Re: [Freesurfer] MeanItensities- PET

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 Ema

Re: [Freesurfer] MeanItensities- PET

External Email - Use Caution 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 subcort

Re: [Freesurfer] MeanItensities- PET

what is your mri_gtmpvc command line? On 6/19/2022 2:22 PM, Bouchra Guelib wrote: External Email - Use Caution 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,  Right-Lateral-Ventr

Re: [Freesurfer] mris_label2annot seed not set

External Email - Use Caution Awesome, thank you for the information! Ben

Re: [Freesurfer] mris_label2annot seed not set

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: External Email - Use Caution Hi Freesurfer experts, While trying

Re: [Freesurfer] SPM to FreeSurfer

That page is  way out of date.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: External Email - Use Caution Apologies for repeat email – I’m getting the following error message, is there something I shou

Re: [Freesurfer] Freeview GUI overlay and registration

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 https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Multi

Re: [Freesurfer] Problem with longitudinal processing

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:

Re: [Freesurfer] using brain mask from older FreeSurfer version on a newer

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: External Email - Use Caution Our lab is moving from FreeSurfer 5.3 to 7.2. We have thousands of scans to do.  I see that

Re: [Freesurfer] MeanItensities- PET

On 6/15/2022 7:40 AM, Bouchra Guelib wrote: External Email - Use Caution 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

Re: [Freesurfer] recon-all -s exited with ERRORS

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 https://surfer.nmr.mgh.harvard.e

Re: [Freesurfer] mri_aparc2aseg bad incorrect ROIs

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: External Email - Use Cautio

Re: [Freesurfer] -hires flag sometimes breaks recon-all

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 w

Re: [Freesurfer] mri_label2vol misaligned for subcortical atlas

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 P

Re: [Freesurfer] How is cache.th40.pos.sig.voxel.mgh computed, exactly?

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 nois

Re: [Freesurfer] Incorporating samseg segmentation into the recon-all pipeline

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 re