-01_T1w.nii.gz right after

Re: [Freesurfer] Problem with recon-all --> nii.gz file not found

, 2023 9:15 AM To: Freesurfer support list Subject: Re: [Freesurfer] Problem with recon-all --> nii.gz file not found * External Email - Caution * External Email - Use Caution Hey again, sorry for my many problems, but this did not work as well (same error) $ recon-all -s sub-04 -i

Re: [Freesurfer] Problem with recon-all --> nii.gz file not found

Ruehr Sent: Friday, January 13, 2023 9:43 AM To: Freesurfer support list Subject: Re: [Freesurfer] Problem with recon-all --> nii.gz file not found External Email - Use Caution Hello, I've tried the echo command, which didn't work. Afterwards I tried -sd: recon-all -s sub-04 -i -sd /h

Re: [Freesurfer] Problem with recon-all --> nii.gz file not found

An: Freesurfer support list Betreff: Re: [Freesurfer] Problem with recon-all --> nii.gz file not found Hi Livia, I’m not sure why your $SUBJECTS_DIR is not recognized. In the same terminal window, 1. echo $SUBJECTS_DIR 2. submit your recon-all If this doesn’t work, you can use -sd flag as sugges

Re: [Freesurfer] Problem with recon-all --> nii.gz file not found

: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Livia Ruehr Sent: Friday, January 13, 2023 7:40 AM To: Freesurfer support list Subject: Re: [Freesurfer] Problem with recon-all --> nii.gz file not found External Email - Use Caution Hi, I've tried it today with the path in the comm

Re: [Freesurfer] Problem with recon-all --> nii.gz file not found

: freesurfer-boun...@nmr.mgh.harvard.edu im Auftrag von Huang, Yujing Gesendet: Donnerstag, 12. Januar 2023 18:25:58 An: Freesurfer support list Betreff: Re: [Freesurfer] Problem with recon-all --> nii.gz file not found Hi Livia, Yes, put /home/lirh717c/Desktop/V5LGN/ in front of .nii

Re: [Freesurfer] Problem with recon-all --> nii.gz file not found

To: Freesurfer support list Subject: Re: [Freesurfer] Problem with recon-all --> nii.gz file not found External Email - Use Caution Dear Yujing, Thank your for your fast reply. So you mean that I need to paste the whole path (home/../../..) before the name of the .nii.gz file in the comm

Re: [Freesurfer] Problem with recon-all --> nii.gz file not found

they are there on this level without any subdirectories...? Best Livia Von: freesurfer-boun...@nmr.mgh.harvard.edu im Auftrag von Huang, Yujing Gesendet: Donnerstag, 12. Januar 2023 17:53:41 An: Freesurfer support list Betreff: Re: [Freesurfer] Problem with recon-all

Re: [Freesurfer] Problem with recon-all --> nii.gz file not found

On Behalf Of Livia Ruehr Sent: Thursday, January 12, 2023 11:31 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] WG: Problem with recon-all --> nii.gz file not found External Email - Use Caution Von: Rühr, Livia Gesendet: Donnerstag, 12. Januar 2

Re: [Freesurfer] Problem with recon-all command in tutorial dataset

External Email - Use Caution Try: export TUTORIAL_DATA=/home/shao/tutorial_data Tim > On August 11, 2020 at 6:51 AM Wei Shao wrote: > > > External Email - Use Caution > > Hi, Freesurfer Team > > My name is Wei Shao, I just a beginner of Freesurfer. As I

[Freesurfer] Problem with recon-all command in tutorial dataset

External Email - Use Caution Hi, Freesurfer Team My name is Wei Shao, I just a beginner of Freesurfer. As I play around with the tutorial data, here is a problem I met, I tried to recon-all the dicoms data as the tutorial instruction practice with the date instructed, but it

Re: [Freesurfer] Problem running recon-all example from installation guide

External Email - Use Caution Hi Andreas, If you want to run recon-all on Bert, I would suggest to copy him to some place where you have write access and use that as the SUBJECTS_DIR. Running FreeSurfer as root is a bad idea and usually leads to trouble later (e.g., the output

