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
