Hello Freesurfer, Thanks Shantanu I was able to convert the .nii to .mgz files . However, about the recon-all command do I run it separately for each .mgz file or run it one time for all .mgz file(which are eight in numbers)? And what command do I use for recon-all? I have tried many but none is working..
Thanks and regards, Sampada On Tue, May 6, 2014 at 11:12 PM, Shantanu Ghosh < shant...@nmr.mgh.harvard.edu> wrote: > sorry > > try: > > cd Users/sampada/Desktop/ > mkdir test > cd test > mri_covert /Users/sampada/Desktop/d2n119495/s400a1001.nii > sampada/Desktop/test/s400a1001.mgz > > Hth, > shantanu > > On Tue, May 6, 2014 11:10 pm, Shantanu Ghosh wrote: > > You don't need the quotation marks in your path > > also, it seems you don't have a directory called > > /Users/sampada/Desktop/test/org > > > > try something like: > > > > cd Users/sampada/Desktop/ > > mkdir test > > cd test > > mri_covert /Users/sampada/Desktop/d2n119495/s400a1001.nii > > sampada/Desktop/test/s400a1001.nii > > > > Hth, > > shantanu > > > > > > On Tue, May 6, 2014 9:50 pm, Dr Sampada Sinha wrote: > >> Hello Shantanu, > >> > >> Many thanks for your reply! This is my exact commandline which I give to > >> free surfer for the 1st of the eight nii files. When i am able to > >> convert > >> this nii to mgz then i will ask how to convert all the eight files at > >> one > >> go. > >> > >> mri_convert '/Users/sampada/Desktop/d2n119495/s400a1001.nii' > >> '/Users/sampada/Desktop/test/mri/org/.mgz' > >> > >> > >> Regards, > >> > >> Sampada > >> > >> > >> On Tue, May 6, 2014 at 6:43 PM, Shantanu Ghosh > >> <shant...@nmr.mgh.harvard.edu > >>> wrote: > >> > >>> can you send your exact mri_convert commandline? > >>> > >>> > >>> On Tue, May 6, 2014 6:11 pm, Dr Sampada Sinha wrote: > >>> > *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 > >>> > >>> > >>> -- > >>> Shantanu Ghosh, Ph.D. > >>> Harvard Medical School & Massachusetts General Hospital > >>> Martinos Center for Biomedical Imaging > >>> -- > >>> Not only is the universe stranger than we think, it is stranger than we > >>> can think. -Werner Heisenberg > >>> > >>> _______________________________________________ > >>> Freesurfer mailing list > >>> Freesurfer@nmr.mgh.harvard.edu > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > -- > > Shantanu Ghosh, Ph.D. > > Harvard Medical School & Massachusetts General Hospital > > Martinos Center for Biomedical Imaging > > -- > > Not only is the universe stranger than we think, it is stranger than we > > can think. -Werner Heisenberg > > > > > > > -- > Shantanu Ghosh, Ph.D. > Harvard Medical School & Massachusetts General Hospital > Martinos Center for Biomedical Imaging > -- > Not only is the universe stranger than we think, it is stranger than we > can think. -Werner Heisenberg > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >
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