Use something like recon-all -s s600a1001 -i s600a1001.mgz -all
On 05/15/2014 02:55 PM, Dr Sampada Sinha wrote: > Hello Shantanu I tried to set up the Subject directory using this > command and it says the following error: > > Last login: Thu May 15 14:49:50 on ttys000 > dhcp020-222-214:~ sampada$ export FREESURFER_HOME=/Applications/freesurfer > dhcp020-222-214:~ sampada$ source $FREESURFER_HOME/SetUpFreeSurfer.sh > -------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 -------- > Setting up environment for FreeSurfer/FS-FAST (and FSL) > FREESURFER_HOME /Applications/freesurfer > FSFAST_HOME /Applications/freesurfer/fsfast > FSF_OUTPUT_FORMAT nii.gz > SUBJECTS_DIR /Applications/freesurfer/subjects > MNI_DIR /Applications/freesurfer/mni > dhcp020-222-214:~ sampada$ cd '/Users/sampada/Desktop/Vaibhav2/' > dhcp020-222-214:Vaibhav2 sampada$ export SUBJECTS_DIR=$PWD > dhcp020-222-214:Vaibhav2 sampada$ recon-all -s s600a1001.mgz '-all' > mkdir: /Users/sampada/Desktop/Vaibhav2/s600a1001.mgz/scripts: Not a > directory > mkdir: /Users/sampada/Desktop/Vaibhav2/s600a1001.mgz/scripts: Not a > directory > cp: > /Users/sampada/Desktop/Vaibhav2/s600a1001.mgz/scripts/build-stamp.txt: > Not a directory > cat: > /Users/sampada/Desktop/Vaibhav2/s600a1001.mgz/scripts/build-stamp.txt: > Not a directory > INFO: FreeSurfer build stamps do not match > Subject Stamp: > Current Stamp: freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 > INFO: SUBJECTS_DIR is /Users/sampada/Desktop/Vaibhav2 > Actual FREESURFER_HOME /Applications/freesurfer > /Users/sampada/Desktop/Vaibhav2/s600a1001.mgz: Not a directory. > > Will you please let me know where I am going wrong? > > Thanks and regards, > > Sampada > > > On Wed, May 14, 2014 at 8:45 PM, Shantanu Ghosh > <shant...@nmr.mgh.harvard.edu <mailto:shant...@nmr.mgh.harvard.edu>> > wrote: > > 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 <mailto: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 > <mailto: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 > <mailto: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 > <mailto: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 > <mailto: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 > <mailto:gr...@nmr.mgh.harvard.edu> > >> >> >>> >> Phone Number: 617-724-2358 <tel:617-724-2358> > >> >> >>> >> Fax: 617-726-7422 <tel:617-726-7422> > >> >> >>> >> > >> >> >>> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > >> >> >>> >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > >> >> >>> >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://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 > <mailto: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 > <mailto: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 > <mailto:Freesurfer@nmr.mgh.harvard.edu> > >> >> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> >> >>> > >> >> >> _______________________________________________ > >> >> >> Freesurfer mailing list > >> >> >> Freesurfer@nmr.mgh.harvard.edu > <mailto: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 > <mailto: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 > <mailto:Freesurfer@nmr.mgh.harvard.edu> > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto: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 <mailto: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 -- 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
