Re: [Freesurfer] recon-all -make all

2020-02-14 Thread Douglas N. Greve
On 2/11/2020 9:26 AM, Benjamin Ineichen wrote: External Email - Use Caution Dear Freesurfer experts, I ran recon-all on 100 subjects. Around 20 of them needed manual corrections of the pial surface on the brainmask.mgz. 1.) Can I run the command: "recon-all -make all- s " on all

[Freesurfer] recon-all -make all

2020-02-11 Thread Benjamin Ineichen
External Email - Use Caution Dear Freesurfer experts, I ran recon-all on 100 subjects. Around 20 of them needed manual corrections of the pial surface on the brainmask.mgz. 1.) Can I run the command: "recon-all -make all- s " on all 100 subjects and it will only recon-all the

Re: [Freesurfer] recon-all -make all error

2018-10-07 Thread Bruce Fischl
Hi Vasudev you don't need the whole path for the -s switch, just the subject ID (in this case it looks like HC13) cheers Bruce On Mon, 8 Oct 2018, Dev vasu wrote: External Email - Use Caution Dear all, I am encountering following error whenever i re-rerun my recon-all on

[Freesurfer] recon-all -make all error

2018-10-07 Thread Dev vasu
External Email - Use Caution Dear all, I am encountering following error whenever i re-rerun my recon-all on cluster,,although i have downloaded new development version of recon-all.makefile, this error persists,kindly let me know what i am doing wrong recon-all -make all -s

[Freesurfer] recon-all -make all error?

2010-12-06 Thread Jeff Sadino
Hello, I am reprocessing a number of subjects from fs 4.5.0 to fs 5.0.0. I am doing this by issuing the recon-all -make all -s subject command. It stops right away with the message: make: Nothing to be done for `all'. There exists the wmparc.stats file from the fs450 recon, but there is no

[Freesurfer] recon-all -make all -s (subject) ERROR

2010-07-19 Thread aekairys
Hi freesurfers, I just got this error while continuing processing of a subject: mri_average: MRIread(/PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-25287/cor-2.img) failed Linux titan 2.6.18-128.el5 #1 SMP Wed Dec 17 11:41:38 EST 2008

Re: [Freesurfer] recon-all -make all -s (subject) ERROR

2010-07-19 Thread Douglas N Greve
is that disk full? doug aekai...@umich.edu wrote: Hi freesurfers, I just got this error while continuing processing of a subject: mri_average: MRIread(/PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-25287/cor-2.img) failed Linux

Re: [Freesurfer] recon-all -make all -s (subject) ERROR

2010-07-19 Thread Douglas N Greve
Are the inputs (001.mgz and 002.mgz) the same size? They have slightly different acquisition parameters, which is not a good sign ... aekai...@umich.edu wrote: Hi again, The disk is not full and attached is the recon-all.log best, Anson K. University of Michigan On Mon, 19 Jul 2010