[Freesurfer] Freesurfer/Freeview Version Compatibility

[Edwards, Vincent]

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Hello,

I have several brains that I sent through recon-all using Freesurfer 7. If I 
wanted to use Freeview on Freesurfer version 5 to do pial/wm/and control point 
edits, would I be able to do recon-all through Freesurfer 7? I assumed that 
since Freeview is a GUI, the version used shouldn't have any actual impact on 
things as long as we returned to version 7 to recon-all. That seemed to be the 
case when someone asked a similar question (the reverse) 

  , but that was many years ago so I wanted to confirm.

Thanks,

Vincent Edwards
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[Freesurfer] mri_cc question

[Dawn Matthews]

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Hello Freesurfer team and thank you for your continued responses to questions.  
My questions pertain to mri_cc, and subsegmentation of the corpus callosum.  In 
prior runs of version 6.0, it seems that aseg outputs the subregions of the 
corpus callosum.  The option for mri_cc also identifies those segments, and 
(Question 1) I wondered if in version 7.4 how that differs from what aseg 
normally outputs?  In addition, (Question 2) with the -f flag to include the 
fornix, does this mean that the fornix is incorporated into the five 
subvolumes, or is the fornix volume calculated separately? (Question 3), For 
the option to set a different number of segmentations, how does that translate 
into the five ‘default’ segments (e.g. Anterior, Mid-Anterior, Central, 
Mid-Posterior, Posterior).  Again, thank you for the team’s continued work.
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[Freesurfer] Create a Binarized ROI for Surface

[Na, Xiaoxu]

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Dear Freesurfer Expert,

We would like to extract mean Cth values for each subject within a own-creaded 
ROI (surface defined), using freeview (for instance). Is it possible to create 
a ROI (i.e. spherical surface) surrounding a particular vertex of an sig.mgh 
file? (and then extract its mean Cth values for each subject)?

I think this is not a new question, and it was posted somehow on 
https://secure-web.cisco.com/15jmZMEaxCepVMfyQImwGR_dFusKbz7ObR8zcE3AMwMwg6FQ-QTkuETE4n5SJPU_y-ULxR0ToQgr0B_LnZ-TU71vd9-uYDXh55K9eVQ23CX9kaJT60pYOX0pH6tJ69K_Ry--XuPl1mkS0Vm-sSsWKWe2iqWjc5l2Y91tqImFy3Fb1NHtO7eCCpFk8I3Th1ljqxlnFLLOdjxe5bNpse_tYAPw-_J4V3X1Y9ONydytuj8eYC1Ly6c51azXalSlz6ZF_Xa9SbBJbXCJ6wvPAnlRqcmLPaBSCkzxpYzHM8250uaUvkwrVXDetf4ppJsTfDiNl/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FQuestionAnswers,
 and 
https://secure-web.cisco.com/1nS4AASSkp9fTCLDzqspNVvBf35PGarlPS708pOXtzpIMD4eASchvVbZLp65PS17HOn4cF-QEOKrz967tFrvqCTjlc-sB9fVuMI1CEUkb5m657oRe3DpyjwX9zSi3drP0cPEFBtrQe-2wfm3lQVO166f3QJao-Pq2XbpVRgo5UBgmt7oKBFbiBCBvj_534G45CEE2U9KkR7EjTPPn1W6w0ur3GGywIbW1Fh8AqeJa-QPpV2hrOWwEiX9Xkh3Dh4lveR2CDXf04WAXrlgdNdDnyqPZDbW1k45Pa1C37Ew1sU8dfqpWbKwdc1z2jO2R6EHx/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg67677.html,
 but I'm still encountering questions.

These commands did run, but together they didn't create a binarized mask with 1 
for the sphere around the coordinates, and 0 for the other voxels. Would you 
recommend what I should change? Thank you so much!

$mri_volsynth --template $SUBJECTS_DIR/fsaverage/surf/lh.thickness --pdf sphere 
--sphere-center -7.4 67.22 60.27 --radius 5 --o delta.sm00.mgh
$mris_fwhm \
--smooth-only \
--subject fsaverage \
--hemi lh \
--i delta.sm00.mgh \
--niters 10 \
--o delta.sm10.mgh
$mri_binarize --i delta.sm10.mgh --min 10e-5 --o delta.sm10.bin.mgh


Regards,
Xiaoxu

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[Freesurfer] Fwd: Case-controls study !

[Martin Juneja]

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Hi FS experts,

I was wondering if someone could help me get the following issue resolved.

Thanks.

-- Forwarded message -
From: Martin Juneja 
Date: Fri, Dec 8, 2023 at 11:03 AM
Subject: Case-controls study !
To: Freesurfer support list 


Hello FreeSurfer experts,

In my case-control study, I have a dataset of 5 healthy controls (HCs) and
one patient (PAT). I was wondering if there is any way to perform GLM for
PAT > HCs on brain morphometry data.

When I tried to follow instructions from here:
https://secure-web.cisco.com/1aK-KNfU8HH_e-fpaIAGAkK_0d2hcDIl4JpjyDUomASQEQQJehjuhA0YYNd1-yCMyLrNtRVInHC0sL4ZGQSm_hx-e7WqN75sm22gAExeDyUksUiv3NFy2UeyAzhzh7cNHQd3Uf5EAsh0E1za-xLWZQArzwTi3Bn_5I9N1UoxsMjYkGv5oZxPiqEXVD5BEsxQiOPkQtZJuTIDOtckipDfTK-LEDpsCXFCAShvieYfbxxg0ec00jOhHeoAyF4ZLaU_-CqhBmbOtWCJUC56qpOxRmizvYekBnUs8Nlzv3M50Fu7V8kklIdu8eSaJSTnIRHLld9QqWlnqRDFQoChfS_1bcQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FGroupAnalysis,
 the
mri_glm fit command gives me the following error:

Class Size and Means of each Continuous Variable

1 HC  5  24.2000   0.6000

2 Tumor  1  50.   1.

ERROR: Class Tumor has 1 members. With 2 variables and using DODS, you need
at least 3 members


It seems at-least three subjects are required in the Tumor category -
because I have age and sex covariates in my fsgd file.


I was wondering if there is any way to still perform the above GLM analysis
or any other alternatives available to compare HCs vs one PAT.


Thanks!
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