[Freesurfer] ERROR: bits = 0 not supported
Hi, I am preprocessing my fMRI data acquired with Philips. when I using the command 'dcmunpack -src . -targ sess01 -run 101 bold nii f.nii .' The error occurred likes below: Found 31 total files. Found 12 unique series: 0 101 301 401 501 601 701 801 901 1001 1101 1201 Subject xxx Date xxx Time 110223 Institution x. 0 Survey unknown unknown unknown unknown unknown unknown ./PS_0002 101 Survey unknown unknown unknown unknown unknown 140 ./XX_0003 301 T1W_3D_TFE_ref unknown unknown unknown unknown unknown 190 ./IM_0004 401 FE_EPI unknown unknown unknown unknown unknown 2835 ./XX_0007 501 FE_EPI_EX1 unknown unknown unknown unknown unknown 2835 ./IM_0008 601 FE_EPI_EX2 unknown unknown unknown unknown unknown 2835 ./IM_0011 701 FE_EPI_EX3 unknown unknown unknown unknown unknown 2835 ./IM_0013 801 FE_EPI_EX4 unknown unknown unknown unknown unknown 2835 ./XX_0016 901 FE_EPI_EX5 unknown unknown unknown unknown unknown 2835 ./XX_0018 1001 FE_EPI_EX6 unknown unknown unknown unknown unknown 2835 ./IM_0019 1101 FE_EPI_EX7 unknown unknown unknown unknown unknown 2835 ./XX_0022 1201 FE_EPI_EX8 unknown unknown unknown unknown unknown 2835 ./XX_0024 mri_convert ./XX_0003 ./bold/101/f.nii --nskip 0 --ndrop 0 nskip = 0 ndrop = 0 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from ./XX_0003... Starting DICOMRead2() dcmfile = ./XX_0003 dcmdir = . WARNING: tag image orientation not found in ./XX_0003 Ref Series No = 101 ERROR: bits = 0 not supported. My os is Linux 16.04 and the Freesurfer's version is 5.3.___ 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.
[Freesurfer] Fwd: FreeSurfer Error: bits = 0 not supported.
-- Forwarded message -- From: Jordi Delgado Date: 2009/10/30 Subject: FreeSurfer Error: bits = 0 not supported. To: freesurfer@nmr.mgh.harvard.edu Hello*, * My name is Jordi Delgado, I work with FreeSurfer on a cluster of machines. Yesterday I sent some subjects to process and for three of them I recived in the Output Log from PBS the following message: * Subject Stamp: freesurfer-Linux-centos4-stable-pub-v4.3.1 Current Stamp: freesurfer-Linux-centos4-stable-pub-v4.3.1 INFO: SUBJECTS_DIR is /nfs/arpon/PROJCT/FXTAS/proc/FREESURFER/OutPBS Actual FREESURFER_HOME /nfs/arpon/SOFTWR/freesurfer Linux td172.pic.es 2.6.18-128.7.1.el5 #1 SMP Mon Aug 24 08:12:52 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux /nfs/arpon/PROJCT/FXTAS/proc/FREESURFER/OutPBS/PCC_030 mri_convert /nfs/arpon/PROJCT/FXTAS/orig/DICOM/T13D/PCC_030/PCC_030_0001 /nfs/arpon/PROJCT/FXTAS/proc/FREESURFER/OutPBS/PCC_030/mri/orig/001.mgz mri_convert /nfs/arpon/PROJCT/FXTAS/orig/DICOM/T13D/PCC_030/PCC_030_0001 /nfs/arpon/PROJCT/FXTAS/proc/FREESURFER/OutPBS/PCC_030/mri/orig/001.mgz $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from /nfs/arpon/PROJCT/FXTAS/orig/DICOM/T13D/PCC_030/PCC_030_0001... Starting DICOMRead2() dcmfile = /nfs/arpon/PROJCT/FXTAS/orig/DICOM/T13D/PCC_030/PCC_030_0001 dcmdir = /nfs/arpon/PROJCT/FXTAS/orig/DICOM/T13D/PCC_030 WARNING: tag ImageNumber not found WARNING: tag image orientation not found Ref Series No = 301 ERROR: bits = 0 not supported. Send email to freesurfer@nmr.mgh.harvard.edu Linux 2.6.18-128.7.1.el5 #1 SMP Mon Aug 24 08:12:52 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Thu Oct 29 18:26:01 CET 2009* After revising the freesurfer implementation and verify that other subjects have been processed correctly I noted that three subjects start their slices numeration with 0001 up to 0172 and the rest started (the correctly finished subjects) by 0002 up to 0171. So I searched this error in the freeSurfer wiki and google and I didn't found anything. What is happening? Is an image problem? Thank you in advance, -- Jordi Delgado Mengual PIC (Port d'Informació Científica) Campus UAB, Edificio D E-08193 Bellaterra, Barcelona Tel: +34 93 581 33 22 Fax: +34 93 581 41 10 http://www.pic.es Avis - Aviso - Legal Notice: http://www.ifae.es/legal.html -- Jordi Delgado Mengual PIC (Port d'Informació Científica) Campus UAB, Edificio D E-08193 Bellaterra, Barcelona Tel: +34 93 581 33 22 Fax: +34 93 581 41 10 http://www.pic.es Avis - Aviso - Legal Notice: http://www.ifae.es/legal.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Fwd: FreeSurfer Error: bits = 0 not supported.
