Re: [Freesurfer] Serious failure of surface reconstruction

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Re: [Freesurfer] Serious failure of surface reconstruction

___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in

[Freesurfer] Serious failure of surface reconstruction

My last email seemed to be too big because of the picture, so I try it without the picture Dear FreeSurfers, after having now completed the automatic Freesurfer reconstruction without error message (with Fressurfer Centos X64 v4.5.0 on a Debian Machine version 5.0.4, see my email from yes

[Freesurfer] Error while loading shared libraries: libtiff.so.3

Dear FreeSurfers, I am running freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 on a Linux Debian machine (for details see below). After running stable till the -autorecon3 step, the process was killed because the shared library libtiff.so.3 was not found in this distribution. We currently t

[Freesurfer] Cerebellum volume analysis

Dear FreeSurfers, I plan to do a cerebellar volume analysis in a rather large clinical sample and thereto originally aimed to follow the instructions of Makris and colleaugues (2003, 2005). Unfortunatly I was not able to get access to all the necessary software and accordingly I am forced to im

[Freesurfer] signal loss in the orbitofrontal cortex

Dear FreeSurfers, in the FreeSurfer cortical parcellation procedure, a volume measure is calculated for the lateral orbitofrontal cortex and in my study population I indeed do find a significant group difference in the volumes of this region. However, there certainly is signal loss of the MR si

[Freesurfer] ROI extraction based on t-values

Dear FreeSurfers, is there an easy way to extract the mean cortical thickness of clusters according to a predefined t-value threshold? I performed a cortical thickness analysis between 3 groups and found some clusters where the groups differed significantly. Now, I would like to extract the mea

[Freesurfer] error in autorecon1

Dear Freesurfers, when I try to run the recon-all flow, it exits at the skull stripping stage in some subjects, giving out error messages like this: register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 GCAhistoScaleImageIntensities: could not find wm pe

[Freesurfer] ROI definition based on cortical parcellation

Dear freesurfers, comparing patient groups I found volume differences in specific cortical regions (using aparc_stats), which I would now like to compare to the results of a classical VBM. Concerning the whole brain analyses, the VBM did not yield comparable results (what might partly be a mat

[Freesurfer] scale factor in talairach transformations

Dear freesurfers, I am new in the list and will start with a hopefully not too stupid question... besides a planned cortical thickness analysis I would like to compare the volumes for some cortical parcellation areas between three groups. As far as I understood the freesurfer-procedures the bra