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 secondsubject, 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 greve@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 greve@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
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 secondsubject, 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 greve@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 greve@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
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 secondsubject, 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 > greve@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 greve@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 greve@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@nmr.mgh.harvard.edu
-
Adam Nitenson -
Douglas N Greve