[Freesurfer] Problem running recon-all example from installation guide

External Email - Use Caution Hello, I am trying to get the examples running as per the FreeSurfer installation guide. I initially got a recon-all not found error which turned out to be due to the lack of tcsh/csh, which I installed (I found this fix in the mailing list) and now

Re: [Freesurfer] problem using recon-all

External Email - Use Caution Several things: 1) The FreeSurfer list is probably not the best place for support for the HCP Pipelines as there is a dedicated user list hcp-us...@humanconnectome.org for this. Folks who support the HCP Pipelines may not monitor the FreeSurfer list

Re: [Freesurfer] problem using recon-all

External Email - Use Caution Actually Im not really sure why Matlab pops up here.. this is ran there is nothing that is Matlab dependent in the PreFreesurfer Pipeline... ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] problem using recon-all

and get back to you Andrew From: Shachar Gal Date: Thursday, February 14, 2019 at 4:31 AM To: "Hoopes, Andrew" , "ts...@rcmd.org" , FS Help Subject: Re: [Freesurfer] problem using recon-all External Email - Use Caution you can ignore the nifti errors in the beginning

Re: [Freesurfer] problem using recon-all

External Email - Use Caution you can ignore the nifti errors in the beginning of the error message, because it was just a small glitch that I solved. the rest of the errors still stand, and are unclear to me.. On Thu, 14 Feb 2019 at 11:09, Shachar Gal wrote: > Hey, > So I

Re: [Freesurfer] problem using recon-all

External Email - Use Caution Hey, So I disabled SIP, and tried to run the subject from the beginning, and sadly I encountered an error while running the PreFreesurfer Pipeline, which worked fine until disabling SIP. This is the error message: ** ERROR (nifti_image_read): short

Re: [Freesurfer] problem using recon-all

of Shachar Gal Reply-To: FS Help Date: Wednesday, February 13, 2019 at 9:24 AM To: "ts...@rcmd.org" Cc: FS Help , Ido Tavor Subject: Re: [Freesurfer] problem using recon-all External Email - Use Caution I am not sure that the issue is with the SIP, because the message says this - &

Re: [Freesurfer] problem using recon-all

External Email - Use Caution I am not sure that the issue is with the SIP, because the message says this - *"freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c"* does not exist in the patches directory, and in fact, it does not exist here -

Re: [Freesurfer] problem using recon-all

External Email - Use Caution Hey Tim, I tried to run the “-E fs_update”, and got this message: rsync -zbrlv --progress --suffix=.1550066275_bak rsync://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c/*

Re: [Freesurfer] problem using recon-all

External Email - Use Caution That being said, this did not help in my case. I had to disable System Integrity Protection. > On February 13, 2019 at 2:08 PM Tim Schäfer wrote: > > > External Email - Use Caution > > The release notes mention this message: > >

Re: [Freesurfer] problem using recon-all

External Email - Use Caution The release notes mention this message: https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes under 'Known issues' and recommend you run 'sudo -E fs_update'. > On February 13, 2019 at 1:45 PM Shachar Gal wrote: > > > External Email -

Re: [Freesurfer] problem using recon-all

External Email - Use Caution ok, so I tried doing what I mentioned above (I used the hcp recon-all version), and when trying to run the FreeSurfer Pipeline, I received this error: dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from:

Re: [Freesurfer] problem using recon-all

External Email - Use Caution Hey Douglas, A couple of question about the patch In order to use it, I need to download the regular Freesurfer version-6, and replace only the scripts that are in the patch? (i.e Make_average_surface, recon_all, conf2hires, longmc) Which recon-all

Re: [Freesurfer] problem using recon-all

If you want to test it out yourself, you can get it from ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/hcp/ On 2/4/19 6:09 AM, Glasser, Matthew wrote: > > External Email - Use Caution > > There is a little more testing we are doing. > > Matt. > > From: Shachar Gal

