Hi Doug, That did the trick! Thanks so much!
-Adam > 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 > > > 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 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.
