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 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 resulted in eight folders (in .img/.hdr format) 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). Is there any special command you are using to convert those files Shantanu?
You can edit dcm2nii.ini file using any text editor after it is created automatically (by running dcm2nii for the first time). It operates like a shell program and can be run from your analysis directory by sourcing it first.
If you look at the dcm2nii file you can use custom settings. To get the output nii as a single file set the SingleNIIFile=1 and 4D=1, otherwise by default you get the img/hdr pairs
If further you want nii.gz instead of nii files, use Gzip=1 setting
If this doesn't work, you could use the Windows version to convert with the same settings that I describe above.
If yes, will you please let me know? Where do you keep your dcm files (iyou don't mind me asking that)? I tried changing the location from Desktop to Applications/freesurfer as well, but its still not working.
The dcm files can be anywhere, you have to source them correctly by providing the correct path. Or drag/drop into the window if you are using the gui.
Thanks and regards,
Sampada
On Mon, Apr 28, 2014 at 7:00 PM, Shantanu Ghosh < shantanu@nmr.mgh.harvard.edu> wrote:
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 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
-- 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
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.
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 the discussion.
see inline for my responses.
Hth, shantanu
On Mon, April 28, 2014 8:27 pm, Dr Sampada Sinha wrote:
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 resulted in eight folders (in .img/.hdr format) 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). Is there any special command you are using to convert those files Shantanu?
You can edit dcm2nii.ini file using any text editor after it is created automatically (by running dcm2nii for the first time). It operates like a shell program and can be run from your analysis directory by sourcing it first.
If you look at the dcm2nii file you can use custom settings. To get the output nii as a single file set the SingleNIIFile=1 and 4D=1, otherwise by default you get the img/hdr pairs
If further you want nii.gz instead of nii files, use Gzip=1 setting
If this doesn't work, you could use the Windows version to convert with the same settings that I describe above.
If yes, will you please let me know? Where do you keep your dcm files (iyou don't mind me asking that)? I tried changing the location from Desktop to Applications/freesurfer as well, but its still not working.
The dcm files can be anywhere, you have to source them correctly by providing the correct path. Or drag/drop into the window if you are using the gui.
Thanks and regards,
Sampada
On Mon, Apr 28, 2014 at 7:00 PM, Shantanu Ghosh < shantanu@nmr.mgh.harvard.edu> wrote:
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 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
-- 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
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.
-- 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@nmr.mgh.harvard.edu
-
Shantanu Ghosh