Hello, I am a new user of the freesurfer platform. I am a high school junior conducting research on brain MRI scans and came across this wonderful platform. However I am not very sure how to proceed with my research - I am trying to find the whole brain Gyrification Index, which I did manually on a different software called ImageJ using multiple image scans of brain slices. Will freesurfer be able to analyze brain scan images and provide a whole brain GI or does it only analyse and provide local GI which is what I found through some forums? If so, are there any tutorials to learn how to do that? Do I need any other software like MatLab to find out the Gyrification Index?
Thank you in advance! Ankita
Hi Ankita
sure, we compute GI. You need to get a good T1-weighted scan with voxels that are about 1mm isotropic, then run it through our recon-all script
cheers Bruce On Mon, 18 Jan 2016, Arindam Chatterjee wrote:
Hello,I am a new user of the freesurfer platform. I am a high school junior conducting research on brain MRI scans and came across this wonderful platform. However I am not very sure how to proceed with my research - I am trying to find the whole brain Gyrification Index, which I did manually on a different software called ImageJ using multiple image scans of brain slices. Will freesurfer be able to analyze brain scan images and provide a whole brain GI or does it only analyse and provide local GI which is what I found through some forums? If so, are there any tutorials to learn how to do that? Do I need any other software like MatLab to find out the Gyrification Index?
Thank you in advance! Ankita
Hi Bruce, Thank you for your prompt response! Sorry for my novice questions - does T1-weighted scan with voxels have to be in a specific format like jpg, dicom or mesh format?
Ankita
On Mon, Jan 18, 2016 at 1:59 PM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Ankita
sure, we compute GI. You need to get a good T1-weighted scan with voxels that are about 1mm isotropic, then run it through our recon-all script
cheers Bruce On Mon, 18 Jan 2016, Arindam Chatterjee wrote:
Hello,I am a new user of the freesurfer platform. I am a high school
junior
conducting research on brain MRI scans and came across this wonderful platform. However I am not very sure how to proceed with my research - I
am
trying to find the whole brain Gyrification Index, which I did manually
on a
different software called ImageJ using multiple image scans of brain
slices.
Will freesurfer be able to analyze brain scan images and provide a whole brain GI or does it only analyse and provide local GI which is what I
found
through some forums? If so, are there any tutorials to learn how to do
that?
Do I need any other software like MatLab to find out the Gyrification
Index?
Thank you in advance! Ankita
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Hi Ankita
dicom is perfect. Just give recon-all a single file from the correct dicom series and it will figure out the rest of them Bruce On Mon, 18 Jan 2016, Arindam Chatterjee wrote:
Hi Bruce, Thank you for your prompt response! Sorry for my novice questions - does T1-weighted scan with voxels have to be in a specific format like jpg, dicom or mesh format? Ankita
On Mon, Jan 18, 2016 at 1:59 PM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Ankita
sure, we compute GI. You need to get a good T1-weighted scan with voxels that are about 1mm isotropic, then run it through our recon-all script cheers Bruce On Mon, 18 Jan 2016, Arindam Chatterjee wrote: > Hello,I am a new user of the freesurfer platform. I am a high school junior > conducting research on brain MRI scans and came across this wonderful > platform. However I am not very sure how to proceed with my research - I am > trying to find the whole brain Gyrification Index, which I did manually on a > different software called ImageJ using multiple image scans of brain slices. > Will freesurfer be able to analyze brain scan images and provide a whole > brain GI or does it only analyse and provide local GI which is what I found > through some forums? If so, are there any tutorials to learn how to do that? > Do I need any other software like MatLab to find out the Gyrification Index? > > Thank you in advance! > Ankita > > _______________________________________________ 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.
Great! Thank you for the prompt response and the pointers. I am going through the tutorials now to learn how to use freesurfer and will try out what you suggested.
Thanks! Ankita
On Mon, Jan 18, 2016 at 2:26 PM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Ankita
dicom is perfect. Just give recon-all a single file from the correct dicom series and it will figure out the rest of them Bruce On Mon, 18 Jan 2016, Arindam Chatterjee wrote:
Hi Bruce, Thank you for your prompt response! Sorry for my novice questions - does T1-weighted scan with voxels have to be in a specific format like jpg,
dicom
or mesh format? Ankita
On Mon, Jan 18, 2016 at 1:59 PM Bruce Fischl <fischl@nmr.mgh.harvard.edu
wrote: Hi Ankita
sure, we compute GI. You need to get a good T1-weighted scan with voxels that are about 1mm isotropic, then run it through our recon-all script cheers Bruce On Mon, 18 Jan 2016, Arindam Chatterjee wrote: > Hello,I am a new user of the freesurfer platform. I am a high school junior > conducting research on brain MRI scans and came across this wonderful > platform. However I am not very sure how to proceed with my research - I am > trying to find the whole brain Gyrification Index, which I did manually on a > different software called ImageJ using multiple image scans of brain slices. > Will freesurfer be able to analyze brain scan images and provide a whole > brain GI or does it only analyse and provide local GI which is what I found > through some forums? If so, are there any tutorials to learn how to do that? > Do I need any other software like MatLab to find out the Gyrification Index? > > Thank you in advance! > Ankita > > _______________________________________________ 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
I am still trying to find the right command line approach to running recon -all. I am sure this is documented somewhere - any pointers?
Do I have to set any environment variables like FREESURFER_HOME etc.for each terminal I try to run freesurfer? Also, can my images be on Google Drive when I try to run recon-all?
Thanks! Ankita
On Mon, Jan 18, 2016 at 2:28 PM Arindam Chatterjee achatter01@gmail.com wrote:
Great! Thank you for the prompt response and the pointers. I am going through the tutorials now to learn how to use freesurfer and will try out what you suggested.
Thanks! Ankita
On Mon, Jan 18, 2016 at 2:26 PM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Ankita
dicom is perfect. Just give recon-all a single file from the correct dicom series and it will figure out the rest of them Bruce On Mon, 18 Jan 2016, Arindam Chatterjee wrote:
Hi Bruce, Thank you for your prompt response! Sorry for my novice questions - does T1-weighted scan with voxels have to be in a specific format like jpg,
dicom
or mesh format? Ankita
On Mon, Jan 18, 2016 at 1:59 PM Bruce Fischl <
fischl@nmr.mgh.harvard.edu>
wrote: Hi Ankita
sure, we compute GI. You need to get a good T1-weighted scan with voxels that are about 1mm isotropic, then run it through our recon-all script cheers Bruce On Mon, 18 Jan 2016, Arindam Chatterjee wrote: > Hello,I am a new user of the freesurfer platform. I am a high school junior > conducting research on brain MRI scans and came across this wonderful > platform. However I am not very sure how to proceed with my research - I am > trying to find the whole brain Gyrification Index, which I did manually on a > different software called ImageJ using multiple image scans of brain slices. > Will freesurfer be able to analyze brain scan images and provide a whole > brain GI or does it only analyse and provide local GI which is what I found > through some forums? If so, are there any tutorials to learn how to do that? > Do I need any other software like MatLab to find out the Gyrification Index? > > Thank you in advance! > Ankita > > _______________________________________________ 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
freesurfer@nmr.mgh.harvard.edu
-
Arindam Chatterjee -
Bruce Fischl