Re: [Freesurfer] Is ICV needed as a covariate if matched between groups

External Email - Use Caution Hi Carly, plus, if I may answer in addition, make sure that the ICV differences are checked with sex as covariate, so that statement of yours is only valid, if analyzed also per sex separately, or with sex as covariate. Next, you should also (onc

[Freesurfer] Question on mri_nu_correct for 3 Tesla data

External Email - Use Caution Hi FreeSurfer specialists, we have problems with a strong non-intensity in 3 Tesla data of GE (mainly temporal poles and occipital area). We managed to rescue the occipital errors by a pre-Bias-field correction using SPM, but would of course try t

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

External Email - Use Caution Hi Saurabh, you have to run (and QC) recon-all before, Best, Philipp Von: freesurfer-boun...@nmr.mgh.harvard.edu im Auftrag von Jindal, Saurabh Gesendet: Donnerstag, 22. April 2021 20:55 An: freesurfer@nmr.mgh

Re: [Freesurfer] Use Hippocampal segmentation sub-nuclei on other brain softwares

External Email - Use Caution Hi Gregorio, you need to transform the *mgz output images accordingy to NIFTIs images. Here is some exemplary shell code for the left hemisphere - operating in a subject's mri folder, using the FS6.0 type of aggregation (if you used FS7.1, you might

[Freesurfer] addon question perl version needed for FS5.3

t; or could they be exchanged by the mni folder of FS6.0 in order to avoid the break of the perl script due to a version problem? Thanks for any hints, Philipp Von: freesurfer-boun...@nmr.mgh.harvard.edu im Auftrag von Saemann, Philipp Gesendet: Montag, 12.

[Freesurfer] perl version needed for FS5.3

External Email - Use Caution Hi all, we have problems in launching the recon-all command of FS5.3 (needed for a reconstruction of old results): during the nu_correct command various perl commands are called with a fix #!/usr/bin/perl -w The primary error is some "Can't used

Re: [Freesurfer] 2mm thick image for hippocampal segmentation.

External Email - Use Caution Hi, I try to answer but Eugenio may also add comments. Several points that are important: - 1.5 Tesla and 1x1x1 mm3 are at the limit of what the algorithm can manage. - Post-aquisition reslicing to a higher resolution does not really increase the

Re: [Freesurfer] license file not working

Freesurfer support list Betreff: Re: [Freesurfer] license file not working Hi Philipp, Can you let us know the OS and version you’re running on? The license format was updated for v6. It should be backwards compatible, but it’s possible it’s not anymore on newer systems. thanks Andrew Fro

[Freesurfer] license file not working

External Email - Use Caution Hi FreeSurfer specalists, for some historical reconstruction I had to download an old FS5.3-Version, on a Linux System, untarred etc. - it seems there was no .license = hidden license file coming with the download, and no license.txt file. I req

Re: [Freesurfer] license file not working

e file? Make sure it >is a simple ascii text file not created under Windows > > >On 08/01/2014 04:10 PM, Saemann Philipp wrote: >> Hello users or support team, >> >> after using FS successfully for some time, now, after >> a trivial command such as >> &

[Freesurfer] license file not working

Hello users or support team, after using FS successfully for some time, now, after a trivial command such as mri_convert -it analyze T1.img -ot mgz 001.mgz an error appears as follows: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from T1.img... -