Freesurfer Mri

[Dorothy Gouldie]

Doesthat mean I have to paste the four lines into a file called "license.txt"? I actually did in this way. I paste the four lines at the end of a file called "license.txt". But when I finish all the steps and check the installation. There is an error popping up:

All in all, installing Freesurfer is not that hard, but installing it in a new linux system is surely a better option than messing with VirtualMachines in Windows. The VM that they offer in their website does not allow to run the commands in files residing in the host machine, which is the point of running a VM in the end.

The current freesurfer 7.2 version has some semblance of a binary installer (.deb package) that worked for me on Ubuntu 18( ). On Windows, in lieu of running Ubuntu in a VirtualBox VM (which includes an X-server), you can use the windows subsystem for linux (WSL) to download and run the default Ubuntu image. Then try to download and run the freesurfer .deb binary installer in Ubuntu. With WSL 1 or 2 you can access the path to your windows home directory mounted in linux ( _wsl). You still need to setup an X server on Windows 10 to work with freeview running in Ubuntu under WSL, but I read that should no longer be necessary with WSL in Windows 11. Once you obtain a freesurfer license ( ) then just set the environment variable FS_LICENSE to the absolute path for the license file, e.g., in your shell init file in Ubuntu (in order for freeview to run).

Hi, I am facing the same problem. When I try to load a freesurfer segmentation (a standard aparc+aseg.mgz) on Ubuntu (either using the importer interface, the load volume interface or a slicerpython command) I will get this error:

The main conclusion is that in the context of an ongoing study, users are discouraged to update to a new major release of either FreeSurfer or operating system or to switch to a different type of workstation without repeating the analysis; results thus give a quantitative support to successive recommendations stated by FreeSurfer developers over the years. Moreover, in view of the large and significant cross-version differences, it is concluded that formal assessment of the accuracy of FreeSurfer is desirable.

Copyright: 2012 Gronenschild et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Funding: This work was supported by the Geestkracht program of the Dutch Health Research Council (ZON-MW, grant number 10-000-1002), and the European Community's Seventh Framework Program under grant agreement No. HEALTH-F2-2009-241909 (Project EU-GEI). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Just like similar neuroimaging packages, new releases of FreeSurfer are issued regularly, fixing known bugs and improving existing tools and/or adding new ones. Each release is accompanied with documentation describing the changes relative to the previous release ( ). However, transition to a new release during the course of a study may affect the results and is therefore discouraged by the developers of FreeSurfer. This potential source of variation in outcome may invalidate comparisons between different studies. As yet, the sources and effect sizes of these variations have never been investigated in detail.

The goal of the present study was to address the above mentioned questions by repeating the automated segmentation on the same workstation and on different workstations using a set of 30 anatomical T1-weighted MRI scans. Three different versions of FreeSurfer were used on a single Hewlett-Packard workstation and several Macintosh workstations running under two different OSX versions. In particular, we aimed to get insight into the variabilities resulting from these different data processing conditions and to compare these with reported accuracy and reliability results and morphological and pathological cerebral changes. Although the developers of FreeSurfer have been explicitly recommending users not to mix FreeSurfer versions, platforms, and OS versions within a study (see public archives at http:/www.mail-archive.com/freesurfernmr.mgh.harvard.edu), to our knowledge this is the first time that the effects of these different processing conditions have been quantified systematically.

The study was approved by the ethics committee of the Maastricht University Medical Center and all participants gave written informed consent in accordance with the committee's guidelines and with the Declaration of Helsinki [15]. All patients were mentally competent to consent as evaluated by trained psychology graduates during the screening and informed consent procedures, i.e., participating patients were fully understanding information disclosures and study procedures.

Two workstations and corresponding operating systems were at our disposal for this study (Table 1). On the Macintosh (Mac) platforms, FreeSurfer used the UNIX shell while on the Hewlett-Packard (HP) platform, LINUX was used (CentOS 5.3). One Mac workstation was configured to run under two different OS versions by means of an external disk. Although OSX 10.6 is able to run in 64 bits mode, we used 32 bits mode only (see next section). By contrast, on the HP platform, CentOS was used in 64 bits mode.

