Oh, I see. So in the calculation of total GM in aseg.stats does it include the hippocampus, although it is not showing on the masks for surface of GM or PIAL? I also tried to calculate total intracranial CSF (ventricles + outer liquor spaces). Is following calculation correct: e TIV - BrainSegNotVent = total intracranial CSF
These calculations are voxels based. I rather prefer a surface based calculation of total intracranial CSF. Is this faisible with freesurfer?
Thanks a lot! Cheers, Kristina
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Tuesday, May 27, 2014 2:24 PM To: Mayer Kristina Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: WG: [Freesurfer] WG: [Fwd: WG: missing temporal lobes]
Hi Kristina
can you please post to the list so others can answer? If you add control points to the temporal WM where you are missing gm it should recover most if not all of it. Hippocampus is not neocortical and isn't supposed to be included. The surfaces are somewhat arbitrary there, and excluded from all subsequent calculations (like total cortical area/volume)
cheers Bruce
On Tue, 27 May 2014, Mayer Kristina wrote:
Dear Bruce How can I get the Hippocampus and the missing parts of GM of the temporal lobe into the PIAL (sufrace mask)? How can I convince freesurfer those parts are belonging to gray matter?
Cheers, Kristina ________________________________________ Von: Mayer Kristina Gesendet: Freitag, 23. Mai 2014 16:11 An: Freesurfer support list; freesurfer-bounces@nmr.mgh.harvard.edu Betreff: AW: [Freesurfer] WG: [Fwd: WG: missing temporal lobes]
Von: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu]" im Auftrag von "Bruce Fischl [fischl@nmr.mgh.harvard.edu] Gesendet: Freitag, 23. Mai 2014 14:52 An: Freesurfer support list Betreff: Re: [Freesurfer] WG: [Fwd: WG: missing temporal lobes]
Hi Kristina
don't add CPs to the gray matter - that will mess everything up! Bruce On Fri, 23 May 2014, Mayer Kristina wrote:
Dear Bruce My dataset is very young (around 2 years of age), I suppose the contrast and size is just different from the default-template of freesurfer. Is there a way to exchange the template (I am thinking of a probabilistic map) without creating an own atlas first? Attached you find screenshots of my work and the recon-log of the same subject. I first run all recon-all steps. Then I added CP where WM was missing. I also added CP in GM region where lost of GM was missing (temporal lobe) to get the pial right. Then I tried to remove the WM which came out too much, for I placed CP in GM regions. Is there another way for it?
Best, Kristina
log 0001339: Fri May 16 08:50:00 CEST 2014 FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer /media/n-NAS_MRI/freesurfer-subjects-dir/0001336 setenv SUBJECTS_DIR /media/n-NAS_MRI/freesurfer-subjects-dir -autorecon2-cp -autorecon3 -subjid 0001336 Linux cs2.kispi.int 3.13.5-103.fc19.x86_64 #1 SMP Mon Mar 3 18:46:36 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
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a!
t/!
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Von: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu]" im Auftrag von "Bruce Fischl [fischl@nmr.mgh.harvard.edu] Gesendet: Donnerstag, 22. Mai 2014 14:10 An: Freesurfer support list Betreff: Re: [Freesurfer] missing temporal lobes
Hi Kristina
that shouldn't be needed. If you upload a dataset we will take a look
cheers Bruce On Thu, 22 May 2014, Mayer Kristina wrote:
Hi there, I tried to put more CP, so all the temporal lobe tissue is in the mask.
This will end up in overestimation of white matter. So in a second step you will have to manually adjust WM mask.
In my dataset, after adjusting WM mask, WM ist still little bit
oversetimated, but at least i am not missing tissue.
When you find a better option, I am glad to learn about. Good luck!
Best, Kristina ________________________________________ Von: freesurfer-bounces@nmr.mgh.harvard.edu
[freesurfer-bounces@nmr.mgh.harvard.edu]" im Auftrag von "Bruce Fischl [fischl@nmr.mgh.harvard.edu]
Gesendet: Donnerstag, 22. Mai 2014 04:35 An: Freesurfer support list Betreff: Re: [Freesurfer] missing temporal lobes
Hi Eileen Does adding control points to both temporal lobes fix it? Cheers Bruce
On May 20, 2014, at 9:34 AM, "Daly, Eileen" eileen.daly@kcl.ac.uk wrote:
Hello all,
We are having trouble with the output after running recon-all -all
-subjid subjectx on our scans.
Registrations and skull striping look okay, but the white matter and
pial surface segmentations leave outportions of the anterior temporal lobe.
After adding control points to the left temporal lobe, we then ran
recon-all -autorecon2 -cp -autorecon3 -subjid subjects.
This made the the left lobe look better, but then we spotted new
missing bits on the right side
anterior temporal lobe.
Any ideas on dealing with these missing temporal lobe issues?
Thanks,
Eileen Daly _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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