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
>
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