Re: [Freesurfer] FS on Ubuntu {Disarmed}

External Email - Use Caution Hello Olga, I have not tried the FS 5.3 binaries on an Ubuntu 20 system, but I suspect some shared library references won’t be resolved there.  Even if the FS 5.3 source were to compile on Ubuntu 20, you would likely get some discrepancy in numeric o

[Freesurfer] Failed tissue type check {Disarmed}

External Email - Use Caution Dear Doug, I have the same issue as the people below. I was wondering if this was solved in the meantime. I ran petsurfer gtmpvc with the psf 0 and no-tfe flags to not do PVC and got the following error in only one of my subjects. When I ran the same

[Freesurfer] recon-all issue in vmPFC with high-res T1/T2 data {Disarmed}

External Email - Use Caution Hi all, I'm encountering an issue with surface reconstruction quality in ventromedial prefrontal cortex, using relatively high resolution (.8mm) T1- and T2-weighted input data to recon-all. I'm using the following command, with Freesurfer 7.1.1 running

[Freesurfer] ERROR HC subfield segmentation_FS7.1.1

External Email - Use Caution Dear FreeSurfer Developers, I would like to run the Hippocampus subfields segmentation on Freesurfer 7.1.1. I am working on a HCP cluster with CentOS 7 (Core). Before running the segmentation on my data, I first tried to run the segmentation on your

Re: [Freesurfer] asegstats2table

Hi Alberto, My name is Devani Cordero, I'm a research technician for the FreeSurfer lab. You can absolutely use asegstats2table. First, what kind of labels did you create? Did you make them based off of a volume such as T1.mgz or did you create them on a surface? Let me know! Devani Devani C

[Freesurfer] Regarding MNI152 TEMPLATE

External Email - Use Caution Dear All, Hope everyone is safe and well. Did anyone you have MNI152 TEMPLATE mainly required for Alzheimer's Diagnosis. Also can anyone help in recommending any tool other than FREESURFER for preprocessing of sMRI scans for Alzheimer's disease but the

Re: [Freesurfer] ERROR HC subfield segmentation_FS7.1.1

Dear Alessio, You need to request approximately 16GB of RAM when you submit your jobs to the cluster. Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: on behalf of "alessiopropos...@libero.it" Reply-To: Free

[Freesurfer] Multiple Frames

Hi FreeSurfer Developers, I am trying to process a few MPRAGE sequences (different sessions), so I can edit the scans. And I am having trouble reconning the .mgz files. I have looked into why my job terminated early and I have attached the message below. The error states that 'input(s) cannot

[Freesurfer] FS on Ubuntu {Disarmed}

External Email - Use Caution Dear colleagues, I am looking for information about installing FS on Ubuntu 20.04. One concern is that we might need to be able to use an older version of FS (e.g. FS 5.3), and from what we can tell that won't even be compatible with Ubuntu 18.0

Re: [Freesurfer] Freesurfer Digest, Vol 202, Issue 30 {Disarmed}

External Email - Use Caution Hi Douglas, Thanks a lot for your kind explanation! With regards Vittal On Thu, Dec 17, 2020 at 8:12 PM wrote: > Send Freesurfer mailing list submissions to > freesurfer@nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wi

Re: [Freesurfer] group analyses {Disarmed}

Sorry, I'm not sure what you mean when you say the volume map is uncorrected On 12/14/2020 10:02 AM, Sara Lyn wrote: External Email - Use Caution And also i'm trying to extract these values from the uncorrected maps not corrected. Is there a way for that? Thank you On Mon, Dec 14, 202

Re: [Freesurfer] group analyses {Disarmed}

If you want to apply etiv correction when extracting the cortical volume with mris_preproc, just add --etiv to the command On 12/14/2020 9:59 AM, Sara Lyn wrote: External Email - Use Caution Hi Thank you for your response. How do I correct this extracted volume for intracranial volume

Re: [Freesurfer] cannot find freesurfer/average/RB_all_2008-03-26.gca with -use-gpu in v5.3 {Disarmed}

External Email - Use Caution Hi Doug, it turns out part of the v5.3 installation had been accidentally deleted. After restoring the file, it works fine, and I am happy to report the the GPU versions work (with CUDA 5). Thanks! Caspar Am Do., 17. Dez. 2020 um 15:37 Uhr schrieb Gre

Re: [Freesurfer] cannot find freesurfer/average/RB_all_2008-03-26.gca with -use-gpu in v5.3

The GPU stuff may or may not work. It was hard to maintain because the GPUs kept changing so much, and it would not surprise me that the code from 5.3 is incompatable with GPUs today. But it looks like the error is that it could not find a file. Does that file actually exist? On 12/12/2020 3:04

Re: [Freesurfer] Error in selxavg3-sess

Are there presentations that are simultaneous? On 12/12/2020 3:19 AM, Nina Khatibi wrote: External Email - Use Caution Hi, I'm using a functional analyse with selxavg3-sess, i have 25 subjects and each subject contains 15 runs, I've done plenty of analyses with different paradigm files

Re: [Freesurfer] HCP_1200 parcellation problems

Sorry, I can't tell from your email what the problem is. Can you elaborate? On 12/9/2020 2:30 PM, najme soleimani wrote: External Email - Use Caution Dear FreeSurfer Developers, I downloaded the HCP_1200 subjects' structural extended data. I am attempting to have equal sized parcellatio

Re: [Freesurfer] need assistance to decode QDEC results

It depends on the order that you specified them. You will have four groups SczUrban SczRural HVUrban HVRural The interaction will be of the form (SczUrban-SczRural)-(HVUrban-HVRural) Look in the y.fsgd to see what the order of the classes is. You can then look in the contrast folder at C.dat to

Re: [Freesurfer] MP2RAGE pial surface edit error

Essentailly, this is a skull strip error, so you may need to remove the skull (ie, non-brain) manually On 12/9/2020 6:25 AM, Elisa Rehbein wrote: External Email - Use Caution Dear Freesurfer experts, we are currently running recon-all for our MP2RAGE images, using Freesurfer 7. Howe

Re: [Freesurfer] Extracted mean timecourse from FS label

I don't know, that msg probably comes from the gifti code we link to. It looks like it is just a warning. Do the output waveforms look ok? On 12/9/2020 6:05 AM, Mason Wells wrote: External Email - Use Caution Hi Experts, I have pre-processed some resting-state date using fMRI prep. I h

Re: [Freesurfer] {Disarmed}

External Email - Use Caution Any tools other than Freesurfer for preprocessing Nifti sMRI scans. Only requirement is it should work on windows. On Thu, 17 Dec 2020, 4:22 pm Laura f, wrote: > Dear Sir or Madam, > I am not longer working with FreeSurfer so I would like to remove m

[Freesurfer] (no subject)

Dear Sir or Madam, I am not longer working with FreeSurfer so I would like to remove my subscription to the mailing list. Thank you, Laura smime.p7s Description: S/MIME cryptographic signature External Email - Use Caution___ Freesurfer m

[Freesurfer] FREESURFER AND NEURONAVIGATOR IMAGE

External Email - Use Caution I need to use freesurfer brain_anat.nii T1 and path.pd.nii (CST WM tract ) in the navigator for neurosurgery. It is necessary to merge the two volume images and to transform it in dicom.Exist a command for that or a procedure in Fressurfer? Or sam