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 _______________________________________________ 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.
