External Email - Use Caution
Hi,
I try to extract FA values from the FSL FA skeleton using the freesurfer aparc.a2009s+aseg+2mm parcellations.
I did the following:
1. Recon-all to obtain --> aparc.a2009s+aseg+2mm
2. TBSS in FSL to obtain --> all_FA_skeletonised
3. Tbss_deproject to split up all_FA_skeletonised into individual skeletons (native space) (*_FA_FA_all_FA_skeletonised.nii.gz)
4. Non-linear transformation of aparc.a2009s+aseg+2mm to subjects' native space (parc2dwi.nii.gz)
5. Creating binary mask for each subjects FA skeleton to exclude 0 voxels (*_FA_skeleton_mask.nii.gz)
6. Extracting FA values using mri_segstats with the following command:
cd subj1/ mri_segstats \ --seg mri/parc2dwi.nii.gz \ --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt \ --i skeletons/SPN01_CMH_0001_01_FA_FA_all_FA_skeletonised.nii.gz \ --mask skeletons/SPN01_CMH_0001_01_FA_skeleton_mask.nii.gz \ --excludeid 0 \ --sum skeletons_FA.stats
The FA values I obtain are around 0.1 which is highly unlikely, especially for regions such as the corpus callosum. Is there some obvious error in my approach? Or can someone recommend a different approach? I would be very grateful for some help!
Thanks, Steph
Stephanie Winkelbeiner, MSc Research Coordinator Psychiatry Research Zucker Hillside Hospital 75-59 263 Street Glen Oaks, NY 11004 Tel: (718) 470-4588 Email: swinkelbei@northwell.edumailto:swinkelbei@northwell.edu
Northwell Health Visit us at Northwell.eduhttp://northwell.edu/
The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege.
Have you checked if the registered segmentation and the FA map align correctly in freeview?
On Nov 23, 2018 1:27 PM, "Winkelbeiner, Stephanie A" Swinkelbei@northwell.edu wrote:
External Email - Use Caution Hi,
I try to extract FA values from the FSL FA skeleton using the freesurfer aparc.a2009s+aseg+2mm parcellations.
I did the following:
1. Recon-all to obtain --> aparc.a2009s+aseg+2mm
2. TBSS in FSL to obtain --> all_FA_skeletonised
3. Tbss_deproject to split up all_FA_skeletonised into individual skeletons (native space) (*_FA_FA_all_FA_skeletonised.nii.gz)
4. Non-linear transformation of aparc.a2009s+aseg+2mm to subjects’ native space (parc2dwi.nii.gz)
5. Creating binary mask for each subjects FA skeleton to exclude 0 voxels (*_FA_skeleton_mask.nii.gz)
6. Extracting FA values using mri_segstats with the following command:
cd subj1/ mri_segstats \ --seg mri/parc2dwi.nii.gz \ --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt \ --i skeletons/SPN01_CMH_0001_01_FA_FA_all_FA_skeletonised.nii.gz \ --mask skeletons/SPN01_CMH_0001_01_FA_skeleton_mask.nii.gz \ --excludeid 0 \ --sum skeletons_FA.stats
The FA values I obtain are around 0.1 which is highly unlikely, especially for regions such as the corpus callosum. Is there some obvious error in my approach? Or can someone recommend a different approach? I would be very grateful for some help!
Thanks, Steph
Stephanie Winkelbeiner, MSc Research Coordinator Psychiatry Research Zucker Hillside Hospital 75-59 263 Street Glen Oaks, NY 11004 Tel: (718) 470-4588 Email: swinkelbei@northwell.edumailto:swinkelbei@northwell.edu
Northwell Health Visit us at Northwell.eduhttp://northwell.edu/
The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege.
freesurfer@nmr.mgh.harvard.edu
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Winkelbeiner, Stephanie A -
Yendiki, Anastasia