Hello freesurfer, thanks for your message. I am doing the recon-all for T1 and T2* structural dataset now I have in all 8 files in the order of (T2>T1>T2>DTI>T@>T2*>T2). I am doing a data analysis of another subject and we have one T1 file s600a1001.mgz. Since my shell is a bash shell, I am running this command for recon-all '-all' process. My two files (T1 and T2*) are in the Vaibhav2 folder. My subject directory is/User/sampada/Desktop/Vaibhav2/s600a1001.mgz and subject id is s600a1001.mgz
sampada$ export FREESURFER_HOME=/Applications/freesurfer dhcp020-222-041:~ sampada$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni dhcp020-223-232:~ sampada$ cd Desktop/Vaibhav2 dhcp020-223-232:Vaibhav2 sampada$ recon-all -s s600a1001.mgz '-all' ERROR: cannot find /Applications/freesurfer/subjects/s600a1001.mgz Even when I make the intermediate directory of mri/orig, its still not recognising the command and shows an error. Thanks and regards, Sampada On Fri, May 9, 2014 at 8:00 PM, Shantanu Ghosh <shant...@nmr.mgh.harvard.edu > wrote: > You should try to run recon_all command with -all flag to run on the > structural T1 dataset. After that you can use the tutorials from the > freesurfer wiki to do a Feat analysis. > > For recon_all you need to specify only the subject and the script > automatically does the rest. Segmentation and parcellation is automatized > (see wiki) > > Hth, > Shantanu > > > On Fri, May 9, 2014 6:26 pm, Dr Sampada Sinha wrote: > > 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 > >> > > > > > -- > 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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