External Email - Use Caution 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 ----------------------------------------------------------------------------------------------------- University of Zurich Dr. Jürgen Hänggi, Ph.D. Department of Psychology Division Neuropsychology Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haen...@psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This email (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this email in error) please notify the sender immediately and destroy this email. Any unauthorised copying, disclosure or distribution of the material in this email is strictly forbidden. ----------------------------------------------------------------------------------------------------- > On 25 Nov 2018, at 14:41, Winkelbeiner, Stephanie A > <swinkel...@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" <ayend...@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" > <swinkel...@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 à aparc.a2009s+aseg+2mm > > 2. TBSS in FSL to obtain à 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: swinkel...@northwell.edu <mailto:swinkel...@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. 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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
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