[Freesurfer] Thickness histogram on labelled region only
I would like to look at the histogram of cortical thickness for the cingulate cortex because I am concerned that the edges next to the corpus callosum have very low thicknesses (and significant regions that are zero) that may be creating some interesting cingulate results we are seeing. I see there is a matlab script to look at the thickness histogram of the entire cortex, but is there a way to create a histogram for just one labeled region at a time? Thanks, Ronald Pierson Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Thickness histogram on labeled region only?
I sent this a while back, but haven't received any suggestions. Would anyone have any ideas or suggestions? I would like to look at the histogram of cortical thickness for the cingulate cortex because I am concerned that the edges next to the corpus callosum have very low thicknesses (and significant regions that are zero) that may be creating some interesting cingulate results we are seeing. I see there is a matlab script to look at the thickness histogram of the entire cortex, but is there a way to create a histogram for just one labeled region at a time? Thanks, Ronald Pierson Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Labeling surface to get thickness from a region
I am following up on some issues where we see some effects we really
don't expect when analyzing our data with qdec. They look like they
could be some slightly bad data from scan issues, segmentation problems,
etc. This is a large set of scans so I would like to script out a
routine to get the thickness values for each vertex in a region, then
look for outliers to help us understand if this is real or a problem.
How can I retrieve the thickness values for all of the vertices in a
region? I am using the routine below, but the labels don't seem to be
the same across subjects - apparently I need to understand how the label
numbers/lists match with the various surfaces. What surfaces, annot
files and label numbers would be the appropriate ones to use for this?
Does the rest make sense?
I have been loading the pial surface and using
Labl_import_annotation aparc.annot
Labl_save 30 l_ROI1
Then in matlab something like:
l_thick = read_curv ('$path/$subject/surf/lh.thickness')
l_roiverts = read_label('$subject,'l_ROI1')
nvert1 = size(l_roiverts)
for k = 1:nvert1(1,1)
ind = l_roiverts(k,1)
l_ROI1Thick(k,1) = l_thick(ind,1);
end
hist(l_ROI1Thick,100)
print -djpeg -f1 -r150 l_ROI1Thick_$subj
Thanks for your time,
Ronald Pierson
Chair of Imaging, PREDICT-HD
Manager, Research and Development
Department of Psychiatry, Carver College of Medicine
W-278 GH, 200 Hawkins Dr
Iowa City, IA 52242
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[Freesurfer] Using a clipped image
We have a large number of scans with excellent, visually inspected and manually trimmed brain masks, so we would like to use these masks to assist the FreeSurfer processing. One way we have experimented with to achieve this is to clip the T1 to remove anything non-brain before importing it into the subject directory. In using brain-clipped T1 images as a starting point for FreeSurfer we notice that the Talairach transform checking is quite far off, scaled badly and rotated downward 10+ degrees in pitch. I assume that this is due to the lack of similarity to the moving image, which includes skull. However, even if we don't modify this transform, the final parcellation looks quite good, and very, very similar to that from using a standard, non-clipped T1 as input. Is there any reason not to use a clipped T1 as input into FreeSurfer? Is the Talairach-based information used for segmentation or parcellation, and are we potentially creating problems? Or would it be better to simply use our mask to trim up the images after autorecon1 (coregistering them into the same image space and clipping them with a custom routine)? Ron Pierson Department of Psychiatry Carver College of Medicine W-278 GH, 200 Hawkins Dr Iowa City, IA 52242 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Using a clipped image
