[Freesurfer] Z-stat - z.mgh

Dear FreeSurfer users I am not able to extract the Z-values as they are not present in my output: z.mgh -- z-stat that corresponds to the significance Are these Z-values always produced (or only in case of two group comparison)? Is there a way to produce this map myself? This is my output afte

Re: [Freesurfer] unit for hippocampus segmentation results

If you mean the new subfield module, then the answer is: cubic mm. Juan Eugenio Iglesias Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of

Re: [Freesurfer] Maps/seed on surafce

Hi Dr. Greve, I used following command for this: mkanalysis-sess -analysis LH_XY.surf.lh -surface fsaverage lh -fwhm 5 -notask -taskreg LH_XYZ.dat 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -mcextreg -polyfit 5 -nskip 4 -fsd bold -TR 3. Thanks. On Wed, Jun 15, 2016 at 3:07 PM, Douglas N Greve w

[Freesurfer] Hippocampal subfields error

Hi all I ran recon-all on data from about 60 participants pre and post an intervention, with the hippocampal subfields flag (e.g. "recon-all -all -subjid SPS01-1910_pre_lazar -hippocampal-subfields-T1"). The recon-all.log file states that the process finished without errors. However, the hippoca

[Freesurfer] Error loading a constructed annotation file

Dear freesurfer experts, I constructed an annotation file using mris_label2annot. I did this several times and every time it worked very well. I was able to use a ctab to define several colors, load my annotation file into freeview, and look at it. Now I tried to construct another annotation fil

Re: [Freesurfer] Error loading a constructed annotation file

Hi Nora you need to send us the complete command line you ran and also the error message and the complete terminal outpu cheers Bruce On Thu, 16 Jun 2016, Bittner, Nora wrote: Dear freesurfer experts,   I constructed an annotation file using mris_label2annot. I did this several times and

Re: [Freesurfer] convert from MNI152 to native space

Hi FS Experts, I'm trying to use the mni152reg command but I get an error that --lta is not recognized. It appears that fslregister doesn't have this option. There was a previous post about this problemhttp://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg41953.html but I can't figure

Re: [Freesurfer] Hippocampal subfields error

I've also gotten this error recently, with T1, T2, and combined T1+T2 hippocampal segmentations. It looks like the files exist at /autofs/cluster/freesurfer/centos6_x86_64/dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf exist, they just don't have the ".ctf" file extension. Matt ___

Re: [Freesurfer] Hippocampal subfields error

Thanks Matt. Did you somehow get it to work or recognize the file without the ctf extension? Thanks Jonathan From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Hibert, Matthew Louis [mhib...@mgh.harvard.edu

[Freesurfer] Job opening: Computational Neuroscience Faculty

Computational Neuroscience Faculty University of Minnesota, Minneapolis, MN, USA The University of Minnesota seeks 2 scientists with documented backgrounds and interests in using brain imaging and computational neuroscience to understand brain function in health and disease. The University of

Re: [Freesurfer] Hippocampal subfields error

No, I just wanted to mention that in case it helps with troubleshooting what went wrong with the new dev version build. Matt From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Greenberg, Jonathan [jgreenbe.

[Freesurfer] Apply mris_apply_reg for a label

Hello everyone, I have a label for the left hemisphere for my subject but I don't understand the syntax to apply mris_apply_reg on this label to obtain the right hemisphere version. mris_left_right_register was performed to get lh.sphere.left_right and lh.sphere.left_right but I don't know how to

Re: [Freesurfer] Apply mris_apply_reg for a label

Hi Alexandre try mri_label2label using the ?h.sphere.left_right cheers Bruce On Thu, 16 Jun 2016, Alexandre Routier wrote: Hello everyone, I have a label for the left hemisphere for my subject but I don't understand the syntax to apply mris_apply_reg on this label to obtain the right hemispher

Re: [Freesurfer] Hippocampal subfields error

Thanks. Has anyone else encountered this error message or knows how it can be solved? Thank you Jonathan From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Hibert, Matthew Louis [mhib...@mgh.harvard.edu] Sent

[Freesurfer] FSFAST- Cerebellum

Hi all, I am trying to extract mean time series BOLD data using FSFAST from Cortical ROIs + sub cortical ROIs and cerebellum. preproc-sess -s rest210 -fsd bold -surface fsaverage lhrh -mni305 -fwhm 6 -per-run -stc odd    mri_segstats --annot fsaverage lh aparc --i rest210/bold/001/fmcpr.odd.sm6.

[Freesurfer] modifying files on older versions of FS

I have successfully processed data with FS v5.3 (linux/CentOS) using recon-all -all. Is it possible to make modifications to the 5.3-generated brainmask.mgz (primarily dura removal) and wm.mgz files using a much older 4.4 version of FS and then re-run recon-all on 5.3 with these modified files.

Re: [Freesurfer] GLM_Fit Question

Hi Freesurfers, I am having a similar problem with the FSGD file as the user indicated at this thread: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg40599.html I am trying to access the script that Doug wrote in order to fix it, however, the link to download the script does not

Re: [Freesurfer] modifying files on older versions of FS

Why would you want to do that? Peace, Matt. From: on behalf of "Alexopoulos, Dimitrios" Reply-To: Freesurfer support list Date: Thursday, June 16, 2016 at 4:06 PM To: Freesurfer support list Subject: [Freesurfer] modifying files on older versions of FS I have successfully processed da

Re: [Freesurfer] modifying files on older versions of FS

We haven't been able to get FS 5.3 (running on a linux server) output to display on our Win 7 PC's using Xming or Exceed X11 emulators. We get errors (below) on all our PCs. Appears to be related to low-end video cards not-supporting openGL. [sge-login1 ~]$ tksurfer GLUT: Fatal Error in tksurfer

[Freesurfer] Brodmann annotation on fsaverage

Hi, Freesurfer has an annotation file for Brodmann areas, which is ?h.PALS_B12_Brodmann.annot. This Brodmann parcellation doesn't seem to be accurate in certain regions (e.g. in retrosplenial and perirhinal cortex). Does anyone have an alternative Brodmann atlas that can be visualized in Freesurfe

Re: [Freesurfer] modifying files on older versions of FS

wow, 4.4, that's pretty old. Not sure, I guess try it Bruce On Thu, 16 Jun 2016, Alexopoulos, Dimitrios wrote: I have successfully processed data with FS v5.3 (linux/CentOS) using recon-all -all.   Is it possible to make modifications to the 5.3-generated brainmask.mgz (primarily dura remov

[Freesurfer] All coordinates of volume of interest

Hi, Is there a way to get all coordinates (x,y,z) of the particular volume of interest (e.g., left-insula, left-thalamus)? Best, Aziz. -- Aziz Nanthaamornphong, Ph.D., Faculty of Technology and Environment Prince of Songkla University, Phuket Campus +66 7627 6716 (v) http://research.te.psu.ac.t