Re: [Freesurfer] [FreeSurfer] recon-all exited with error - watershed error

024 16:58:18 To: Freesurfer support list Subject: [Freesurfer] [FreeSurfer] recon-all exited with error - watershed error External Email - Use Caution Dear FS experts, I am encountering an error when running recon-all. I followed the FAQ <https://se

Re: [Freesurfer] [FreeSurfer] recon-all exited with error

: Freesurfer support list Subject: Re: [Freesurfer] [FreeSurfer] recon-all exited with error Hi Krystal, Can you try running recon-all without ‘-parallel’ flag? Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Krystal Xiwing Yau Sent: Saturday, February 18, 2023 7:45 PM To

Re: [Freesurfer] [FreeSurfer] recon-all exited with error

; mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Huang, Yujing mailto:yhuan...@mgh.harvard.edu>> Sent: 17 February 2023 01:47:15 To: Freesurfer support list Subject: Re: [Freesurfer] [FreeSurfer] recon-all exited with error recon-all failed to create the symbolic links. H

Re: [Freesurfer] [FreeSurfer] recon-all exited with error

rom: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Krystal Xiwing Yau Sent: Thursday, February 16, 2023 9:15 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] [FreeSurfer] recon-all exited with error External Email - Use Caution Dear FreeSurfer experts, I ran the command &

Re: [Freesurfer] recon-all exited with error

You have two inputs, 001.mgz and 002..mgz, and it looks like they have different sizes. They must be the same size On 8/22/2020 3:36 PM, Dalton Bermudez wrote: External Email - Use Caution ERROR: MultiRegistration::loadMovables: images have different voxel sizes.   Currently not suppo

[Freesurfer] recon-all exited with error

External Email - Use Caution ERROR: MultiRegistration::loadMovables: images have different voxel sizes. Currently not supported, maybe first make conform? Debug info: size(1) = 1, 1, 1 size(0) = 1, 0.976562, 0.976562 error: No such file or directory error: MultiRegistration::

Re: [Freesurfer] recon-all exited with error

Hi there I uploaded these last week to the file drop and used Bruce's email as it said it requires a ".nmr.mgh.harvard.edu" email type. Please let me know if you received icbm-202 and icbm-205 as tar.gz files. As I mentioned, I was able to get surfaces for both of these but they seemed to end at

Re: [Freesurfer] recon-all exited with error

You can send it to either my email (ahoo...@mgh.harvard.edu) or Bruce’s best, Andrew On Jan 19, 2018, at 10:12 AM, Trisanna Sprung-Much mailto:trisanna.sprung-m...@mail.mcgill.ca>> wrote: thanks Andrew. I had seen that and will give it a go - just wanted to m

Re: [Freesurfer] recon-all exited with error

thanks Andrew. I had seen that and will give it a go - just wanted to make sure that my recipient email would be the FreeSurfer support list. Trisanna On Fri, Jan 19, 2018 at 9:59 AM, Hoopes, Andrew wrote: > Hi Trisanna, > > Okay - if your file is less than 2GiB, I suggest sending your data via

Re: [Freesurfer] recon-all exited with error

Hi Trisanna, Okay - if your file is less than 2GiB, I suggest sending your data via the Martinos file drop (directions at the bottom of this page: https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange). best Andrew On Jan 18, 2018, at 11:53 AM, Trisanna Sprung-Much mailto:trisanna.sprung-

Re: [Freesurfer] recon-all exited with error

Hi Andrew Thank you for your response. I gave it a go and still no luck, unless I am missing something completely obvious here trisanna@kaplan:~/data-01/freesurfer/freesurfer_6.0/ICBM_305$ ftp surfer.nmr.mgh.harvard.edu Connected to surfer.nmr.mgh.harvard.edu. 220-This is the Martinos Center Anon

Re: [Freesurfer] recon-all exited with error

Hi Trisanna, Try running 'quote PASV' in ftp before running 'put' - that should hopefully clear up this issue. best, Andrew On Jan 17, 2018, at 4:03 PM, Trisanna Sprung-Much mailto:trisanna.sprung-m...@mail.mcgill.ca>> wrote: Sorry, Bruce. ignore my last email. Not sure what happened there.

