Hi Adam, the problem is that the original fmc.nii was generated with an error because of the lack of disc space. But the file itself exists and has a creation date after f.nii, so preproc-sess did not know that there was anything wrong with it and did not try to regenerate it. Try deleting fmc.nii and re-running.
doug Adam Nitenson wrote: > Hi Doug, > > My original email was sent to the freesurfer list. > > Here is the more detailed terminal info: > > FREESURFER_HOME: /usr/local/freesurfer/stable4 > > Build stamp: freesurfer-Linux-centos4_x86_64-stable-v4.5.0-20100311 > > RedHat release: CentOS release 5.5 (Final) > > Kernel info: Linux 2.6.18-194.8.1.el5 x86_64 > > NMR Center info (/space/freesurfer exists): > > machine: audrey > > SUBJECTS_DIR: /cluster/roffman/users/MTH_Study > > PWD: /cluster/roffman/users/MTH_Study > > ssh audrey > setenv SUBJECTS_DIR /cluster/roffman/users/MTH_Study > cd /cluster/roffman/users/MTH_Study > > I had already ran all of the unpacking commands through recon-all without > fail (see old email below for first subject; MTH20007AA). These were done > using the SUBJECTS_DIR /autofs/space/seymour_001/users/MTH_Study. After > that, we had bought a TB in the new cluster, and I copied all of the > seymour 1 data there. So, I then switched to SUBJECTS_DIR: > /cluster/roffman/users/MTH_Study, as running the preproc-sess for the > other subject using the directory /cluster/roffman/users/folate_subjects > worked fine. > > The failed command was: preproc-sess -s MTH20007AA -fwhm 5 > > with the error: > > niiRead(): error reading from 012/fmc.nii > ERROR: Read 40, expected 64 > ERROR: mri_fwhm failed > ERROR: spatialsmooth-sess failed > > -Adam > > > > >> Hi Adam, what is the command line you ran and the directory you ran it >> from? What was your SUBJECTS_DIR? In general, you should send this >> information each time you write. You might want to look at >> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting for other ways to improve >> your bug reports. Also, please start to send these kinds of things to >> martinos-tech or the freesurfer list. >> >> thanks >> >> doug >> >> >> Adam Nitenson wrote: >> >>> Hi Doug, >>> >>> Using the new storage cluster with extra space allows the second >>> subject, FB0011060AA to preprocess, but I'm still having issues with >>> the first MTH20007AA. I'm getting the following error now: >>> >>> niiRead(): error reading from 012/fmc.nii >>> ERROR: Read 40, expected 64 >>> ERROR: mri_fwhm failed >>> ERROR: spatialsmooth-sess failed >>> >>> Again, the raw data source is >>> /cluster/archive/288/siemens/TrioTim-35101-20100916-143244-437000 >>> >>> -Adam >>> >>> >>> >>> >>> >>>> Ah, yea, it's probably space issues. Let me know if more space does >>>> not fix the problem. >>>> >>>> doug >>>> >>>> On 9/23/10 7:37 AM, Adam Nitenson wrote: >>>> >>>> >>>>> Sure. I would also like to note that after I sent that email, I >>>>> realized >>>>> that I only had 508 KB left in Seymour 1, so I don't know if these >>>>> errors >>>>> could have been generated due to a lack of space. We just purchased a >>>>> block of space on the new storage cluster, but haven't used it yet. >>>>> >>>>> If you think it might still be something else....here are the commands >>>>> (after sourcing, etc). >>>>> >>>>> FIRST SUBJECT >>>>> >>>>> unpacksdcmdir -src >>>>> /cluster/archive/288/siemens/TrioTim-35101-20100916-143244-437000 >>>>> -targ >>>>> /autofs/space/seymour_001/users/MTH_Study/MTH20007AA -run 5 MPRAGE COR >>>>> blah >>>>> >>>>> unpacksdcmdir -src >>>>> /cluster/archive/288/siemens/TrioTim-35101-20100916-143244-437000 >>>>> -targ >>>>> /autofs/space/seymour_001/users/MTH_Study/MTH20007AA -fsfast -run 12 >>>>> bold >>>>> nii f.nii -fsfast -run 13 bold nii f.nii -fsfast -run 14 bold nii >>>>> f.nii >>>>> -fsfast -run 15 bold