The volumes are presented by FreeSurfer in the form of tables and labeled voxels. The tabulated volumes are more accurate than the voxel volumes because they are corrected for partial volume effects. Both types of volumes were used in our analysis (see Document S1 for more details).

In order to compare the results with accuracy results previously reported by Lehmann and colleagues [5], a few white matter and grey matter regions were merged to produce a whole gyrus or lobe (left and right), such as medial-inferior temporal gyrus (MITG), superior temporal gyrus (STG), and temporal lobe (TempL). Simarly, total ventricle volume (Ventr) was constructed (left+right added together). In this manner, a total of 7 composite volumes were assembled. (The respective segmentation labels were kindly provided to us by Dr. Manja Lehmann, University College London, UK, see Document S1 for more details).

In total, we computed 190 (sub)cortical volumes (185 for v5.0.0) and 68 CT values. It should be noted that no manual corrections were made to any of the FreeSurfer results in order to ensure a valid analysis. However, a visual inspection was performed to check the segmentations.

Three versions of FreeSurfer were used: v4.3.1, released on 19 May 2009, version v4.5.0, released on 11 August 2009, and version v5.0.0, released on 16 August 2010. For the Mac workstations these are 32 bits versions (due to problems to build some third party libraries in 64 bits mode on the Mac), whereas for the HP workstation these are 64 bits versions.

The experiments where carried out on multiple Mac workstations and a single HP workstation. Experiments 1 and 2 were designed (1) to disclose any difference between runs on the same workstation and between runs on different workstations and (2) to reveal any interference between parallel running streams. Experiment 3 provided insight into the effects of different versions of FreeSurfer. In experiments 1 to 3, OSX 10.5.8 was used on the Mac workstations. Finally, the effects of different Mac OSX versions were investigated in experiment 4 for all FreeSurfer versions used.

Several statistical measures were employed to quantify the effects studied, such as mean difference and standard deviation, and the coefficient of variation (COV), defined as the percentage standard deviation relative to the mean. In addition, we computed the measure of spatial overlap of a structure, also known as similarity index (SI) or Dice coefficient [29]. Its range is between 0 (no overlap) and 1 (complete overlap). Finally, the intra-class correlation coefficient, ICC, based on the one-way random effects model [30] was calculated. More details can be found in Document S1.

For the statistical analysis, the paired Student t test was applied, since each time the outcome of two conditions was compared. We considered two levels of statistical significance, both corrected for multiple comparisons. The first level was set to p

No differences were detected between repeated single runs nor between single runs and parallel runs on the same workstation and for the same FreeSurfer and OS version. For the same OS version, all Mac workstations produced identical results. However, differences were revealed between:

The differences are presented in more detail below, starting with an overview and subsequently zooming in on specific structures and data processing comparisons. For the volume measurements, only voxel volumes are considered since the results for tabulated volumes were very similar.

A complete overview in the form of colored cells for all comparisons is illustrated in Figure 1 (voxel volume) and Figure 2 (CT). With such reproduction, reminiscent of a DNA microarray, one can get a good impression of the results at a glance. By far the most colored cells were found for the cross-version comparisons (v4.3.1 vs. v5.0.0 and v4.5.0 vs. v5.0.0).

As described above, the level of statistical significance after correction for multiple comparisons depends on the data processing contrast being considered, see Table 2. It turned out that for the volumes, significant differences were derived only for the cross-version contrasts v5.0.0 vs. the two earlier versions (both Mac and HP). However, for CT, significant differences were found also for some other data processing comparisons. If FDR correction was applied to the volume results, then almost all the colored cells for the cross-version contrasts v5.0.0 vs. v4.3.1/v4.5.0 (both Mac and HP) in Figure 1 represent significant differences. In fact, about half of the 178 structures were significant. With a conservative Bonferroni correction, about a quarter of the structures were significant. For CT rather similar results were obtained: about half/a quarter of the 68 cortical structures were significant after FDR/Bonferroni correction in case of the cross-version contrasts v5.0.0 vs. v4.3.1/v4.5.0 (both Mac and HP). Furthermore, in case of the HP vs. Mac and Mac OSX 10.6 vs. OSX 10.5 contrasts, significant CT differences were found for versions v4.3.1 and v4.5.0, whereas no significant CT differences were present at all for version v5.0.0.

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