Re: [Freesurfer] Max threshold marked as '-inf' in cluster summary file

can you send the cluster summary file? On 11/24/2019 7:09 PM, Bronwyn Overs wrote: External Email - Use Caution Hi Kersten, Following on from Douglas's reply, you may remember my analysis as I forwarded you some files in October (see

Re: [Freesurfer] PetSurfer questions

what ligand are you using? Do you expect it to be higher in GM and in WM? What are the values in the gtm.stats file relative to when you run it without PVC? How did you choose 5 as the --psf? On 11/26/2019 2:53 AM, Soo-Jong Kim wrote: External Email - Use Caution Dear FreeSurfer

Re: [Freesurfer] [recon-all] [use of -T2] Does only -autorecon3 use -T2?

Yes, the T2 is only used to refine the pial surface On 11/26/2019 5:14 PM, Billah, Tashrif wrote: Hi all, Is -T2 used only in -autorecon3 as shown here: recon-all -subject subjectname -T2 /path/to/T2_volume -T2pial -autorecon3 In

Re: [Freesurfer] extract lgi

yes, see https://surfer.nmr.mgh.harvard.edu/fswiki/LGI On 11/26/2019 2:07 AM, An Lijun wrote: External Email - Use Caution Dear Yanyan, Actually you could refer to the freesurfer tutorial firstly. Best Regards, An Lijun Lin Yanyan mailto:linyan...@outlook.com>> 于2019年11月26日周二

[Freesurfer] [recon-all] [use of -T2] Does only -autorecon3 use -T2?

Hi all, Is -T2 used only in -autorecon3 as shown here: recon-all -subject subjectname -T2 /path/to/T2_volume -T2pial -autorecon3 In other words, if I do: recon-all -subject subjectname -i /path/to/input_volume -T2 /path/to/T2_volume

[Freesurfer] Postdoctoral Opportunity at Brigham and Women’s Hospital – Harvard Medical School

Postdoctoral Opportunity at Brigham and Women’s Hospital – Harvard Medical School The Department of Neurology at Brigham and Women’s Hospital (BWH) and Harvard Medical School (HMS) in Boston, Massachusetts, has an opening for highly qualified individuals at the post-doctoral level to work on

Re: [Freesurfer] (no subject)

External Email - Use Caution Thank you! I have a gca for subcortical and two gcs (lh/rh) for cortical structures. I created an annot (rh/lh) and a mgz using mris_ca_label and mri_ca_label for parcellation/segmentation stats. For the PET analysis I have the following problem: If

[Freesurfer] Freesurfer dev version: Hyppocampus, amygdala and thalamus segementation

External Email - Use Caution Dear Freesurfer devs, We are considering segmenting with the Freesurfer 6 dev version the hippocampus, the amygdala and the thalamus of several subjects who have already done the recon-all. Since we have a T1 image and T2 image with smaller voxel

Re: [Freesurfer] How do I fix this white matter boundary issue? {Disarmed}

External Email - Use Caution This addressed my concern! Thank you for the insight. From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Greve, Douglas N.,Ph.D. [dgr...@mgh.harvard.edu] Sent: Friday,

Re: [Freesurfer] V1 length

Hi Melissa, You can now measure the length of a path on surfaces in the development version of freeview. You can download the dev build here: https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview On the surface panel, click on "Path/Custom Fill" icon and draw the path. Then hold the

[Freesurfer] freeview parallelized binary

External Email - Use Caution Hello, We recently noticed freeview on the MGH cluster was using multiple cores when loading niftis, however, our local installation only uses one core when loading the same nifiti. Is it possible to get access to this freeview binary or the source

Re: [Freesurfer] Using pre-segmented results

Hi Jordi yes, this should be possible. You might need to run recon-all in stages though. Although if you set the wm.mgz values from SPM to 255 and 1 (not 0) recon-all should detect them as "edits" and retain them cheers Bruce On Tue, 26 Nov 2019, Jordi Huguet wrote: External

[Freesurfer] Using pre-segmented results

External Email - Use Caution Hi there, I wonder if its somehow possible to feed FreeSurfer's recon-all with pre-existing segmented maps (based on prior segmentation procedure e.g. SPM or ANTs) to "improve" FreeSurfer results. For some images I am working with the FreeSurfer's WM