du -h /tmp/ shows 256GB available, so that doesn’t seem to be it. Is the “not found” error telling me that a binary is not found, or that some expected output file is not found? I was looking for /bin/imtest and /bin/remove_ext, and those binaries indeed do not exist, but we’ve run Freesurfer on another dataset (but on another workstation, but neither were those two binaries to be found on that workstation).
Is your /tmp space full?
On 04/15/2016 12:54 PM, Mcnorgan, Christopher wrote:
I was hoping the developers might be able to help with a problem I'm having with a sub-step of preproc-sess.
I executed the following:
preproc-sess -s FS_T1_501 -surface self lhrh -fwhm 6 -per-run -fsd bold
In the relevant output, I see mktemplate-sess completed, followed by a call to mkbrainmask-sess, which eventually reported:
# ---------- Using FSL's BET to Extract Brain------------------ # /home/chris/ubfs/cpmcnorg/openfmri/booth/FS_T1_501/bold bet.fsl /tmp/mkbrainmask_2623/in.nii /tmp/mkbrainmask_2623/brain -m -f 0.1 /usr/local/freesurfer/bin/bet.fsl: 1: /usr/local/freesurfer/bin/bet.fsl: /bin/remove_ext: not found /usr/local/freesurfer/bin/bet.fsl: 1: /usr/local/freesurfer/bin/bet.fsl: /bin/remove_ext: not found /usr/local/freesurfer/bin/bet.fsl: 1: /usr/local/freesurfer/bin/bet.fsl: /bin/imtest: not found /usr/local/freesurfer/bin/bet.fsl: 153: [: =: unexpected operator /usr/local/freesurfer/bin/bet.fsl: 231: /usr/local/freesurfer/bin/bet.fsl: /bin/bet2: not found
/********************************************** * Chris McNorgan * Assistant Professor * Department of Psychology * University at Buffalo, * The State University of New York * http://ccnlab.buffalo.edu/ * Office: 716.645.0236 * Lab: 716.645.0222 **********************************************/
Can you run
/mkbrainmask-sess//-debug -s FS_T1_501 //-fsd bold/ |& tee dng.log and send me dng.log ?
doug
On 04/18/2016 04:51 PM, Mcnorgan, Christopher wrote:
du -h /tmp/ shows 256GB available, so that doesn’t seem to be it. Is the “not found” error telling me that a binary is not found, or that some expected output file is not found? I was looking for /bin/imtest and /bin/remove_ext, and those binaries indeed do not exist, but we’ve run Freesurfer on another dataset (but on another workstation, but neither were those two binaries to be found on that workstation).
Is your /tmp space full?
On 04/15/2016 12:54 PM, Mcnorgan, Christopher wrote:
//>/I was hoping the developers might be able to help with a problem I'm />/having with a sub-step of preproc-sess./ /I executed the following: />//>/preproc-sess -s FS_T1_501 -surface
self lhrh -fwhm 6 -per-run -fsd bold />//>/In the relevant output, I see mktemplate-sess completed, followed by a />/call to mkbrainmask-sess, which eventually reported: />//>/# ---------- Using FSL's BET to Extract Brain------------------ # />//home/chris/ubfs/cpmcnorg/openfmri/booth/FS_T1_501/bold />/bet.fsl /tmp/mkbrainmask_2623/in.nii /tmp/mkbrainmask_2623/brain -m -f 0.1 />//usr/local/freesurfer/bin/bet.fsl: 1: />//usr/local/freesurfer/bin/bet.fsl: /bin/remove_ext: not found />//usr/local/freesurfer/bin/bet.fsl: 1: />//usr/local/freesurfer/bin/bet.fsl: /bin/remove_ext: not found />//usr/local/freesurfer/bin/bet.fsl: 1: />//usr/local/freesurfer/bin/bet.fsl: /bin/imtest: not found />//usr/local/freesurfer/bin/bet.fsl: 153: [: =: unexpected operator />//usr/local/freesurfer/bin/bet.fsl: 231: />//usr/local/freesurfer/bin/bet.fsl: /bin/bet2: not found/
/**********************************************
- Chris McNorgan
- Assistant Professor
- Department of Psychology
- University at Buffalo,
- The State University of New York
- http://ccnlab.buffalo.edu/
- Office: 716.645.0236
- Lab: 716.645.0222
**********************************************/
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Mcnorgan, Christopher