Re: [Freesurfer] contrast-FSGD question

External Email - Use Caution Hi Doug, The FSGD looks like the attached. For the contrast: [ 0 0 0 0 0.5 -0.5 -0.5 0.5 0 0 0 0], to model the 3-way interaction between Class and the new multiplied continuous interaction variable controlling for eTIV. That brainmap, where we

[Freesurfer] FreeSurfer VM Password

External Email - Use Caution Dear, Hi, Can I have the pass code to open the image FS_7_2_0_Ubuntu_18_04_06.ova.7z

Re: [Freesurfer] FreeSurfer VM Password

External Email - Use Caution Dear, Hi, Can I have the pass code to open the image FS_7_2_0_Ubuntu_18_04_06.ova.7z

Re: [Freesurfer] dcmunpack behavior with scouts

External Email - Use Caution Hi Sebastien. The BIDS you are getting is because I did some code restructuring yesterday. If you point me to the script Doug gave you, I can do a merge. Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Proulx, Jean Sebastien

Re: [Freesurfer] dcmunpack behavior with scouts

External Email - Use Caution It seems to be working fine: -keep-scouts does keep the scouts and removing it discards the scouts. There was some errors for some runs but they were the same for dcmunpack as distributed in dev so I did not bother investigating further. I had to

Re: [Freesurfer] Error Sourcing Freesurfer

External Email - Use Caution You could also try directly sourcing the FS-711 like this: if using bash: source /usr/local/freesurfer/nmr-stable711-env-bash if using csh: source /usr/local/freesurfer/nmr-stable711-env From:

Re: [Freesurfer] SynthSeg terminates with 'std::bad_alloc' error when using --threads option (>1)

External Email - Use Caution Seems like you're running out of memory when using more than 1 threads. Can you allocate more memory to the VM? You can also try running Synthseg without the --robust flag? From: freesurfer-boun...@nmr.mgh.harvard.edu

Re: [Freesurfer] Error Sourcing Freesurfer

External Email - Use Caution Hi Isabella, 'fs-stable711-env-autoselect' should be the string passed to fsenv script. For example, to source 7.2.0 release: If you are using csh: source /cluster/freesurfer/fsenv.csh 7.2.0 If you are using bash: source /cluster/freesurfer/fsenv.sh

Re: [Freesurfer] Error Sourcing Freesurfer

External Email - Use Caution Hi Avnish, Here is the output: pwd /homes/2/it090 ls /usr/local/freesurfer 6.0.0fs-stable6-env-autoselect 6.0.1fs-stable710-env-autoselect 7.0.0fs-stable711-env-autoselect

Re: [Freesurfer] mri_normalize error MP2RAGE

External Email - Use Caution The current versions of FS require an intensity normalization step be run on 7T data prior to running it through FS. I have used SPM VBM for this, but I think samseg should work too, eg, samseg --i t1.mgz --o samseg Then use

Re: [Freesurfer] Error Sourcing Freesurfer

External Email - Use Caution Could you post the ouitput of these two commands: pwd ls /usr/local/freesurfer Best, Avnish From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Turco, Isabella Sent: Tuesday, May 2, 2023 10:55 AM To:

[Freesurfer] mri_synthseg problem with CT... freesurver v 7.3.2

External Email - Use Caution Hi: I downloaded some CT from OASIS 4 database... I tried to segment it using mri_synthseg (freesurfer v 7.3.2)... But I got bad results... Only I got the segmentation of one region of the brain... Also, I do the crop of the image, and the threshold

[Freesurfer] Error Sourcing Freesurfer

External Email - Use Caution Hello, When trying to source Freesurfer version 7.1.1 using the command below, I'm getting the error "No such file or directory." source /usr/local/freesurfer/fs-stable711-env-autoselect Any guidance on potential solutions would be much appreciated!

Re: [Freesurfer] QDEC Alternative

External Email - Use Caution no plans for a new gui. you might look up qdecr. this is a 3rd party altenative that uses R; I've never used it myself, so I don't know how well it works on voxel-wise analysis or if there is a gui On 5/1/2023 2:00 PM, Lauren Stephens wrote:   

[Freesurfer] FreeSurfer VM Password

External Email - Use Caution Dear, Hi, Can I have the pass code to open the image FS_7_2_0_Ubuntu_18_04_06.ova.7z