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:~
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
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
You are using with the extension .mgz thats wrong
try:
recon-all -s s600a1001 -all
and as Markus suggests, use the -s flag for the subject directory
Hth,
Es
On Thu, May 15, 2014 6:00 pm, Dr Sampada Sinha wrote:
Hello Shantanu,
Thanks for your mail, but the error is still the same:
Last
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
(T2T1T2DTIT@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
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,
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
Hi Sampada
the recon-all script is designed to analyze T1-weighted structural data.
Once that has been done, it can be used to facilitate fMRI analysis. Is
that what you are trying to do? What are the 8 volumes?
cheers
Bruce
On Fri, 9 May 2014, Dr Sampada Sinha wrote:
Hello Freesurfer,
*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
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. *
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
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,
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
You could also try the nipy version. works real well with Snow Leopard OS
shantanu
On Mon, April 28, 2014 9:09 pm, Shantanu Ghosh wrote:
Hi Sampada,
Please cc the freesurfer list when answering/asking questions so others
can answer too. And also people with similar issues will benefit from
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
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
You can convert Dicom using MRICroN with the dcm2nii utility
shantanu
On Mon, April 28, 2014 6:55 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
Hello Shantanu,
Thanks for your reply.I tried using that as well. And it says that the file
is only 'read' file. I used chmod on unix but still its not working with
dcm2nii. Interstingly, when I used mriconvert software for this,it
converted all the dcm files to .img/.hdr files. This process
Hi Sampada,
Please cc the freesurfer list when answering/asking questions so others
can answer too. And also people with similar issues will benefit from the
discussion.
see inline for my responses.
Hth,
shantanu
On Mon, April 28, 2014 8:27 pm, Dr Sampada Sinha wrote:
Hello Shantanu,
Thanks
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