[Freesurfer] Post list

External Email - Use Caution Hi, I want to send mail Best Öğr. Gör. Dr. Halil Aziz Velioğlu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] about to segmentation

External Email - Use Caution Hi Mr/Mrs, I want to segment substantia nigra, nucleus ruber (red nucleus) and subthalamic nucleus in Freesurfer. These regions are not in aseg.stats file. So how can I segment these regions? Is there any pipeline or scripts? Best regard, -- Öğr. Gö

Re: [Freesurfer] segmentThalamicNuclei.sh exited with error

Dear Dalton, Did you install the Matlab 8.4 runtime as explained in the wiki? Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: on behalf of Dalton Bermudez Reply-To: Freesurfer support list Date: Thursday, 21

Re: [Freesurfer] Freesurfer 4.5 on Ubuntu 18.04 ?

External Email - Use Caution Hello Paulo, I could be wrong, but I don’t see that freesurfer 4 contains or shipped with any ./lib directory with its own copies of needed libraries like libvtk*, libtcl*, etc.   On Ubuntu, those libraries are installed on the system under /usr/lib/

Re: [Freesurfer] Recon-all Error

External Email - Use Caution > On November 21, 2019 at 7:56 PM "Greve, Douglas N.,Ph.D." > wrote: > [...] > But the error you are > seeing appears to be that the mritotal program cannot be found (not a > computational problem or problem with your data). But it is strange that

Re: [Freesurfer] Map fMRI data onto surface

What is the blue? The best way to dispaly it is to show the fMRI in gray scale with the surfaces overlaid on it. What exactly is the input pa0292_S004_bis_matrix_new_1_preprocessed_output_crop.nii.gz? How was it created? Can you verify that the orientation is correct? You can load it in FreeVie

Re: [Freesurfer] Question about the input for longitudinal processing pipeline

Do you have a "norm" mprage? On 11/21/19 3:49 PM, Darko Komnenić wrote: > > External Email - Use Caution > > Thanks a lot for the reply and the suggestions, Douglas! These scans > are at 3T. > Best, > Darko > > -- > > Message: 4 > Date: Wed, 20 Nov

Re: [Freesurfer] Map fMRI data onto surface

Why are you using --t1? If this is fmri, it should be --t2 On 11/21/19 3:27 PM, An wrote: > > External Email - Use Caution > > The image in the previous email uses the command tkregisterfv to > visualize the registration result after step2 bbregister, where I > uncheck the boxes of the s

Re: [Freesurfer] Question about the input for longitudinal processing pipeline

External Email - Use Caution Thanks a lot for the reply and the suggestions, Douglas! These scans are at 3T. Best, Darko > -- > > Message: 4 > Date: Wed, 20 Nov 2019 22:45:18 + > From: "Greve, Douglas N.,Ph.D." > Subject: Re: [Freesurfer] Question

[Freesurfer] segmentThalamicNuclei.sh exited with error

External Email - Use Caution Dear Freesurfer Support Team, I am trying run the file segmentThalamicNuclei.sh to segment the thalamic nuclei on a subject. I am using the following command line: /usr/local/freesurfer/bin/segmentThalamicNuclei.sh 00_0086 $SUBJECTS_DIR. However, the p

Re: [Freesurfer] Map fMRI data onto surface

It is hard to say from that image, but it does not look registered to me. - your bbregister command is not valid as it is, please give the full command - please send the bbregister log file - to look at the registration, use tkregisterfv. It will show the surfaces over the fMRI On 11/21/19 1:20

Re: [Freesurfer] Recon-all Error

I don't generally discourage it, but I don't think many people use it, and so it might not be maintained that well. But the error you are seeing appears to be that the mritotal program cannot be found (not a computational problem or problem with your data). But it is strange that you could run

[Freesurfer] freesurfer linux-ppc build

External Email - Use Caution Hello, Is there an available freesurfer linux power pc (Power 9) build? I can not find any information about this online. If not , I have been working on making one and would like to know if anyone else has any progress ... Thanks, Ryan Schneider Bo

Re: [Freesurfer] Recon-all Error

External Email - Use Caution Thank you, Douglas, for your fast reply. I have used -3T option for all my dataset (>80 subject so far) and it worked well for all except for this subject. Do you generally discourage using this option? I thought it does some normalization/denoising for

Re: [Freesurfer] Map fMRI data onto surface

35% sounds high to me. Did you actually check the registration You can always load the the fMRI as an overlay in freeview, try tksurferfv subject lh inflated -ov fmri-sampled-on-lh.mgz Also, please include command lines you used On 11/21/19 10:03 AM, An wrote: > > External Email - Use Cau

Re: [Freesurfer] Substantia nigra delineation

Sorry, we don't have tools to segment substantia nigra. Hopefully coming soon On 11/21/19 4:34 AM, Aline Delva wrote: > > External Email - Use Caution > > Dear, > > We would like to delineate the substantia nigra using a 3D Sag BRAVO > and a 3D Sag FLAIR in freesurfer. > > What is the op

[Freesurfer] Map fMRI data onto surface

External Email - Use Caution Hi there, I want to map the intensities of the fMRI 4D volumes onto its surface in order to get the functional values on each vertex in each frame. I have done the following steps for achieving this: 1. ran recon-all on its anatomical volume. 2. regis

Re: [Freesurfer] Freesurfer 4.5 on Ubuntu 18.04 ?

External Email - Use Caution Hello-- Good morning. Thank you very much for your email. Yes we have the license file. When we didn't have the license file, we would get an error about missing license file. (base) pbaptist@clps-pb1:/var/tmp/freesurfer4$ ls ASegStatsLUT.txt bin

[Freesurfer] Substantia nigra delineation

External Email - Use Caution Dear, We would like to delineate the substantia nigra using a 3D Sag BRAVO and a 3D Sag FLAIR in freesurfer. What is the optimal method to do this? We already performed recon all and unfortunately SN was not segmented. Yours sincerely, Delva Aline,