[Freesurfer] Error during decompression of DICOM JPEG compressed series

External Email - Use Caution Hi FS team, I am used to run Freesurfer v6.0 on a Ubuntu 18.04 workstation and everything runs well for most of the subjects that I process so first thanks for this great tool. I am facing an issue with a JPEG compressed DICOM series that I am not ab

Re: [Freesurfer] Error during decompression of DICOM JPEG compressed series

External Email - Use Caution I am using bash shell but I tried with many others as mentioned in my first post (zsh, tcsh, csh, sh) and nothing worked so far... - Mail original - De: "Douglas N. Greve,Ph.D." À: freesurfer@nmr.mgh.harvard.edu Envoyé: Mardi 2 Octobre 2018

[Freesurfer] Freeview coordinates

External Email - Use Caution Hi Freesurfer team, Sorry to ask a new question about FreeSurfer coordinates (I know it has been debated multiple times reading old messages) but I am still confused with all these spaces. I have a very simple use case in Freeview, when I load the T1

Re: [Freesurfer] Freeview coordinates

External Email - Use CautionHi Bruce,Thanks for the tip.When I run the command on 'lh.white' surface for example, I don't get an affine transform but a simpler one:vox2ras-tk:-1  0 0  128 0  0 1 -128 0 -1 0  128 0  0 0  1So when I apply this transform to a pixel position (152, 66, 7

Re: [Freesurfer] Freeview coordinates

External Email - Use Caution Hi Ruopen and Bruce, indeed I fixed the transform multiplication and now I am able to get the good coordinates. Thanks for your help! Best, Florent - Mail original - De: "Ruopeng Wang" À: freesurfer@nmr.mgh.harvard.edu Envoyé: Vendredi 26 O

[Freesurfer] Cannot disable the topology correction

External Email - Use Caution Hi FS team, I am having an error when disabling (-nofix) the topology correction with the recon-all command. The "-nofix" option is skipping the topology correction as expected but then the next step is failing because "?h.orig" file does not exist.

Re: [Freesurfer] Cannot disable the topology correction

External Email - Use Caution Hi Douglas, thanks for your answer. I agree that desabling the topology correction is not recommended but I am dealing with subjects having many lacunar infarcts that impact this step (running for more than 2 days sometimes and leading to segmentatio

[Freesurfer] Infant FreeSurfer issues

External Email - Use Caution Hi FreeSurfer team, I’ve been using the Infant FreeSurfer pipeline on 3DT1 sequences for few weeks now on infants from 0.4 to 5.4 years-old. I know Infant FreeSurfer is recommended for 0-2 years old infant but standard FreeSurfer was failing due to

[Freesurfer] Infant FreeSurfer: volumes

External Email - Use Caution Hi FreeSurfer team, I using the latest version of Infant FreeSurfer to assess brain volumes on very young kids. When looking at the brain volume (aka 'BrainSegVolNotVent') extracted from the aseg statistical file I got a very different volume than do

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] SAMSEG and statistics

External Email - Use Caution Hi FreeSurfer community, I recently discovered the SAMSEG application in the FreeSurfer 7.2.0 release and started to give a try on few subjects were FreeSurfer was having a hard time to segment brain structures (due to poor contrast). So I have few q

[Freesurfer] Infant FreeSurfer: volumes extraction without surface

External Email - Use Caution Hi FreeSurfer team, I've been using Infant FreeSurfer for several very young subjects and it works pretty well. But after reviewing the generated surfaces, it looks like pial surface is not extended to fit the cortical grey matter as you can see here