Re: [Freesurfer] Hypothalamus segmentation - Freesurfer 7.1

Hi Alex, After sourcing the dev distribution, can you run: fspython -m pip install h5py==2.10.0 This is an unfortunate bug with older versions of keras and newer versions of h5py, but we’ll be upgrading our internal scripts soon to deal with this. Thanks for point this out - I’ll put a note in

Re: [Freesurfer] Hypothalamus segmentation - Freesurfer 7.1

External Email - Use Caution Thank you for your help! I have tested the hypothalamus segmentation on the development version of FS, and this was the error output that I got (see below). How should I proceed to fix this? :~/Documents$ mri_segment_hypothalamic_subunits --s UCL55003

Re: [Freesurfer] white matter volume

External Email - Use Caution If that's the correct way to do it then yes since I don't know about this. If not, is the volume of white matter obtained from freesurfers glmfit group analyses? On Tue, Feb 2, 2021 at 11:39 AM Douglas N. Greve wrote: > sorry, still don't understand.

Re: [Freesurfer] white matter volume

sorry, still don't understand. do you want to get the volume of WM from DTI? On 2/2/2021 11:19 AM, Sara Lyn wrote: External Email - Use Caution Hi Dr Greve, Instead of using DTI to get at the FA/MD etc measures is there a way to get at the volume of the white matter? Best, Sara On

Re: [Freesurfer] white matter volume

External Email - Use Caution Hi Dr Greve, Instead of using DTI to get at the FA/MD etc measures is there a way to get at the volume of the white matter? Best, Sara On Tue, Feb 2, 2021 at 10:54 AM Douglas N. Greve wrote: > Not sure what you mean > > On 2/1/2021 12:32 PM, Sara L

Re: [Freesurfer] Failed tissue type check {Disarmed}

External Email - Use Caution Hi Doug, I tried these fixes but they still give me the error message below. I did replace it in the gtmseg.ctab though -- should it be perhaps the seg.ctab in the aux folder ? Thanks, Julie On Tue, 12 Jan 2021 at 10:37, Julie Ottoy wrote: > Hi Dou

Re: [Freesurfer] Fwd: label to surface

I've never done it in FS, but you might be able to do it with mris_convert using -c option and specifying a gifti as an output On 2/1/2021 8:19 PM, Sam W wrote: External Email - Use Caution Hi! Just pinging. Is there a way to get the surface+overlay file as mentioned above using free

Re: [Freesurfer] White matter parcellation

The subcortical GM structures are obtained from the whole brain segmentation (Fischl, Neuron, 2002). The segmentation of the WM is performed by taking the label of the closest point on cortex (Salat, Neuroimage, 2009) On 2/1/2021 1:52 PM, Graterol Pérez, José Alberto wrote: Extern

Re: [Freesurfer] cortical thickness ROI

Yes, you can use mris_apply_reg to map the label/annotation back to the individual, then mri_label2vol to map it into the DTI space, then use mri_segstats to extract the mean value from the ROI On 2/1/2021 1:15 PM, Sara Lyn wrote: External Email - Use Caution Hi Freesurfer developers

Re: [Freesurfer] white matter volume

Not sure what you mean On 2/1/2021 12:32 PM, Sara Lyn wrote: External Email - Use Caution Hi, Is there a way to get at the white matter volume from a group analysis? Sara ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://m