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Hi Yununs,
thanks for your mail:
There are no fixed and hard thresholds for these metrics (e.g., SNR). It really
depends on the sample and image characteristics. More important than the
absolute values is the distribution of these values across case
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Hi,
I am using freesurfer. I have gone through with the installation and
diagnostics and everything works fine. FOr example, using the command
recon-all --help in terminal yields a bunch of directions. Yet, when I
enter something like: recon-all -s ber
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Thanks a lot Kersten
On Wednesday, November 22, 2023 at 02:04:33 PM GMT+3:30, Diers, Kersten
/DZNE wrote:
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Hi Yununs,
thanks for your mail:
There are no fixed and hard thresholds for these m
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Hi
I am unable to add an additional scan FGATIR during thalamic segmentation. For
example I have a subject in the freesurfer/subjects directory that does
thalamic segmentation without adding the additional scan but not with the
attached code. I trie
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Dear freesurfer team,
I want to overlay the activation map that I got from SPM on the inflated
surface. The command I use is:
"mri_vol2surf--mov spmT_funcmap.nii --ref
subj01/mri/orig.mgz. --regtk.dat--hemi rh --ofloderna
Dear Amrita,
Please insert your subject directory between your subject name(sub-19253779)
and your FGATIR scan (sub-19253779/mri/FGATIR.nii.gz).
If you running your code from the subjects directory, which seems to be the
case, it would simply be:
segmentThalamicNuclei.sh sub-19253779 . sub-19253
did you look at the results (eg, the aseg)? Can you send the
recon-all.log file?
On 11/19/2023 11:18 PM, June Kang wrote:
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Hello,
According to the FAQ for earlier version of Freesurfer (maybe 6.x),
the instruction is below.
First you must run only -a
They are not
On 11/20/2023 6:01 AM, yunus soleymani wrote:
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Hi Freesurfers,
I wanted to know if the Freesurfer volume results are already
normalized by the total intracranial volume or if I should normalize
it for each subject myself.
Thanks for your answ
If the difference is only between 3.0761 and 3.0327, then that is
acceptably small to disregard.
On 11/21/2023 10:40 AM, 笹林大樹 wrote:
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Dear Dr. Greve,
I trust this message finds you well. I wanted to follow up on the
inquiry I posted to the FreeSurfer mail
You can use something like
mri_convert orig.mgz -at mri/talairach.m3z orig-in-mni305.mgz
This is nonlinear. It takes you to the mni305 space.
On 11/21/2023 11:45 AM, P Pieperhoff wrote:
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Hi Yujing,
thank you for your help! But I think, this is only the affi
You can use mri_vol2surf, something like
mri_vol2surf --closest-vertex x y z coords ltafile surf outfile
where xyz is a coordinate (eg, the center or edge or you lesion).
coords: 1=scanner,2=tkreg (you can pick the xyz from the freeview
scanner or tkreg ras)
if these coordinates are in the same s
yes, sending the full log file will be helpful. My guess is that the
surfaces got out of synch (eg, if you had done edits).
On 11/21/2023 8:15 PM, Mark Wagshul wrote:
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Dear Freesurfer experts,
Hi. Hoping someone can give me some guidance in how to proceed
You are not going to be able to register the partial FoV directly to
mni152. You can register the partial FoV to a full FoV within subject
and then the full FoV to mni152, then concatenate the registrations
together.
On 11/22/2023 8:01 AM, Spapens, Jeltje (NP) wrote:
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Have you tried adjusting the threshold. Open the configure overlay
option. Also, sending a pic would be helpful (and the contents of tk.dat)
On 11/22/2023 11:29 AM, Atena Akbari wrote:
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Dear freesurfer team,
I want to overlay the activation map that I got
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[image: Screenshot 2023-11-22 at 1.32.53 PM.png]
doesn't allow me to adjust the threshold to negative values, for example
t-values between -3 and 3.
On Wed, Nov 22, 2023 at 1:26 PM Douglas N. Greve
wrote:
> Have you tried adjusting the threshold. Op
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Hi Reza,
The lesion class in samseg is a bit special, as the internal lesion
probabilities are thresholded (using the value passed on via the
--threshold flag, or a default value 0.3 if you didn't use that flag) to
obtain the voxels labeled as 99 in th
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Dear Dr. Greve,
Thank you for your answer!
I found this helpful.
Best,
Daiki Sasabayashi
> 2023/11/22 13:06、Douglas N. Greve のメール:
>
> If the difference is only between 3.0761 and 3.0327, then that is acceptably
> small to disregard.
>
> On 11/21/
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Dear Freesurfer experts,
I have run the following command:
recon-all -s sub-1001 -localGI -no-isrunning
However, I got the error message as below.
>> Warning: Input argument must be a character vector.
> In ver (line 41) In freesurfer_read_surf (li
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Hi everybody,
We are pleased to announce that the application portal is still open for the
NIH funded 2024 session of the course, “Training in Advanced Statistical
Methods in Neuroimaging and Genetics”.
We hope you pass this email on to your local ne
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Hello Freesurfers,
My name is Mirsol and I am currently trying to obtain FA values from
particular hippocampus subfields by registering our fractional anisotropy
map (FA.nii.gz) from dt_recon command and our hippocampus segmentations
from the command s
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Dear Freesurfer Experts,
I did group-level analysis in MNI305 space. Then I output the summay via
command 'mri_volcluster' as follows:
mri_volcluster --in ./sig.nii.gz --thmin ${thvoxel} --sign ${sigsignTemp}
--cwpvalthresh 0.05 --minsize 273 --fwhm
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