[Freesurfer] VM passcode

External Email - Use Caution Hello there What is the password to open the archive zip file when downloading the virtual machine? Thanks Bea ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Thalamic nuclei exited with ERRORS

External Email - Use Caution For MacOS, the 7.2.0 release was done on MacOS 10.14.6 and it will check for Matlab runtime MCRv84 which you install with R2014b as the argument to fs_install_mcr For MacOS, the 7.3.2 release was done on MacOS 10.15.7 and it will check for Matlab

Re: [Freesurfer] Thalamic nuclei exited with ERRORS

External Email - Use Caution Hi again, Just wanted to confirm the randomness of the issue… and see if there was any potential explanation for this. I decided to go back from scratch, using a copy of my scans processed with FS5.3. I re-ran the thalamic nuclei pipeline from

Re: [Freesurfer] FSFAST first level covariates

External Email - Use Caution Sorry if I was unclear. The analysis we have set up will allow me to test for the difference between self and non self valence slope, but I’m also interested in testing for the slope of valence alone (identifying the brain regions associated with

Re: [Freesurfer] FSFAST first level covariates

sorry, you lost me there ... On 8/31/2022 12:39 PM, Angela Fang wrote: External Email - Use Caution That makes sense! And if we wanted to identify brain regions associated with valence (across self/non-self) that is unique from condition 2, can we add a 5^th condition? Maybe we can

Re: [Freesurfer] sclimbic sometimes does not detect left basal forebrain

I'm not sure but I have a guess. EAch stage of the unet has an intensity normalization step where the intensity of all voxels are spread uniformly over a range. I suspect that the bright, meaningless voxels are causing the meaningful voxels to be forced into too small of a range causing

Re: [Freesurfer] Bus error using VM (#@# Nu Intensity Correction)

External Email - Use Caution Hard to look at the error w/o a core dump file, but I suspect “bus error” is from the VM and not from commands in the recon-all acting differently during your 2nd run. It reads like you created a shared folder for the VM to use, and set SUBJECTS_DIR

Re: [Freesurfer] FSFAST first level covariates

External Email - Use Caution That makes sense! And if we wanted to identify brain regions associated with valence (across self/non-self) that is unique from condition 2, can we add a 5th condition? Maybe we can code self as 2 and non-self as 1 so that condition 2 (self*valence)

Re: [Freesurfer] sclimbic sometimes does not detect left basal forebrain

External Email - Use Caution thank you! One last question hopefully on this matter. I dont fully understand still why the percentile flag would affect the subcortical regions? the bias field was only in the front and back of the brain. Thanks, Miriam

[Freesurfer] LENS-Italy Postdoc Opportunity

Hi all, The biophotonics group at LENS is looking for a biologist to study human brain neuroanatomy using fluorescence microscopy techniques. Please see the below posting. Feel free to forward to anyone you know who might be interested. Thanks, Jocelyn The biophotonics group at LENS, is

Re: [Freesurfer] midsagittal mask

Oh, sorry, mri_cc From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Sam W Sent: Wednesday, August 31, 2022 9:57 AM To: Freesurfer support list Subject: Re: [Freesurfer] midsagittal mask External Email - Use Caution Hi Bruce, Thank you for the response! Which freesurfer

Re: [Freesurfer] midsagittal mask

mri_cc. Look in the recon-all.log file for an example command line. You may want to change the output file so that you do not overwrite what is there. On 8/31/2022 9:56 AM, Sam W wrote: External Email - Use Caution Hi Bruce, Thank you for the response! Which freesurfer command do I

Re: [Freesurfer] Thalamus segmentation - segmented thalamus looks bigger than brain.mgz would indicate

I don't think the brain.mgz is the right one to look at as it has already been partially segmented. Compare against the norm.mgz (or nu.mgz) instead. It is really hard to determine where the lateral boundaries are in thalamus On 8/31/2022 2:46 AM, Thalhammer, Melissa wrote: External

Re: [Freesurfer] midsagittal mask

External Email - Use Caution Hi Bruce, Thank you for the response! Which freesurfer command do I need to run with -t 0? Best regards, Sam On Sat, Aug 27, 2022 at 3:44 AM Fischl, Bruce wrote: > I don’t think we ever write out the mid-sagittal plane, but we do compute > it

Re: [Freesurfer] samseg dice score is low

External Email - Use Caution Hello again, I use Freesurfer-Samseg for MS lesion segmentation(cross-sectional). I use the T1 and Flair for this. (just these are inputs) I registered *flair and t1 to DIR *for every patient. (My manual lesion masks are on DIR imaging.) I controlled