remove the quotation marks from '-all' and try again e.g. recon-all -s s600a1001.mgz -all
Hth, S. On Thu, May 15, 2014 2:55 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> 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 >> >> 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 >> > _______________________________________________ > 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
