[Freesurfer] mri_gtmpvc error: failed tissue type check

Dear Freesurfer community, An error has occured while applying PET partial volume correction using mri_gtmpvc. A snippet from the log file: Reading /projects/PET/recon/ID247/mri/gtmseg.lta Replacing 18 ERROR: CheckSegTissueType() tissue type for seg 29 Left-undetermined not set Failed tissue

Re: [Freesurfer] mri_gtmpvc error: failed tissue type check

I followed the processing workflow as described in PETSurfer wiki and gtmseg.mgz was created using gtmseg script as described. I ran this processing for over 100 subjects and only one has failed. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.ed

[Freesurfer] Content of PET gtm.stats.dat file

Hello FreeSurfer Developers, I have run mri_gtmpvc command to perform PET PVC (partial volume correction) where input data has 4 frames (dynamic). The output volume as gtm.nii.gz has 4 frames as well which means that PVC was performed for each frame separately. However, gtm.stats.dat file has o

[Freesurfer] PET ROI analysis

?Hello FreeSurfer Developers, I have done partial volume correction of PET data as described in PETSurfer stream. Now, I want to extract a mean intensity value of my ROI for each subject. This ROI is defined in the fsaverage space and saved as a label. What would be the best way to do it? Shou

[Freesurfer] LME model and contrast

Dear freesurfer team, I’m trying to use freesurfer LME tools to check whether baseline BMI scores (BMI scores at the first timepoint) have a statistically significant effect/impact on longitudinal thickness changes accounting for baseline age and gender. The model I’m thinking of is: Y_ij = b0

[Freesurfer] hippocampal subfields stats

Dear Freesurfer Developers, I’ve run the new longitudinal hippocampal subfields segmentation using Freesurfer’s developer version. Then I decided to extract stats for each hierarchy: HBT, FS60 and CA. I used the following command, for example: mri_segstats —seg lh.hippoAmygLabels-T1.long.v20.C

[Freesurfer] Longitudinal TRACULA study

Hi, I want to clarify some aspects longitudinal TRACULA processing before processing my data. For example, I have 3 timepoints of data of the same participant: sub101_01 sub101_02 sub101_03 All of these have structural and diffusion data (same scanner, same acquisition parameters). I processe

[Freesurfer] LME model and contrast for longitudinal covariate and different scanners

External Email - Use Caution Dear Freesurfer experts, I have some doubts while running LME analysis on longitudinal data. The main goal is to check whether longitudinal BMI scores have any impact on the longitudinal cortical thickness changes. The model I’m thinking of is as fo

[Freesurfer] Turn off bias field correction for SAMSEG

External Email - Use Caution Dear FreeSurfer team, Is there a way to turn off the bias field estimation and correction while running SAMSEG? I have images that are bias field corrected and would be great to skip this extra bias field estimation. Thanks in advance. Best, Donata

[Freesurfer] Reliability and sensitivity of two whole-brain segmentation approaches − ASEG and SAMSEG

External Email - Use Caution A new pre-print paper comparing two FreeSurfer’s whole-brain segmentation methods - ASEG and SAMSEG is now available (see the link below). The study is of great interest to many researchers in the field, providing new insights and guiding the selecti

[Freesurfer] Putamen and claustrum

External Email - Use Caution Dear FreeSurfers, I had a look at the RB_all_2020-01-02.gca atlas and there was no probabilistic information regarding the claustrum. However, in the mailing archive I have found the following: "On 2 May 2017, at 17:57, Douglas Greve wrote: […] Pu