I wonder if anybody could help please?
1. I have converted DICOM to NIFTI and then when I try to apply mri_convert command to change it to .mgz; i cant locate the converted file!
2. When I try and create directories of the patient within subjects subfolder; it says ‘permission denied’. I then used the sudo command to prepare directories.But then i cant move .mgz file (which is not found) into the mri subfolder of the patient.
3. Thus i cannot apply the command recon-all.
Is there any easy way to get the DICOM to load on to freesurfer without all this hassle?
I am grateful for your help.
Anand
Hi Anand
you will need write permissions to a dir, after which you can just run:
recon-all \ -i <path to a single dicom file in the right series> \ -s <subject id> \ -sd <dir for all your subjects> \ -all
No need to convert to nifti or anything cheers Bruce
On Sat, 10 Dec 2016, anand iyer wrote:
I wonder if anybody could help please?
- I have converted DICOM to NIFTI and then when I try to apply mri_convert
command to change it to .mgz; i cant locate the converted file!
- When I try and create directories of the patient within subjects
subfolder; it says ‘permission denied’. I then used the sudo command to prepare directories.But then i cant move .mgz file (which is not found) into the mri subfolder of the patient.
- Thus i cannot apply the command recon-all.
Is there any easy way to get the DICOM to load on to freesurfer without all this hassle?
I am grateful for your help.
Anand
Thanks for your prompt reply.
I still cant figure it out.
All the DICOM files for T1 brain volume are on a folder on the desktop. How do i get permission to a dir? I’d be grateful for your reply.
Thanks,
Anand Anand Iyer
On 10 Dec 2016, at 22:23, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Anand
you will need write permissions to a dir, after which you can just run:
recon-all \ -i <path to a single dicom file in the right series> \ -s <subject id> \ -sd <dir for all your subjects> \ -all
No need to convert to nifti or anything cheers Bruce
On Sat, 10 Dec 2016, anand iyer wrote:
I wonder if anybody could help please?
- I have converted DICOM to NIFTI and then when I try to apply mri_convert
command to change it to .mgz; i cant locate the converted file! 2. When I try and create directories of the patient within subjects subfolder; it says ‘permission denied’. I then used the sudo command to prepare directories.But then i cant move .mgz file (which is not found) into the mri subfolder of the patient. 3. Thus i cannot apply the command recon-all. Is there any easy way to get the DICOM to load on to freesurfer without all this hassle? I am grateful for your help. Anand
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.
Hi Anand
I can't help you getting permission - that you have to sort out with your IT staff or whomever owns the desktop
cheers Bruce On Sat, 10 Dec 2016, anand iyer wrote:
Thanks for your prompt reply. I still cant figure it out.
All the DICOM files for T1 brain volume are on a folder on the desktop. How do i get permission to a dir? I’d be grateful for your reply.
Thanks,
Anand Anand Iyer
On 10 Dec 2016, at 22:23, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:Hi Anand
you will need write permissions to a dir, after which you can just run:
recon-all \ -i <path to a single dicom file in the right series> \ -s <subject id> \ -sd <dir for all your subjects> \ -all
No need to convert to nifti or anything cheers Bruce
On Sat, 10 Dec 2016, anand iyer wrote:
I wonder if anybody could help please? 1. I have converted DICOM to NIFTI and then when I try to apply mri_convert command to change it to .mgz; i cant locate the converted file! 2. When I try and create directories of the patient within subjects subfolder; it says ‘permission denied’. I then used the sudo command to prepare directories.But then i cant move .mgz file (which is not found) into the mri subfolder of the patient. 3. Thus i cannot apply the command recon-all. Is there any easy way to get the DICOM to load on to freesurfer without all this hassle? I am grateful for your help. Anand
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.
Thanks.
I’m not that IT savvy; I own my desktop, but just cant figure this software out. Im not a software guy, but a doctor!
Apologies for wasting your time!
Anand Iyer
On 10 Dec 2016, at 22:50, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Anand
I can't help you getting permission - that you have to sort out with your IT staff or whomever owns the desktop
cheers Bruce On Sat, 10 Dec 2016, anand iyer wrote:
Thanks for your prompt reply. I still cant figure it out. All the DICOM files for T1 brain volume are on a folder on the desktop. How do i get permission to a dir? I’d be grateful for your reply. Thanks, Anand Anand Iyer
On 10 Dec 2016, at 22:23, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:Hi Anand you will need write permissions to a dir, after which you can just run: recon-all \ -i <path to a single dicom file in the right series> \ -s <subject id> \ -sd <dir for all your subjects> \ -all No need to convert to nifti or anything cheers Bruce On Sat, 10 Dec 2016, anand iyer wrote:
I wonder if anybody could help please? 1. I have converted DICOM to NIFTI and then when I try to apply mri_convert command to change it to .mgz; i cant locate the converted file! 2. When I try and create directories of the patient within subjects subfolder; it says ‘permission denied’. I then used the sudo command to prepare directories.But then i cant move .mgz file (which is not found) into the mri subfolder of the patient. 3. Thus i cannot apply the command recon-all. Is there any easy way to get the DICOM to load on to freesurfer without all this hassle? I am grateful for your help. Anand
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
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.
no worries. It's just that I literally can't help you with permissions issues. That's a local setup issue that you need to sort out there. Bruce
On Sat, 10 Dec 2016, anand iyer wrote:
Thanks. I’m not that IT savvy; I own my desktop, but just cant figure this software out. Im not a software guy, but a doctor!
Apologies for wasting your time!
Anand Iyer
On 10 Dec 2016, at 22:50, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:Hi Anand
I can't help you getting permission - that you have to sort out with your IT staff or whomever owns the desktop
cheers Bruce On Sat, 10 Dec 2016, anand iyer wrote:
Thanks for your prompt reply. I still cant figure it out. All the DICOM files for T1 brain volume are on a folder on the desktop. How do i get permission to a dir? I’d be grateful for your reply. Thanks, Anand Anand Iyer On 10 Dec 2016, at 22:23, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Anand you will need write permissions to a dir, after which you can just run: recon-all \ -i <path to a single dicom file in the right series> \ -s <subject id> \ -sd <dir for all your subjects> \ -all No need to convert to nifti or anything cheers Bruce On Sat, 10 Dec 2016, anand iyer wrote: I wonder if anybody could help please? 1. I have converted DICOM to NIFTI and then when I try to apply mri_convert command to change it to .mgz; i cant locate the converted file! 2. When I try and create directories of the patient within subjects subfolder; it says ‘permission denied’. I then used the sudo command to prepare directories.But then i cant move .mgz file (which is not found) into the mri subfolder of the patient. 3. Thus i cannot apply the command recon-all. Is there any easy way to get the DICOM to load on to freesurfer without all this hassle? I am grateful for your help. Anand _______________________________________________ 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
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@nmr.mgh.harvard.edu
-
anand iyer -
Bruce Fischl