Re: [Freesurfer] problem using recon-all

External Email - Use Caution There is a little more testing we are doing. Matt. From: Shachar Gal mailto:gal.shac...@gmail.com>> Date: Monday, February 4, 2019 at 3:32 AM To: Matt Glasser mailto:glass...@wustl.edu>> Cc: Freesurfer support list

Re: [Freesurfer] problem using recon-all

External Email - Use Caution hey, is there any update regarding the release of the FreeSurfer 6 HCP-compatible version? cheers, Shachar On Mon, 14 Jan 2019 at 14:58 Shachar Gal wrote: > thanks, > hope it'll work > anyway, looking forward for the version 6 release > > cheers, >

Re: [Freesurfer] problem using recon-all

External Email - Use Caution thanks, hope it'll work anyway, looking forward for the version 6 release cheers, Shachar On Mon, 14 Jan 2019 at 14:08 Glasser, Matthew wrote: > Ubuntu 14.04 should still work. > > Matt. > > From: Shachar Gal > Date: Monday, January 14, 2019 at

Re: [Freesurfer] problem using recon-all

External Email - Use Caution Ubuntu 14.04 should still work. Matt. From: Shachar Gal mailto:gal.shac...@gmail.com>> Date: Monday, January 14, 2019 at 5:43 AM To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>>, Matt Glasser mailto:glass...@wustl.edu>>, Ido

Re: [Freesurfer] problem using recon-all

External Email - Use Caution if the problem is with the versions, maybe downgrading my OS for now will do the trick? do you happen know what is the latest ubuntu that is compatible with the 5.3-HCP version? does this also occur in centOS? thanks On Sun, 13 Jan 2019 at 17:46

Re: [Freesurfer] problem using recon-all

behalf of Shachar Gal mailto:gal.shac...@gmail.com>> Reply-To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Sunday, January 13, 2019 at 9:46 AM To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] problem using reco

[Freesurfer] problem using recon-all

External Email - Use Caution hello, I using the HCP FreeSurfer Pipeline (using FreeSurfer 5.3-HCP version) on ubuntu, and I encounter this error (copying from the recon-all.log) ___ #@# Talairach Sun Jan 13 17:35:07 IST 2019

Re: [Freesurfer] Problem with Recon-All for Volmetric

you mean not to generate surfaces/parcellations/thickness? I guess you could run -autorecon1 -autorecon2. That would do the start of the surface stuff, but not much (and not long) cheers Bruce On Tue, 30 May 2017, Becker, Valerie wrote: Hi all, Forgive me, as I' new at this, but I cant

Re: [Freesurfer] Problem with Recon-All for Volmetric

you can run it with -autorecon1 -autorecon2 On 05/30/2017 04:00 PM, Becker, Valerie wrote: > > Hi all, > > > Forgive me, as I' new at this, but I cant seem to quite make heads or > tails of the Recon-all page with instructions on how to divide it the > commands. We're just trying to run

[Freesurfer] Problem with Recon-All for Volmetric

Hi all, Forgive me, as I' new at this, but I cant seem to quite make heads or tails of the Recon-all page with instructions on how to divide it the commands. We're just trying to run individual volumetric analyses at the moment. Is there a way to do that with a recon- proc? So as to shorten

Re: [Freesurfer] Problem running recon-all in newly installed Ubuntu 16.04LTS

Hi Bruce, Many thanks. The PC has nominally 8Gb of RAM. The recon-all.log gives the following totalusedfree shared buff/cache available Mem:8142944 1081848 6041324 44260 1019772 6725212 Swap: 8353788

Re: [Freesurfer] Problem running recon-all in newly installed Ubuntu 16.04LTS

Hi Nasos how much RAM is on your new PC? cheers Bruce On Wed, 7 Dec 2016, Nasos Petridis wrote: > Hello freesurfer experts, > > I've recently set up a PC running Ubuntu 16.04LTS and tried to run a > freesurfer version which was running well on another PC (also running > Ubuntu 16.04LTS)...the

