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 <shantanu@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 < shantanu@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 <shantanu@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 > > <greve@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 > >> greve@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