[Freesurfer] Inflated surface

Hi everyone , Recently surface check have been bothering me ,and I cannot quickly find surface error . Unintentionally I read such a sentence "The inflated surface is good to look at when checking to see if you need to make edits to the wm.mgz volume. You'll notice as you inspect this surface that

[Freesurfer] surface check

Hi everyone , After "recon-all"，how to determine quickly the quality of whiter matter segmentation ,surfaces(e.g. whiter matter surface and pial surface) and topological fix ? what anatomy should be paid more attention? Best regards? Xin-Fa Shi . ___ Fr

[Freesurfer] Registration

After 'recon-all' ,how to check its accuracy of registration ? what anatomy should be paid more attention ? Best regards . Xin-Fa Shi . ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfe

[Freesurfer] Visual Check

Hi everyone, After pre-process "recon-all"，what parts of its process need to check visually ?how to determine its necessity for check ? and how to check them ? Could you provide me for a guide or pipeline? Best regards. Xin-Fa Shi. ___ Freesurfer maili

[Freesurfer] QDEC, Correction for multiple comparisons

Hello,everyone Your reply said I can't use alphasim with qdec.By the way ,Could I use alphasim in other ways in FreeSurfer,for example command line ? Best regards. Xin-Fa Shi. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.

[Freesurfer] (no subject)

Hello,everyone Your reply said I can't use alphasim with qdec.By the way ,Could I use alphasim in other ways in FreeSurfer,for example command line ? Best regards. Xin-Fa Shi. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.

[Freesurfer] QDEC, Correction for multiple comparisons

Hi ,everyone I have found only two methods(i.e FDR,Monte Carlo simulation) of correcting for multiple comparisons in QDEC .However ,I didn't get any results on my data after correction .Therefore I want to try alphasim corrcetion.So I am wondering if QDEC can achieve it .If so . how can I do it ?

[Freesurfer] QDEC, Correction for multiple comparisons

Hi ,everyone I have found only two methods(i.e FDR,Monte Carlo simulation) of correcting for multiple comparisons in QDEC .However ,I didn't get any results on my data after correction .Therefore I want to try alphasim corrcetion.So I am wondering if QDEC can achieve it .If so . how can I do it ?

[Freesurfer] ERROR:dimension mismatch between X and contrast con.mtx

Hi everyone, I get this error when running group analysis of cortical thickness by command-line: xin-fa@xinfa--PC:/media/E/FREESURFER/VisualData$ mri_glmfit --y lh.group_differ.thickness.10.mgh --fsgd group_differ.fsgd dods --C con.mtx --surf fsaverage lh --cortex --glmdir lh.group_differ.glmdir

[Freesurfer] recon-all input

Hello, Now I have a subject data,including 156 dicom images(MR0001~MR0156),amd they were converted into a .nii.gz file(eg.CON_T1_01.nii.gz) .I am wondering whether they are the same : recon-all -i MR1.dcm -s con01 -all recon-all -i CON_T1_01.nii.gz -s con01 -all Many Regards. Xin-Fa Shi. _

[Freesurfer] cortical thickness analysis

Hi , I want to make a cortical thickness analysis ,and could you provide me for a user guide or tool ? Regards. Xin-Fa Shi. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The in