Hi Jordi, does this happen if you run it on a local machine? Is it repeatable? Where did you get the dicom from? cheers Bruce On Fri, 30 Oct 2009, Jordi Delgado wrote: > -- Forwarded message -- > From: Jordi Delgado > Date: 2009/10/30 > Subject: FreeSurfer Error: bits = 0 not supported. > To: freesurfer@nmr.mgh.harvard.edu > > > Hello*, > * > My name is Jordi Delgado, I work with FreeSurfer on a cluster of machines. > Yesterday I sent some subjects to process and for three of them I recived in > the Output Log from PBS the following message: > * > Subject Stamp: freesurfer-Linux-centos4-stable-pub-v4.3.1 > Current Stamp: freesurfer-Linux-centos4-stable-pub-v4.3.1 > INFO: SUBJECTS_DIR is /nfs/arpon/PROJCT/FXTAS/proc/FREESURFER/OutPBS > Actual FREESURFER_HOME /nfs/arpon/SOFTWR/freesurfer > Linux td172.pic.es 2.6.18-128.7.1.el5 #1 SMP Mon Aug 24 08:12:52 EDT 2009 > x86_64 x86_64 x86_64 GNU/Linux > /nfs/arpon/PROJCT/FXTAS/proc/FREESURFER/OutPBS/PCC_030 > > mri_convert /nfs/arpon/PROJCT/FXTAS/orig/DICOM/T13D/PCC_030/PCC_030_0001 > /nfs/arpon/PROJCT/FXTAS/proc/FREESURFER/OutPBS/PCC_030/mri/orig/001.mgz > > mri_convert /nfs/arpon/PROJCT/FXTAS/orig/DICOM/T13D/PCC_030/PCC_030_0001 > /nfs/arpon/PROJCT/FXTAS/proc/FREESURFER/OutPBS/PCC_030/mri/orig/001.mgz > $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ > reading from /nfs/arpon/PROJCT/FXTAS/orig/DICOM/T13D/PCC_030/PCC_030_0001... > Starting DICOMRead2() > dcmfile = /nfs/arpon/PROJCT/FXTAS/orig/DICOM/T13D/PCC_030/PCC_030_0001 > dcmdir = /nfs/arpon/PROJCT/FXTAS/orig/DICOM/T13D/PCC_030 > WARNING: tag ImageNumber not found > WARNING: tag image orientation not found > Ref Series No = 301 > ERROR: bits = 0 not supported. > Send email to freesurfer@nmr.mgh.harvard.edu > Linux 2.6.18-128.7.1.el5 #1 SMP Mon Aug 24 08:12:52 EDT 2009 x86_64 x86_64 > x86_64 GNU/Linux > > recon-all exited with ERRORS at Thu Oct 29 18:26:01 CET 2009* > > After revising the freesurfer implementation and verify that other subjects > have been processed correctly I noted that three subjects start their slices > numeration with 0001 up to 0172 and the rest started (the correctly finished > subjects) by 0002 up to 0171. So I searched this error in the freeSurfer > wiki and google and I didn't found anything. What is happening? Is an image > problem? > > Thank you in advance, > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