Re: [Freesurfer] recon-all exited with error

Sorry, Bruce. ignore my last email. Not sure what happened there. I now am trying to upload icbm-205.tar.gz (the subject that failed) but I get the following and it happens over and over. Any idea what the problem could be? trisanna@kaplan:~$ cd data-01/freesurfer/freesurfer_6.0/ICBM_305/ trisann

Re: [Freesurfer] recon-all exited with error

Hi Trisanna there are a bunch of files, but they all look like they are empty: r--r--r-- 1 ftpftp 0 Jan 17 14:24 ICBM_305.tar -r--r--r-- 1 ftpftp 0 Jan 17 14:41 ICBM_305.tar.gz -r--r--r-- 1 ftpftp 0 Jan 17 15:12 icbm-205.tar.gz cheers Bruce On Wed, 17 Jan 2018, T

Re: [Freesurfer] recon-all exited with error

Thanks Bruce. I have uploaded it but I would like to confirm that you received the ICBM_305.tar. For some reason I was not able to compress it any further. To clarify, subjects 205 and now subject 202 have both failed after surface extraction. best Trisanna -- Ph.D. Candidate McGill University I

Re: [Freesurfer] recon-all exited with error

you can put it on our ftp site: https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange On Tue, 16 Jan 2018, Trisanna Sprung-Much wrote: > Hi Bruce > Thanks for the speedy reply. Should I attach it here or is there a place I > can upload it to? > > best > Trisanna > > -- > Ph.D. CandidateM

Re: [Freesurfer] recon-all exited with error

Hi Bruce Thanks for the speedy reply. Should I attach it here or is there a place I can upload it to? best Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Tue, Jan 16, 2018 at 11:44 AM, Bruce Fischl wrote: > hmmm, I've never seen label2label cor

Re: [Freesurfer] recon-all exited with error

hmmm, I've never seen label2label core dump before. Can you tar, gzip and upload the entire subject dir? On Tue, 16 Jan 2018, Trisanna Sprung-Much wrote: > Hi there > > I ran Freesurfer 6.0 on a subject last night and it took about 12 hours > (seemed to get to the very end) and then exited wit

Re: [Freesurfer] recon-all exited with error.

Hello Z K, Thank you. I will do it later and update you. Best, Paul On Mon, Mar 6, 2017 at 9:07 AM, Z K wrote: > Hello Paul, > > I've been trying to replicate it the issue on my Mac without any success. > But I do have what might be a potential solution ide like you to try. Could > you please >

Re: [Freesurfer] recon-all exited with error.

Hello Paul, I've been trying to replicate it the issue on my Mac without any success. But I do have what might be a potential solution ide like you to try. Could you please source freesurfer, then run the following command. $> sudo -E fs_update (This will update a freesurfer file on your machi

Re: [Freesurfer] recon-all exited with error.

Hello Z K, Were you able to fix the bug? Best, Paul On Fri, Mar 3, 2017 at 12:14 PM, Z K wrote: > Im looking into this now, but I think their might be a bug when using > the -parallel flag on Mac platforms. I should have a fix shortly. I will > let you know. > > On 03/03/2017 12:10 PM, miracle o

Re: [Freesurfer] recon-all exited with error.

Thanks. Z K Best, Paul On Fri, Mar 3, 2017 at 12:14 PM, Z K wrote: > Im looking into this now, but I think their might be a bug when using > the -parallel flag on Mac platforms. I should have a fix shortly. I will > let you know. > > On 03/03/2017 12:10 PM, miracle ozzoude wrote: > > Thanks Anto

Re: [Freesurfer] recon-all exited with error.