[Freesurfer] Problem running recon-all in newly installed Ubuntu 16.04LTS

Hello freesurfer experts, I've recently set up a PC running Ubuntu 16.04LTS and tried to run a freesurfer version which was running well on another PC (also running Ubuntu 16.04LTS)...the nightly build for centos6 of 2016-09-03. I'm running the recon-all script. While running mri_ca_register,

Re: [Freesurfer] Problem with recon-all

Hi Mads yes, you should be able to use mri_convert to change it to .mgz format and name it brainmask.mgz, after which I think it will look as if you've manually edited it and it will be applied cheers Bruce On Mon, 12 Oct 2015, Mads Jensen wrote: > I got a skullstrippen mask from another

Re: [Freesurfer] Problem with recon-all

I got a skullstrippen mask from another pipeline to remove the noise in the MP2RAGE. Is it possible to give that to the recon-all? it is either a mnc or nii thanks, mads On 5 October 2015 at 23:11, Andre van der Kouwe wrote: > I think the standard MP2RAGE only

Re: [Freesurfer] Problem with recon-all

Hi and thanks for the fast reply. Pardon my ignorance, but I am not sure that the PD images are? thanks, mads On 5 October 2015 at 21:59, Bruce Fischl wrote: > Hi Mads > > my guess is that this is a problem with the MP2RAGE. We don't see this in > the mprage or

Re: [Freesurfer] Problem with recon-all

Hi Mads my guess is that this is a problem with the MP2RAGE. We don't see this in the mprage or memprage. Can you look at the PD images in that region? Is the PD close to 0? Maybe you can threshold it out? That region is usually very dark on an mprage cheers Bruce On Mon, 5 Oct 2015, Mads

Re: [Freesurfer] Problem with recon-all

I think the standard MP2RAGE only generates the T1 image on the scanner. With the Bloch simulation you can also figure out PD but the online image analysis doesn't do it. On 10/05/2015 04:21 PM, Bruce Fischl wrote: > I thought mp2rage lets you derive a proton-density (PD) weighted image, > but

[Freesurfer] Problem with recon-all

Hi, I got a problem with recon-all of T1's. The problem is that the surfaces extent into what is essential noise, see linked images. The problem is reoccurring in all the subjects I have ran so far, so I was wondering if there could be a generic fix or if it will be necessary to fix each recon

Re: [Freesurfer] Problem with recon-all

I thought mp2rage lets you derive a proton-density (PD) weighted image, but I could be wrong. I'll cc Andre van der Kouwe who will know On Mon, 5 Oct 2015, Mads Jensen wrote: > Hi and thanks for the fast reply. > > Pardon my ignorance, but I am not sure that the PD images are? > > thanks, >

[Freesurfer] Problem with recon-all

Dear FS experts, I have a problem with the command recon-all. In many cases when I use it on the same brain's MRI, on the CLUSTER COMPUTING INFRASTRUCTURE, about 40% of my jobs finish without erros while the other are killed at the command nu_currect, as you can see from the file.log in

Re: [Freesurfer] Problem running recon-all with option -qcache

Hi Doug, Indeed, you are right, I forgot to run recon-all -autorecon3. It is not well documented that after running -autorecon2-wm one should also run -autorecon3. I had the impression that this portion was executed automatically by -autorecon2-wm. Ed On 2 Feb 2011, at 18:03, Douglas N Greve

Re: [Freesurfer] Problem running recon-all with option -qcache

Thanks for the suggestion Ed. I've just added the text below to http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Troubleshooting. If you know of another place where it would be useful, please let us know. doug Note that after you run recon-all with the -autorecon2-wm flag, you will still

[Freesurfer] Problem running recon-all with option -qcache

Hi, A serious error was encountered in running recon-all with option -qcache. The error occurred during execution of mri_surf2surf and the message was: number of vertices in ../subjectID/surf/lh.thickness does not match surface (141969,131763). It means the number of vertices in

