Re: [Freesurfer] [EXTERNAL] Re: extracting FA from FA_skeletonised with freesurfer parcellation
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Hi Anastasia,
I have checked and they do align. However the freesurfer parcels naturally cover more of the brain than the FA skeletons. I was wondering if this was the problem?
Therefore I added a binary mask of the FA skeletons.
I also tried subtracting the parcels from the FA skeletons with fslmaths to make sure that only the area of the skeleton is read out. But that doesn't give convincing results either.
Anyone having other suggestions?
Thanks, Steph
Sent from my Samsung Galaxy smartphone.
-------- Original message -------- From: "Yendiki, Anastasia" AYENDIKI@mgh.harvard.edu Date: 23/11/18 17:50 (GMT-05:00) To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [EXTERNAL] Re: [Freesurfer] extracting FA from FA_skeletonised with freesurfer parcellation
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: 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/
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Dear Stephanie
what happens with the FA values when you
1. use all_FA map instead of only the skeletonised map (all_FA_skeletonised)
2. did you check whether mri_segstats computes the average while simultaneously excludes voxels of the mask where no skeleton is defined, e.g. does fslstats reports similar low FA values when you used the -M option?
Good luck Cheers Jürgen
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On 25 Nov 2018, at 14:41, Winkelbeiner, Stephanie A Swinkelbei@northwell.edu wrote:
External Email - Use CautionHi Anastasia,
I have checked and they do align. However the freesurfer parcels naturally cover more of the brain than the FA skeletons. I was wondering if this was the problem?
Therefore I added a binary mask of the FA skeletons.
I also tried subtracting the parcels from the FA skeletons with fslmaths to make sure that only the area of the skeleton is read out. But that doesn't give convincing results either.
Anyone having other suggestions?
Thanks, Steph
Sent from my Samsung Galaxy smartphone.
-------- Original message -------- From: "Yendiki, Anastasia" AYENDIKI@mgh.harvard.edu Date: 23/11/18 17:50 (GMT-05:00) To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [EXTERNAL] Re: [Freesurfer] extracting FA from FA_skeletonised with freesurfer parcellation
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:
Hi,
I try to extract FA values from the FSL FA skeleton using the freesurfer aparc.a2009s+aseg+2mm parcellations.
I did the following:
Recon-all to obtain à aparc.a2009s+aseg+2mmTBSS in FSL to obtain à all_FA_skeletonisedTbss_deproject to split up all_FA_skeletonised into individual skeletons (native space) (*_FA_FA_all_FA_skeletonised.nii.gz)Non-linear transformation of aparc.a2009s+aseg+2mm to subjects’ native space (parc2dwi.nii.gz)Creating binary mask for each subjects FA skeleton to exclude 0 voxels (*_FA_skeleton_mask.nii.gz)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.statsThe 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.edu mailto:swinkelbei@northwell.edu
Northwell Health
Visit us at Northwell.edu http://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.
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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
You don't want to be averaging zero voxels, so masking makes sense.
When you click on the voxels inside one of those segmentation regions (e.g. one of the CC regions) in freeview, are the FA values that you see high?
On Nov 25, 2018 8:42 AM, "Winkelbeiner, Stephanie A" Swinkelbei@northwell.edu wrote:
External Email - Use Caution
Hi Anastasia,
I have checked and they do align. However the freesurfer parcels naturally cover more of the brain than the FA skeletons. I was wondering if this was the problem?
Therefore I added a binary mask of the FA skeletons.
I also tried subtracting the parcels from the FA skeletons with fslmaths to make sure that only the area of the skeleton is read out. But that doesn't give convincing results either.
Anyone having other suggestions?
Thanks, Steph
Sent from my Samsung Galaxy smartphone.
-------- Original message -------- From: "Yendiki, Anastasia" AYENDIKI@mgh.harvard.edu Date: 23/11/18 17:50 (GMT-05:00) To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [EXTERNAL] Re: [Freesurfer] extracting FA from FA_skeletonised with freesurfer parcellation
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: 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.
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.
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So, I initially did that with the all_FA_skeletonised and got values around 0.6 for the Cc as expected. Interestingly enough though, when I do the same with the individual FA_skeletons that I obtained with the tbss_deproject command the values are around 0.1...
Could you think of a reason why that is?
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia Sent: Monday, November 26, 2018 1:58 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [EXTERNAL] Re: extracting FA from FA_skeletonised with freesurfer parcellation
External Email. Use Caution. You don't want to be averaging zero voxels, so masking makes sense.
When you click on the voxels inside one of those segmentation regions (e.g. one of the CC regions) in freeview, are the FA values that you see high?
On Nov 25, 2018 8:42 AM, "Winkelbeiner, Stephanie A" <Swinkelbei@northwell.edumailto:Swinkelbei@northwell.edu> wrote:
External Email - Use Caution
Hi Anastasia,
I have checked and they do align. However the freesurfer parcels naturally cover more of the brain than the FA skeletons. I was wondering if this was the problem?
Therefore I added a binary mask of the FA skeletons.
I also tried subtracting the parcels from the FA skeletons with fslmaths to make sure that only the area of the skeleton is read out. But that doesn't give convincing results either.
Anyone having other suggestions?
Thanks, Steph
Sent from my Samsung Galaxy smartphone.
-------- Original message -------- From: "Yendiki, Anastasia" <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> Date: 23/11/18 17:50 (GMT-05:00) To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [EXTERNAL] Re: [Freesurfer] extracting FA from FA_skeletonised with freesurfer parcellation
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.edumailto:Swinkelbei@northwell.edu> wrote: 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.
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.
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.
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Winkelbeiner, Stephanie A -
Yendiki, Anastasia