Im looking into this now, but I think their might be a bug when using the -parallel flag on Mac platforms. I should have a fix shortly. I will let you know. On 03/03/2017 12:10 PM, miracle ozzoude wrote: > Thanks Antonin. I also have different error when running another > subject. Recon fails in

Re: [Freesurfer] recon-all exited with error.

Dear Paul, yes, this is the modification of FREESURFER_HOME you need to do (using setenv command if you are using tcsh). Regards, Antonin Hey Antonin, Thank you. hence, the right path should be "setenv FREESURFER_HOME /opt/freesurfer-6.0.0/freesurfer " Best, Paul. On Thu, Mar 2, 2017 at 5:41

Re: [Freesurfer] recon-all exited with error.

Hey Antonin, Thank you. hence, the right path should be "setenv FREESURFER_HOME /opt/freesurfer-6.0.0/freesurfer " Best, Paul. On Thu, Mar 2, 2017 at 5:41 PM, Antonin Skoch wrote: > Dear Paul, > > the slash problem prevents to properly create symbolic link to fsaverage in > your SUBJECTS_DIR.

Re: [Freesurfer] recon-all exited with error.

Dear Paul, the slash problem prevents to properly create symbolic link to fsaverage in your SUBJECTS_DIR. Then, the mri_label2label could not find the fsaverage label file since symbolic link for fsaverage does not exist, hence produces the error.log you are attaching. Regards, Antonin Tha

Re: [Freesurfer] recon-all exited with error.

Thanks Antonin. Also, I got this error.log file in my label folder. Do you think it is due to the slash problem? Best, Paul On Thu, Mar 2, 2017 at 4:38 PM, Antonin Skoch wrote: > Dear Paul, > > I suppose the clue is following messages from your recon-all.log file: > > FREESURFER_HOME /opt/freesu

Re: [Freesurfer] recon-all exited with error.

Dear Paul, I suppose the clue is following messages from your recon-all.log file: FREESURFER_HOME /opt/freesurfer-6.0.0/freesurfer/ and cd /net/synapse/nt/mozzoude/processing/freesurfer/176_003_120326; ln -s /opt/freesurfer-6.0.0/freesurfer//subjects/fsaverage; cd - ln: failed to create symb

Re: [Freesurfer] recon-all exited with error: reading lh.BA1_exvivo.label

>> >> HTH - Don >> >> >> >> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [mailto: >> freesurfer-boun...@nmr.mgh.harvard.edu] *On Behalf Of *Vaz pandolfo, >> Renata >> *Sent:* Thursday, July 07, 2016 8:05 AM >> *To:* freesurfer@nmr.mgh.harvard.ed

Re: [Freesurfer] recon-all exited with error: reading lh.BA1_exvivo.label

.harvard.edu [mailto: > freesurfer-boun...@nmr.mgh.harvard.edu] *On Behalf Of *Vaz pandolfo, > Renata > *Sent:* Thursday, July 07, 2016 8:05 AM > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* [Freesurfer] recon-all exited with error: reading > lh.BA1_exvivo.label > > > >

Re: [Freesurfer] recon-all exited with error: reading lh.BA1_exvivo.label

@nmr.mgh.harvard.edu Subject: [Freesurfer] recon-all exited with error: reading lh.BA1_exvivo.label Dear FreeSurfer developers, I am running recon-all on a healthy subject and I am also trying to get the hippocampal subfields segmentation. On the mri directory there is no hippocampus output, and the recon-all exited

Re: [Freesurfer] Recon all exited with error

Hi Hassan you need to look at the lh.orig.nofix and the lh.inflated.nofix to see what is going on. Typically this happens if there is some massive topological defect caused by e.g. the skull or cerebellum being attached to the wm. cheers Bruce On Sat, 25 Apr 2015, Hassan bakhshi wrote:

[Freesurfer] Recon all exited with error

Hi, I was running 6 individual and all six couldn't finish at the "Fix Topology lh" . I ran them again but again at this stage they got error. the status file is attached. recon-all-status.log Description: Binary data ___ Freesurfer mailing list Free