Re: [Freesurfer] Problem running recon-all with option -qcache

Hi Ed, that subject is out-of-synch (maybe it got aborted). You'll need to re-run some portion of recon-all depending upon where in the stream it aborted. doug Ed Gronenschild wrote: Hi, A serious error was encountered in running recon-all with option -qcache. The error occurred during

Re: [Freesurfer] problem on recon-all

Xiaoying, There are directions for how to do this located here: https://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ?highlight=%28FAQ%29#SkullStrippingOptions Allison -- On Fri, 12 Mar 2010, Xiaoying Tang wrote: Hi all, When we do recon-all, we usually do autorecon1, autorecon2,

Re: [Freesurfer] problem on recon-all

Hi Allison, You are so helpful. Thanks a lot. Best, Xiaoying - Original Message - From: Allison Stevens astev...@nmr.mgh.harvard.edu Date: Friday, March 12, 2010 7:43 am Subject: Re: [Freesurfer] problem on recon-all To: Xiaoying Tang xta...@jhu.edu Cc: freesurfer@nmr.mgh.harvard.edu

[Freesurfer] problem on recon-all

Hi all, When we do recon-all, we usually do autorecon1, autorecon2, and autorecon3 in sequence. But now suppose I have already have a very good skull-stripped subject. I mean I don't need to do skull-stripping with freesurfer. But I want to get greymatter and white matter, which are generated

Re: [Freesurfer] Problem with recon-all on the tutorial data (bert)

Dear Bruce, I have tried running mri_ca_register again twice with the following cases: Case 1: on VirtualBox with 9.2GB available free disk space. I gave 1GB RAM to this Virtual Machine. Case 2: on Ubuntu installed on a machine with 2 core Dual 2.5Ghz , 4G RAM, and 6GB free disk space.

[Freesurfer] Problem with recon-all on the tutorial data (bert)

Dear Freesurfers, I have had a problem when running recon-all on your tutorial data (bert). Please find following the content of recon-all.log: *$Id: mris_sphere.c,v 1.47 2007/03/08 18:36:08 greve Exp $* * $Id: mrisurf.c,v 1.557.2.19 2009/08/05 22:10:21 nicks Exp $*

Re: [Freesurfer] Problem with recon-all on the tutorial data (bert)

Hi Long, have you run out of disk space? Bruce On Tue, 24 Nov 2009, L wrote: Dear Freesurfers, I have had a problem when running recon-all on your tutorial data (bert). Please find following the content of recon-all.log: *$Id: mris_sphere.c,v 1.47 2007/03/08 18:36:08 greve Exp $* * $Id:

[Freesurfer] problem with recon-all

hi folks - I'm trying to get freesurfer (the latest Tiger snapshot) working on my mac but I'm having a problem with recon-all.  If I try to apply it to the bert data included in the distribution, it seems to set up ok but then it doesn't actually do anything.  here is the output from

[Freesurfer] problem with recon-all

when i source: Setting up environment for FreeSurfer/FS-FAST FREESURFER_HOME /usr/local/freesurfer/dev FSFAST_HOME /usr/local/freesurfer/dev/fsfast SUBJECTS_DIR/space/sake/3/users/inverse/subjects FUNCTIONALS_DIR /usr/local/freesurfer/dev/sessions MINC_BIN_DIR

Re: [Freesurfer] problem with recon-all

I modified recon-all to try to autodetect the input format (but introduced a bug). It should work if you add -COR to the command-line. In the mean time I'll fix my mistake. doug Tamara Knutsen wrote: when i source: Setting up environment for FreeSurfer/FS-FAST FREESURFER_HOME

[Freesurfer] Problem running recon-all

Hello everyone, I have recently upgraded my OS from RedHat Linux 9 to RedHat Enterprise edition. After that, I'm getting the following error when I run : $ recon-all -sid -stage1 ### INFO: SUBJECTS_DIR is /home/edamaraju/freesurfer/subjects