Thanks! Yes, that makes perfect sense - looking at: http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable Ron -Original Message- From: Nick Schmansky [mailto:ni...@nmr.mgh.harvard.edu] Sent: Thursday, January 28, 2010 3:04 PM To: Bruce Fischl Cc: Pierson, Ronald K; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Using a clipped image i forgot to add: dont use the skull-stripped image as input. your's just gets inserted after -autorecon1 to replace brainmask..mgz n. On Thu, 2010-01-28 at 15:59 -0500, Nick Schmansky wrote: > you could break it apart: > > recon-all -s subjid -autorecon1 -noskullstrip > > cp brainmask.auto.mgz > cp brainmask.auto.mgz brainmask.mgz > > recon-all -s subjid -autorecon2 -autorecon3 > > n. > > > > On Thu, 2010-01-28 at 15:31 -0500, Bruce Fischl wrote: > > Hi Ron, > > > > we do use the talairach for things like estimating icv, so that would > > concern me a bit. I don't think there is a straightforward way to insert > > the skull stripped image into our stream though. Maybe Nick has a better > > idea? > > > > Bruce > > > > > > On Thu, 28 Jan 2010, > > Pierson, Ronald K wrote: > > > > > We have a large number of scans with excellent, visually inspected and > > > manually trimmed brain masks, so we would like to use these masks to > > > assist the FreeSurfer processing. One way we have experimented with to > > > achieve this is to clip the T1 to remove anything non-brain before > > > importing it into the subject directory. In using brain-clipped T1 > > > images as a starting point for FreeSurfer we notice that the Talairach > > > transform checking is quite far off, scaled badly and rotated downward > > > 10+ degrees in pitch. I assume that this is due to the lack of > > > similarity to the moving image, which includes skull. However, even if > > > we don't modify this transform, the final parcellation looks quite good, > > > and very, very similar to that from using a standard, non-clipped T1 as > > > input. Is there any reason not to use a clipped T1 as input into > > > FreeSurfer? Is the Talairach-based information used for segmentation or > > > parcellation, and are we potentially creating problems? Or would it be > > > better to simply use our mask to trim up the images after autorecon1 > > > (coregistering them into the same image space and clipping them with a > > > custom routine)? > > > > > > > > > > > > Ron Pierson > > > > > > > > > > > > Department of Psychiatry > > > > > > Carver College of Medicine > > > > > > W-278 GH, 200 Hawkins Dr > > > > > > Iowa City, IA 52242 > > > > > > > > > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Longitudinal processing edits
I apologize if this has been covered before, but I wanted to make sure I understand the best way to edit at the appropriate times during the longitudinal stream. 1) Run recon-all -all on each scan 2) If needed, control points are chosen on the individual scans, and recon-all using the -cp option 3) Run the -base processing for the subject 4) WM and brain (pial) edits are done on the base, rerun as needed 5) Final longitudinal processing of each scan I assume the final processing of the individual scans should need very little manual intervention, since the control points and edits will be carried through to that stage. Is this correct, or have I oversimplified or missed something? Ronald Pierson Administrative Chair of Imaging, PREDICT-HD Manager, Research and Development Department of Psychiatry, Carver College of Medicine W-278 GH, 200 Hawkins Dr Iowa City, IA 52242 ___ 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] Editing annotations
Forgive me if this has been covered before, but I was unable to find an answer after searching for a bit. I have been considering editing the final surface parcellation for those scans that have problems in certain areas. Can these corrections then be used to correct the surface registration for the input into Qdec? Also, to test out the editing process I have been simply importing the annot file, editing the labels, then exporting it. Is this the correct thing to do, and is there a tutorial anywhere about this kind of editing? Thanks, Ronald Pierson ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Combining two regions
I apologize if this has been asked and answered before, but I wish to combine rostral and caudal middle frontal gyri for a summary measure. To find the average thickness of the entire region, will it be weighted by the surface area or by the number of vertices? Avg_MidFront = ((CaudThick*NumVertsCaud) + (RostThick*NumVertsRost) / (NumVertsCaud + NumVertsRost)) Or Avg_MidFront = ((CaudThick*SurfAreaCaud) + (RostThick*SurfAreaRost) / (SurfAreaCaud + SurfAreaRost)) Thanks, Ronald Pierson Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