nii f.nii -fsfast -run 16 bold nii f.nii -fsfast >>>>> -run >>>>> 17 bold nii f.nii >>>>> >>>>> cd $SUBJECTS_DIR >>>>> >>>>> recon-all -i >>>>> /autofs/space/seymour_001/users/MTH_Study/MTH20007AA/MPRAGE/005 -s >>>>> MTH20007AA -force >>>>> >>>>> recon-all -autorecon-all -s MTH20007AA >>>>> >>>>> preproc-sess -s MTH20007AA -fwhm 5 (FAILED) >>>>> >>>>> >>>>> SECONDS SUBJECT >>>>> >>>>> unpacksdcmdir -src >>>>> /cluster/archive/288/siemens/TrioTim-35101-20100917-142812-643000 >>>>> -targ >>>>> /autofs/space/seymour_001/users/folate_subjects/FB0011060AA -run 5 >>>>> MPRAGE >>>>> COR blah >>>>> >>>>> unpacksdcmdir -src >>>>> /cluster/archive/288/siemens/TrioTim-35101-20100917-142812-643000 >>>>> -targ >>>>> /autofs/space/seymour_001/users/folate_subjects/FB0011060AA -fsfast >>>>> -run >>>>> 13 bold nii f.nii -fsfast -run 14 bold nii f.nii -fsfast -run 15 bold >>>>> nii >>>>> f.nii -fsfast -run 16 bold nii f.nii -fsfast -run 17 bold nii f.nii >>>>> -run >>>>> 18 bold nii f.nii >>>>> >>>>> cd $SUBJECTS_DIR >>>>> >>>>> recon-all -i >>>>> /autofs/space/seymour_001/users/folate_subjects/FB0011060AA/MPRAGE/005 >>>>> -s >>>>> FB0011060AA -force >>>>> >>>>> recon-all -autorecon-all -s FB0011060AA >>>>> >>>>> preproc-sess -s FB0011060AA -fwhm 5 (FAILED) >>>>> >>>>> Let me know if you need any more info. >>>>> >>>>> Thanks, >>>>> >>>>> Adam >>>>> >>>>> >>>>> >>>>>> Adam, can you send a pointer to the data to me? >>>>>> >>>>>> doug >>>>>> >>>>>> Adam Nitenson wrote: >>>>>> >>>>>> >>>>>>> Hello freesurfers, >>>>>>> >>>>>>> I am trying to unpack a couple of recent subjects in Stable 4. I ran >>>>>>> all >>>>>>> steps through recon-all without error. However, when I try to run >>>>>>> the >>>>>>> next >>>>>>> step, preproc-sess, it keeps failing. >>>>>>> >>>>>>> This is the command I enter: >>>>>>> >>>>>>> preproc-sess -s FB0011060AA -fwhm 5 >>>>>>> >>>>>>> It works for about 30 seconds, and then I get the following in >>>>>>> return >>>>>>> >>>>>>> niiRead(): bad number of dimensions (0) in >>>>>>> 013/tmp.mc-afni2.15211/outvol.nii.gz >>>>>>> reading info from 013/f.nii... >>>>>>> $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ >>>>>>> reading from 013/tmp.mc-afni2.15211/outvol.nii.gz... >>>>>>> ERROR: converting output >>>>>>> Invalid null command. >>>>>>> ERROR: mc-sess failed >>>>>>> >>>>>>> the error for the other subject was slightly different: >>>>>>> >>>>>>> niiRead(): error reading from 013/tmp.mc-afni2.15452/outvol.nii.gz >>>>>>> reading info from 012/f.nii... >>>>>>> $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ >>>>>>> reading from 013/tmp.mc-afni2.15452/outvol.nii.gz... >>>>>>> ERROR: Read 14, expected 64 >>>>>>> ERROR: converting output >>>>>>> Invalid null command. >>>>>>> ERROR: mc-sess failed >>>>>>> >>>>>>> Any idea what might be going on? I've done these same steps many >>>>>>> times >>>>>>> for >>>>>>> processing data and have not before received this error. >>>>>>> >>>>>>> Thanks! >>>>>>> >>>>>>> Adam Nitenson, B.S. >>>>>>> Brain Genomics Lab >>>>>>> Massachusetts General Hospital >>>>>>> _______________________________________________ >>>>>>> Freesurfer mailing list >>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>> -- >>>>>> Douglas N. Greve, Ph.D. >>>>>> MGH-NMR Center >>>>>> gr...@nmr.mgh.harvard.edu >>>>>> Phone Number: 617-724-2358 >>>>>> Fax: 617-726-7422 >>>>>> >>>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>> Adam Nitenson, B.S. >>>>> Brain Genomics Lab >>>>> Massachusetts General Hospital >>>>> >>>>> >>>>> >>>>> >>>> >>> Adam Nitenson, B.S. >>> Brain Genomics Lab >>> Massachusetts General Hospital >>> >>> >>> >>> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> >> >> >> > > > Adam Nitenson, B.S. > Brain Genomics Lab > Massachusetts General Hospital > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
