Re: [Freesurfer] Infant FreeSurfer: volumes

External Email - Use Caution Hi FreeSurfer team, would anyone have some information regarding my question arounf Infant FreeSurfer volumes? Thanks for your help. Best, Florent - Mail original - De: k3...@free.fr À: freesurfer@nmr.mgh.harvard.edu Envoyé: Lundi 14 Juin 20

[Freesurfer] Research Assistant Position in ECoG Lab (New York)

External Email - Use Caution Dear all, The human intracranial EEG (iEEG/ECoG) Laboratory for Human Brain Mapping at the Feinstein Institutes for Medical Research – Hofstra Northwell School of Medicine is looking for one research assistant with earliest start date in July 2021. T

Re: [Freesurfer] Issues with recon-all hanging

External Email - Use Caution Hi Doug, Sorry, I didn't explain it clearly. We are running recon-all on our MPRAGE anatomical data, which is collected at 0.75mm^3 (this is in the 7T scanner in Bay 2 of the Martinos Center). We are specifying recon-all to run using the 1mm MNI temp

[Freesurfer] Problem to run recon-all in one subject

External Email - Use Caution Dear Freesurfer's experts I am trying to run recon-all -all in a subject and it seems there is a problem I do not know how to solve. rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop $ recon-all -s sub-001_ses-BSL -i /home/rosalia/Desktop/ARTICO/sub-001_se

Re: [Freesurfer] Problem to run recon-all in one subject

External Email - Use Caution Hi Bruce, Yes, I noticed that I did not include the extension by error. Sorry for this childish error. Kind regards, Rosie On Mon, Jun 21, 2021 at 5:06 PM Fischl, Bruce wrote: > Hi Rosalia > > > > Does /home/rosalia/Desktop/ARTICO/sub-001_ses-B

Re: [Freesurfer] Problem to run recon-all in one subject

Hi Rosalia Does /home/rosalia/Desktop/ARTICO/sub-001_ses-BSL_T1w exist? Shouldn’t it have an extension like .nii.gz or .mgz? Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Rosalia Dacosta Aguayo Sent: Monday, June 21, 2021 10:49 AM To: Freesurfer support list Subject:

Re: [Freesurfer] Problem to run recon-all in one subject

No worries, it happens to all of us 😊 Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Rosalia Dacosta Aguayo Sent: Monday, June 21, 2021 11:07 AM To: Freesurfer support list Subject: Re: [Freesurfer] Problem to run recon-all in one subject External Email - Use Caution

[Freesurfer] question about partial volume corrections with PETSurfer

External Email - Use Caution Dear PetSurfer and Freesurfer Developers, I would like to run partial volume corrections on amyloid PET images (from ADNI) with PetSurfer. I have downloaded the amyloid PET images that were intensity normalized to the cerebellar GM. However, I not

[Freesurfer] Recon-all for multiple cases

External Email - Use Caution Hello FreeSurfer specialists, I am new to FreeSurfer and I am trying to learn how to run the basic recon-all command for multiple subjects at once. Could someone help me with what the command would look like to run a folder full of .nii files (e.g.,

[Freesurfer] Help with LGI pipeline output - Freeview

External Email - Use Caution Dear FreeSurfer experts, Hope that everyone is well and having a great Monday. I am having some trouble opening the outputs for the LGI pipeline via Freeview - could someone please help me with this? I tried using + editing the code available on the

Re: [Freesurfer] Recon-all for multiple cases

Hi Spencer Are 01.nii and 02.nii MRI volumes for different subjects? Do you have only a single volume/subject? If so, you would recon-all on each one individually. Something like: recon-all -i /01.nii -s subj01 -sdir -all if you have 8 cores and enough ram you can run 8 subjects at the same t

[Freesurfer] Hippocampal Subfields/ASEG

External Email - Use Caution Hello, I have a couple of questions concerning the hippocampal subfield extractions as well as the hippocampus extraction included in ASEG. I have looked around and tried to find as much information as possible about the two but I can't seem to find a

Re: [Freesurfer] Hippocampal Subfields/ASEG

External Email - Use Caution Hello Yiota, the whole hippocampus value is a sum of all subregions except for the hippocampal fissure - best try to reproduce this in an example. The recon-all pipeline also delivers a total hippocampal volume, but it is an entity/result of its o

Re: [Freesurfer] Hippocampal Subfields/ASEG

External Email - Use Caution Hi Philipp, Thank you very much! This was very helpful! Best, Yiota On Mon, Jun 21, 2021 at 3:38 PM Saemann, Philipp wrote: > External Email - Use Caution > > Hello Yiota, > > > the whole hippocampus value is a sum of all subregions except