You should set your SUBJECTS_DIR variable to the directory with all the subjects. Edit the .bashrc/.tcshrc/.cshrc by replacing the current one with SUBJECTS_DIR /User/sampada/Desktop/Vaibhav2/
and then run recon-all S. On Wed, May 14, 2014 7:47 pm, Dr Sampada Sinha wrote: > 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 >> > _______________________________________________ > 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
