You're dicom file is jpeg compressed which FS version 5.3 does not handle. Get the two files from below
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/dcmdjpeg.fs ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_convert Copy into $FREESURFER_HOME/bin (make a backup of mri_convert first) rehash and try again doug On 04/01/2015 01:14 PM, A-reum Min wrote: > Hello > My name is areum. > I've got a problem while freesurfer subjects reconstruction. > I have 37 subjects(control+patient) data. > Number of each subject dicom file is 244. > my FREESURFER_HOME is /usr/local/freesurfer > my SUBJECTS_DIR is /usr/local/freesurfer/subjects/PISA_SPGR > (K-1 image is each subjects file(contained dicom file), K-3 image is > subject(no.1)'s 244 dicom file.) > When i type > [areum@localhost 1]# recon-all -i > /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm -i > /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071580.dcm -all -s subj001 > (subj001 means that contain the first subjects reconstructed data) > then, error occured.. > > Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects/PISA_SPGR > Actual FREESURFER_HOME /usr/local/freesurfer > Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 > 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux > /usr/local/freesurfer/subjects/PISA_SPGR/subj001 > mri_convert /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm > /usr/local/freesurfer/subjects/PISA_SPGR/subj001/mri/orig/001.mgz > mri_convert /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm > /usr/local/freesurfer/subjects/PISA_SPGR/subj001/mri/orig/001.mgz > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > reading from /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm... > Starting DICOMRead2() > dcmfile = /usr/local/freesurfer/subjects/PISA_SPGR/1/I0071579.dcm > dcmdir = /usr/local/freesurfer/subjects/PISA_SPGR/1 > Ref Series No = 3 > Found 246 files, checking for dicoms > Found 244 dicom files in series. > First Sorting > Computing Slice Direction > Vs: -0.8 0 0 > Vs: -1 0 0 > Second Sorting > Counting frames > nframes = 1 > nslices = 244 > ndcmfiles = 244 > PE Dir = ROW (dicom read) > TransferSyntaxUID: --1.2.840.10008.1.2.4.70-- > ERROR: the pixel data cannot be loaded as it is JPEG compressed. > (Transfer Syntax UID: 1.2.840.10008.1.2.4.70) > jpegUID: --1.2.840.10008.1.2.4-- > Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 > 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux > recon-all -s subj001 exited with ERRORS at Wed Apr 1 02:17:23 JST 2015 > For more details, see the log file > /usr/local/freesurfer/subjects/PISA_SPGR/subj001/scripts/recon-all.log > To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > * Question 1.* > Is the SUBJECTS_DIR correct path? > (PISA_SPGR file contained 37 each subjects file) > * Question 2.* > I think that '-i' converted dicom file to mgz format. So, i type the > recon-all -i /first of a collection of 244 files directory -i /second > of a collection of 244 files directory -all -s subj001 ... is it right? > If i type the top two images, then automatically 244 images > reconstruction? > I have 37 subjects files (K-1 image) > > * Question 3.* > If i recon my each subjects data, then do I have to change the > path(SUBJECTS_DIR) each time to change the subject file? > ex) file number (1) is subject1's dicom, file number (2) is subject2' > dicom file so, am i just finished (1)data , do i change my > SUBJECTS_DIR path for recon to subjets data(2) ? ) > * Question 4.* > As you can see that K-6 image is subject dicom jpeg... > can i use this one? or convert another format image? > > > _______________________________________________ > 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ 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.
