[Freesurfer] Fwd: recon-all error: matlab gives: Unrecognized function or variable 'make_outer_surface'.

External Email - Use Caution If you have not already done so, I would try installing and using the newest version of theMatlab runtime environment that the 7.4.1 release was tested with, i.e. R2019b. Once you have set $FREESURFER_HOME, then run the fs_install_mcr script

Re: [Freesurfer] Fwd: recon-all error: ltMNIreadEx: could not open file transforms/talairach.xfm

You did not tell recon-all to do anything:) Try adding -all to your command line On 11/13/19 2:10 PM, Dalton Bermudez wrote: > > External Email - Use Caution > > > > -- Forwarded message - > From: *Dalton Bermudez* > > Date: Wed, Nov 13,

Re: [Freesurfer] Fwd: recon-all error: ltMNIreadEx: could not open file transforms/talairach.xfm

External Email - Use Caution Dear Bruce, This is the command I ran with my own data: recon-all -subjid 00_0086 -i RAW/00_0086/ns_00_0086_3T_T1w_MPR1.nii -i RAW/00_0086/ns_00_0086_3T_T1w_MPR2.nii The whole output can be found in the recon-all.log attached below On Wed, Nov 13,

Re: [Freesurfer] Fwd: recon-all error: ltMNIreadEx: could not open file transforms/talairach.xfm

Hi Dalton you need to give us a lot more information. What command did you run? What was the full output? cheers Bruce On Wed, 13 Nov 2019, Dalton Bermudez wrote: External Email - Use Caution -- Forwarded message - From: Dalton Bermudez Date: Wed, Nov

[Freesurfer] Fwd: recon-all error: ltMNIreadEx: could not open file transforms/talairach.xfm

External Email - Use Caution -- Forwarded message - From: Dalton Bermudez Date: Wed, Nov 13, 2019 at 1:54 PM Subject: recon-all error: ltMNIreadEx: could not open file transforms/talairach.xfm To: Dear FreeSurfer Developers, I am attempting to obtain a average

[Freesurfer] Fwd: recon-all error: ERROR! FOV=272.000 > 256

Hi FS team, I encountered recon-all error and I want to solve the problem or find alternative method. As you can see forwarded mail thread, I asked about the problem before but i couldn’t any clear answer.. Would you suggest someone to advice me how to deal with the problem? Thanks, Juhyoung

Re: [Freesurfer] Fwd: recon-all error

Dear Patricia, this is I suppose the last issue concerning symbolic links, related with part of code starting with following comment:  # if fsaverage is not in subjects dir, put it there I think that the most straightforward  solution of this issue is to manually copy the fsaverage subject to

Re: [Freesurfer] Fwd: recon-all error

Hi Antonin, I edited recon-all file, but another error was reported. This error concerns symbolic links, too. Is there any way I could make it work on this virtual machine? I coud try to substitute all ln commands with cp or something like that. Thanks. Patricia 2017-04-04 13:43 GMT+02:00

Re: [Freesurfer] Fwd: recon-all error

Dear Patricia, see this thread: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg51797.html Your working directory probably resides on the filesystem which does not support symbolic links. You probably could workaround this by editing your recon-all and replace line set cmd2 =

Re: [Freesurfer] Fwd: Recon-all Error

Hi Hassan you need to add some directives to recon-all to tell it what to do. For example, if you add -all to your command line it will do everything it knows how to (pretty much) cheers Bruce On Wed, 4 Mar 2015, Hassan bakhshi wrote: HI, Im using freesurfer newly, i have a folder of a

[Freesurfer] Fwd: Recon-all Error

HI, Im using freesurfer newly, i have a folder of a subject's MRI's named 139942 I tried to run recon-all of a File named I000 The point is to get Superior temporal gyrus thickness. but it show an error and stop working. i looked up archive of FAQ's but i didnt anything usefull. There

Re: [Freesurfer] Fwd: recon-all error

Bruce, Thanks for your help. I will forward this to the MNI mailing list and see if they can help. Cheers, Kate On Tue, Oct 14, 2014 at 10:46 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Kate so something is going wrong with the MNI NU correct tool. Maybe someone on the FS list

Re: [Freesurfer] Fwd: recon-all error

Hi Kate so something is going wrong with the MNI NU correct tool. Maybe someone on the FS list knows how to fix this, but if not you might want to check with the MNI people cheers Bruce On Tue, 14 Oct 2014, Kate Riggall wrote: Hi Bruce, The output is as follows:

Re: [Freesurfer] Fwd: recon-all error

Hi Kate can you run: cd /home/fsuser/host/Sprachlernen/Subjects/Y03/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz and send us the full screen output? thanks Bruce On Tue, 14 Oct 2014, Kate Riggall wrote: Hello,   I am using

Re: [Freesurfer] Fwd: recon-all error

Hi Bruce, The output is as follows: fsuser@xubuntu-VirtualBox:~$ cd /home/fsuser/host/Sprachlernen/Subjects/Y03/mri fsuser@xubuntu-VirtualBox:~/host/Sprachlernen/Subjects/Y03/mri$ mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz