[Freesurfer] Hypothalamus segmentation - Freesurfer 7.1

External Email - Use Caution Dear Freesurfer experts, I am having some trouble getting the hypothalamus segmentation recognized on the command line for FreeSurfer 7.1.0. Is it even available for this version? If not, will it work on the 6.0 or the 7.1.1 version? Thanks and stay s

[Freesurfer] Tkregister2 resolution difference

External Email - Use Caution Dear FreeSurfer, Hi, I'm Yuelin, a graduate student from Caltech. I came across an issue using the Tkregister2 registration GUI: the target scan are always rendered with much lower resolution than the movable scan. This difference in resolution makes

Re: [Freesurfer] Freesurfer recon all

Hi Rahul No, sorry, I cannot. Can you post some pictures of the wm.mgz? And/or the inflated.nofix? Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Paul, Rahul Sent: Friday, January 29, 2021 4:20 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer recon a

Re: [Freesurfer] Freesurfer recon all

Hi Bruce, Is it possible to do a zoom call for troubleshooting with me and my PI today? Rahul From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Fischl, Bruce Sent: Friday, January 29, 2021 12:35 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Free

Re: [Freesurfer] Voxel-wise volumes vs APARC volumes

External Email - Use Caution mris_preproc --qdec-long RossQdecFinal30May.txt --target fsaverage --hemi lh --meas volume --out lh.Rossvolume.mgh The vertex-wise analyses were run with 5 mm smoothing, but the graph I showed below was created with the unsmoothed data. Thanks for t

Re: [Freesurfer] Parallel computing for recon-all

If you are using slurm, then you have to allocate the number of CPUs when you run sbatch, otherwise, you will get only one CPU regardless of how many are tell recon-all to use. On 1/29/2021 1:16 PM, Wei Shao wrote: External Email - Use Caution Hi, Freesufer experts Sorry for the lat

Re: [Freesurfer] Parallel computing for recon-all

External Email - Use Caution Hi, Freesufer experts Sorry for the late reply, I have tried again with openmp 8 flag and added the cpus-per-task=16 for a subject. I have cut the recon-all processing time from 06:17:14 to 03:32:21! So excited. By the way, Could you help me to unders

Re: [Freesurfer] Fw: Freesurfer recon all

You'll have to find and remove the defect manually. It is probably cerebellum that is still attached or maybe a piece of dura or skull. There is some info on defects here http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview You can also run defect2seg --s subject shoul

Re: [Freesurfer] Freesurfer recon all

Hi Rahul That typically means that something has gone wrong, like too much skull being left around. The timing of the defect correction is quadratic in the size of the largest defect, so quite fast for small ones, but very very slow for big ones (and less likely to be correct when done). Look

Re: [Freesurfer] FW: FW: T1 Recon-all error: CTABWriteFileASCII; could not open file for writing

Hi Flavia, At the moment, freesurfer needs access to /tmp in order to cache temporary processing files. Can you reach out to your system admin as to why you don’t have write access to /tmp, and perhaps they will grant you access? Best, Andrew From: freesurfer-boun...@nmr.mgh.harvard.edu on b

Re: [Freesurfer] Voxel-wise volumes vs APARC volumes

What is your mris_preproc comman? On 1/28/2021 5:34 PM, Mark Wagshul wrote: External Email - Use Caution Dear Freesurfer experts, I’m stuck on something which I think has to do with how Freesurfer calculates volumes, but can’t quite wrap my head around it, hopefully you can enlighte

Re: [Freesurfer] Using mri_surf2surf to split files

Try this page https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslFeatFreeSurfer It is pretty old, but maybe it still works On 1/28/2021 5:46 PM, Karan Desai wrote: External Email - Use Caution Yes, I have attached a link to the previous correspondence from the Freesurfer mailing

Re: [Freesurfer] Parallel computing for recon-all

No, all the results are fine. By "broken" I mean that it might crash in places that it would not have crashed in v6 or that it just would not have been running in parallel when you think it was. On 1/28/2021 3:48 PM, Michael Krause wrote: > External Email - Use Caution > > On 1/28/21 6: