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mri_gtmpvc --i ADNI-PET.nii --reg template.reg.lta --psf 6 --seg gtmseg.mgz
--default-seg-merge --auto-mask 1 .01 --mgx .01 --o gtmpvc.output
I am trying to do like that.
I tried to change the --seg gtmseg.mgz by aparc+aseg.mgz to obtain the 45
what is your mri_gtmpvc command line?
On 6/19/2022 2:22 PM, Bouchra Guelib wrote:
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These are the missing regions in which I want to obtain their SUVr.
Left-Lateral-Ventricle, Left-Inf-Lat-Vent,
3rd-Ventricle, 4th-Ventricle, Left-vessel,
You can try removing --default-seg-merge, but it may fail.
It can compute a relative SUV (relative to a give n ROI). By default,
this will be pons, but you can chose others. SUV requires knowing things
like the patients weight.
On 6/19/2022 4:15 PM, Bouchra Guelib wrote:
External
On 6/15/2022 1:26 PM, Kuo, Yi-Ling wrote:
Hello,
The below solutions sounded like data need to be analyzed with
Freesurfer individually to get the registration file?
The anatomical must be analyzed in FS, but not the fMRI. See eg
That page is way out of date. Try this one
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModal_freeview
On 6/15/2022 5:47 PM, Rachel Wagner wrote:
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Apologies for repeat email – I’m getting the following error message,
is there something I
You can ignore that. That was put in by a contractor who put it into
every source file that did not set the random see. No randomness is used
in this program, so you are safe
On 6/16/2022 9:58 AM, Benjamin Deck wrote:
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Hi Freesurfer experts,
While trying
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Awesome, thank you for the information!
Ben
You can run something like
samseg --t1w /path/to/input/volume --s subject --recon
This will run recon-all but using samseg to do the initial steps,
including the segmentation of course
We don't have a lot of experience using this as preprocessing to the
surface-based analysis, so look at your
from mri_glmfit-sim --help
csdbase.sig.voxel.mgh - the sig volume corrected for multiple
comparisons on a voxel-wise basis. The threshhold and sign are
irrelevant. The value at each voxel is the corrected -log10(p-value) for
that voxel.
It is computed from a simulation in which gaussian
It looks like there are a lot of defects as I see a lot of these messages
An extra large defect has been detected...
This often happens because cerebellum or dura has not been removed from
wm.mgz.
This may cause recon-all to run very slowly or crash.
if so, see
How was H-O_subcortical_parcellation_thr50.nii created? Those
instructions are for when you have a segmentation in the FS conformed
space and you want to get them back to the native space. So your
segmentation must be in FS conformed space of the individual
On 6/10/2022 6:49 PM, Christopher
The -hires performs all operations in 0.7mm space whereas leaving it off
causes recon-all to "conform" the volume so that it is 256^3 and 1mm^3.
If you want more help with this, send the log file
On 6/10/2022 6:58 PM, Schneider, Christoph wrote:
Hi,
I have 7T MP2RAGE data of 25 individuals
I'm not sure what is happening. Does cortex have label value that are
just not in the LUT or are the values 0?
Try adding --aseg aseg.presurf.hypos
If you need more help,make sure to include the full terminal output
On 6/13/2022 4:49 PM, Benjamin Deck wrote:
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On 6/15/2022 7:40 AM, Bouchra Guelib wrote:
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Hi,
I wonder if someone can help me to do something similar to that:
" the mean intensity of each FreeSurfer region (ROI) for the 45
subcortical and the 68 cortical regions were assessed the mean
intensity of
You should be able to run 7.2 on top of the 5.3 and at will take all
your edits (make a copy of your 5.3 data first:)
On 6/14/2022 5:26 PM, Aaron Tanenbaum wrote:
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Our lab is moving from FreeSurfer 5.3 to 7.2. We have thousands of
scans to do. I see
When you say they are growing rather than shrinking, do you mean in the
longitudnial recon-all run? The reason I ask is that you only mention
the base and cross. When you do the longitudinal analysis, you need to
do cross, then base, then long.
On 6/15/2022 11:43 AM, Wittayer, Matthias wrote:
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