*Hello freesurfer* *Sorry for the personal message Shantanu. *
*I managed to convert my dicom to nifti using mricron software, though had to make some changes to the preferences. * *About the dcmunpack: The user manual on dcmunpack on fs site says that the unpackdcmdir is used only to unpack Siemens dicom files. We use Phillips infinity for our PET scan.* *I am very new to Unix, free surfer and neuroimaging, so couldn't understand what nipy would do...* *My FS is working fine as when I typed tkmedit bert orig.mngz for volume view it was displaying image.* *But the when I tried to convert my .nii files to .mgz format , I get the following error:* Last login: Tue May 6 10:40:32 on ttys000 dhcp020-222-117:~ sampada$ export FREESURFER_HOME=/Applications/freesurfer dhcp020-222-117:~ sampada$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni dhcp020-222-117:~ sampada$ mri_convert '/Users/sampada/Desktop/d2n119495/s400a1001.nii' '/Users/sampada/Desktop/test/mri/org/.mgz' mri_convert /Users/sampada/Desktop/d2n119495/s400a1001.nii /Users/sampada/Desktop/test/mri/org/.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /Users/sampada/Desktop/d2n119495/s400a1001.nii... TR=7.10, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.0268034, -0.99958, 0.0110098) j_ras = (0.0381548, 0.0120287, 0.999199) k_ras = (0.998912, 0.0263618, -0.0384612) writing to /Users/sampada/Desktop/test/mri/org/.mgz... mghWrite(/Users/sampada/Desktop/test/mri/org/.mgz, -1): could not open file ERROR: failure writing /Users/sampada/Desktop/test/mri/org/.mgz *Will you please let me know what command I need to use to mri convert and recon all of my files? * I* have 8 .nii files (in the order of T1>T2>T1>T2>DTI>T1(resting stage)>T2 (in the order of the acquisition acquired at the time of experiment).* *Thanks and regards,* *Sampada* On Tue, Apr 29, 2014 at 12:17 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu > wrote: > > Have you tried using dcmunpack? You run it twice, once without any > output to get a list of runs in the folder. The 2nd with how you want > the data converted. Run it with --help to get more info > doug > > On 04/28/2014 06:55 PM, Dr Sampada Sinha wrote: > > Hello I have only recently started the fmri data analysis and I > > downloaded freesurfer point by point from martinos site and > > incorporated the license file as well into the Applications/freesurfer > > directory. I have run into the first problem and that is of data > > conversion. My file is in dcm format and I have 11,000 dcm files to > > convert. However, before I was using Jamaan Alghamadi created gui and > > it is not able to convert the mri dcm files. Then I shifted to UNIX > > and again it is saying error. > > > > My file is on the desktop and I have given it subject id as Grace. My > > directory to the dcm file is '/Users/sampada/desktop/Grace. > > > > My terminal look like this before I proceed with the file conversion > > > > Last login: Mon Apr 28 15:10:13 on ttys001 > > > > dhcp020-223-179:~ sampada$ export > FREESURFER_HOME=/Applications/freesurfer > > > > dhcp020-223-179:~ sampada$ source $FREESURFER_HOME/SetUpFreeSurfer.sh > > > > -------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 -------- > > > > Setting up environment for FreeSurfer/FS-FAST (and FSL) > > > > FREESURFER_HOME /Applications/freesurfer > > > > FSFAST_HOME /Applications/freesurfer/fsfast > > > > FSF_OUTPUT_FORMAT nii.gz > > > > SUBJECTS_DIR /Applications/freesurfer/subjects > > > > MNI_DIR /Applications/freesurfer/mni > > > > > > > > Will anyone please let me know what I am doing wrong? I will be very > > grateful for any input. > > > > > > Thanks and regards, > > > > > > Sampada > > Senior research support specialist > > Molecular and neuroimaging department > > Department of Psychiatry > > 451, biomedical research building > > University at Buffalo (south campus) > > Buffalo, NY-14216 > > > > > > > > > > > > _______________________________________________ > > 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. > >
_______________________________________________ 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.
