Re: [Freesurfer] freesurfer results QC

External Email - Use Caution 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

[Freesurfer] Help

External Email - Use Caution 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

Re: [Freesurfer] freesurfer results QC

External Email - Use Caution Thanks a lot Kersten On Wednesday, November 22, 2023 at 02:04:33 PM GMT+3:30, Diers, Kersten /DZNE wrote: External Email - Use Caution Hi Yununs, thanks for your mail: There are no fixed and hard thresholds for these m

[Freesurfer] Unable to add FGATIR during thalamic segmentation

External Email - Use Caution 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

[Freesurfer] issue with mri_vol2surf

External Email - Use Caution 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

Re: [Freesurfer] Unable to add FGATIR during thalamic segmentation

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

Re: [Freesurfer] run recon-all with already skull-stripped data

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: External Email - Use Caution Hello, According to the FAQ for earlier version of Freesurfer (maybe 6.x), the instruction is below. First you must run only -a

Re: [Freesurfer] total intracranial volume

They are not On 11/20/2023 6:01 AM, yunus soleymani wrote: External Email - Use Caution 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

Re: [Freesurfer] Fwd: About Mean LGI value

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: External Email - Use Caution Dear Dr. Greve, I trust this message finds you well. I wanted to follow up on the inquiry I posted to the FreeSurfer mail

Re: [Freesurfer] Transformation of volume images

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: External Email - Use Caution Hi Yujing, thank you for your help! But I think, this is only the affi

Re: [Freesurfer] Distance Measurement After recon-all

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

Re: [Freesurfer] recon-all error - MRISlabel2Mask()

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: External Email - Use Caution Dear Freesurfer experts, Hi. Hoping someone can give me some guidance in how to proceed

Re: [Freesurfer] Boundary based registration on partial FoV to MNI space

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: External Email -

Re: [Freesurfer] issue with mri_vol2surf

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: External Email - Use Caution Dear freesurfer team, I want to overlay the activation map that I got

Re: [Freesurfer] issue with mri_vol2surf

External Email - Use Caution [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

Re: [Freesurfer] Question about lesions output of samseg

External Email - Use Caution 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

Re: [Freesurfer] About Mean LGI value

External Email - Use Caution 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/

[Freesurfer] Errors in LGI command

External Email - Use Caution 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

[Freesurfer] Late applications due by Nov 30th: NIH R25 Course Training in Advancd Statistical Methods in Neuroimaging and Genetics, Salt Lake City, Utah, April 15-26, 2024.

External Email - Use Caution 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

[Freesurfer] vol2subfield troubleshoot

External Email - Use Caution 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

[Freesurfer] No ROI name in summary of MNI305 group analysis

External Email - Use Caution 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