Re: [Freesurfer] Linear mixed model for longitudinal data

External Email - Use Caution Hi Julian, please see my responses below. Best, Kersten Am 04.03.2022 um 14:11 schrieb Julian Macoveanu mailto:julian.macove...@gmail.com>>: External Email - Use Caution (Apologies for reposting due to lack of answer) Dear all, This is my

[Freesurfer] hypothalamic nuclei question

External Email - Use Caution I am trying to run the hypothalamic subunits segmentation but I am getting an error message (see below). I have FS7.2 installed on Ubuntu 18.04 (hippocampal and thalamic nuclei work fine). This error occurs even after changing the voxel size to 1x1x1

Re: [Freesurfer] hypothalamic nuclei question

Dear Niels, Would it be possible to share T1w_acpc_dc_restore_1mm.nii.gz with us so we can try on our end? Cheers, Eugenio Juan Eugenio Iglesias http://www.jeiglesias.com On 9 Mar 2022, at 09:16, Niels Janssen mailto:njans...@ull.edu.es>> wrote: External Email - Use Caution I

Re: [Freesurfer] run_samseg output folder permissions error

External Email - Use Caution This seems to have something to do with the image read/write tools in FS's Python tools not being able to handle ushort pixel types. One way around this would be to convert the input image into e.g., floats before calling samseg, but for a real fix in t

Re: [Freesurfer] mri_glmfit error: MatrixMultiplyD(): m2 is null

The problem is that your design matrix is badly scaled. The eTIV values are much larger than the group membership (value=1). Try subtracting the mean of the eTIV and dividing by the stddev to normalize it. On 2/25/2022 8:07 PM, 정현우 wrote: External Email - Use Caution Hi Dr. Greve,

Re: [Freesurfer] Hippocampal segmentation Matlab crash

External Email - Use Caution Tried it, but I still get the same error. -- Caitlin Bowman, Ph.D. Assistant Professor of Psychology University of Wisconsin-Milwaukee From: on behalf of "Hoopes, Andrew" Reply-To: Freesurfer support list Date: Tuesday, March 8, 2022 at 3:18 PM To

Re: [Freesurfer] Permission denied error from -localGI

Do you have permission to /scratch? Does it exist? On 3/2/2022 9:50 AM, Billah, Tashrif wrote: Hi all, We are trying to run recon-all with -localGI but running into an unknown permission denied error: $ recon-all -s sub-1001 -localGI ``` make_outer_surface('/path/to/FS_SUBJECTS_DIR/sub-100

Re: [Freesurfer] GLM analysis - volume and surface area

Can you just ask the question again so I don't have to sort it out myself? On 3/2/2022 3:30 PM, Laura Willers de Souza wrote: External Email - Use Caution Sorry about that! I'm resending with previous emails. The first message below is the one you didn't know how to respond to becau

Re: [Freesurfer] bbregister dependencies recon-all

You pretty much have to run it through to the end. You can try using mri_coreg (this is the first step of bbregister). It does not need anything but two images and will  run in  a few min. On 3/3/2022 5:24 AM, Guillem París wrote: > External Email - Use Caution > > Hello, > > I'm trying

Re: [Freesurfer] Error: inputs cannot have multiple frames

It means that you have two frames in the 001.mgz file. Sometimes this happens with multiecho mprages. If this  is the case, you can convert your input to a single frame with mri_concat --rms file.mgz --o file.rms.mgz Then use file.rms.mgz as the input to recon-all On 3/3/2022 12:04 AM, HYE JUNG

Re: [Freesurfer] ERROR: Flag -sveres unrecognized

What version are you trying to run? selxavg-sess has been depricated for years. Try selxavg3-sess On 3/3/2022 10:59 AM, CALLACHAND Muntasir wrote: External Email - Use Caution Hi, I have a problem when i try to run the function selxavg-sess

Re: [Freesurfer] Using T1 FLAWS in recon-all

never heard of FLAWS. My good search says that it is WM and CSF suppression, so it probably won't work. On 3/4/2022 6:10 AM, Mathilde Pichon wrote: External Email - Use Caution Hello, I know T1 MPRAGE is the prefered format to perform a recon-all segmentation. But some of my patien

Re: [Freesurfer] recon-all errors after mri_pretess

Does this fail every time like this? It looks like it just abruptly stopped. Does anything print out to standard error? On 3/4/2022 11:18 AM, Alexopoulos, Dimitrios wrote: External Email - Use Caution Hi, we’re running FS 7.2 ‘recon-all -all’ on a subject and are getting errors on ou

Re: [Freesurfer] Cutting the Full Surface

In FreeView Click on the brain with scissors icon ("Cut"), select your points, then "Cut Closed Line",    make sure the cusror is in the patch, then hit "Fill Uncut Area", then save as a patch On 3/7/2022 12:03 PM, Francesca Strappini wrote: External Email - Use Caution Dear FreeSu

Re: [Freesurfer] Cutting the Full Surface

External Email - Use Caution Thank you! On Wed, Mar 9, 2022, 19:28 Douglas N. Greve wrote: > In FreeView > Click on the brain with scissors icon ("Cut"), select your points, then > "Cut Closed Line", >make sure the cusror is in the patch, then hit "Fill Uncut Area", then > s

[Freesurfer] Atlas of primary motor and auditory cortex

External Email - Use Caution Hello Freesurfer experts, I ran the recon-all command and got all the .label files for the segmentations of the cortical areas. However, I have some questions about the label for primary motor and auditory cortex. - I found two types of labels asso

[Freesurfer] Oracle VM - SSH

External Email - Use Caution Hello FS experts I'm using freesurfer with the oracle VM and I need to SSH in from my host machine, I see that openSSH is installed on the VM, but haven't been able to get in. Does anyone have experience with/ advice for this? Thanks in advance Zo

Re: [Freesurfer] Oracle VM - SSH

External Email - Use Caution Hello Zoe, The VM is not setup out of the box with an IP address you can use to remotely login to from an outside machine.  It uses (or piggy-backs off) the existing network connection from the host machine.   This enables the VM to boot w/o needing

Re: [Freesurfer] recon-all permissions problems

External Email - Use Caution Hello Giuseppe, Try the same command (with lowercase w) or use a+w and then enter your password, $ sudo chmod -R  a+w  $SUBJECTS_DIRPassword: … then test to see if it works to create a file there, i.e., it should not report permission denied ... $ touc

Re: [Freesurfer] mri_glmfit error: MatrixMultiplyD(): m2 is null

External Email - Use Caution Hi Dr. Greve, Thank you very much for your solution. That solved the problem. I genuinely appreciate your support! Best, Hyunwoo Jeong 2022년 3월 10일 (목) 오전 2:52, Douglas N. Greve 님이 작성: > The problem is that your design matrix is badly scaled. The e