[Freesurfer] problem mri_convert

Dear FreeSurfers, On one of our Linux machines we encounter the following error message when calling mri_convert: /lib64/libz.so.1: no version information available (required by mri_convert) /usr/lib64/libstdc++.so6: version GLIBCXX_3.4.11 not found (required by mri_convert) Mri_convert has w

[Freesurfer] Extract values in ROI to ascii file

Dear Freesurfers, I am using mris_convert to obtain per vertex thickness values in an ascii file. What I would like to do is to limit the requested area to a certain region of interest using a label file. Is this possible? (analogous to mris_anatomical_stats where a label flag can be given?).

[Freesurfer] including a vertex-specific covariate in mri_glmfit

Dear Freesurfers, I have a question about mri_glmfit for surface analyses. I have until now used covariates which provided one value for each subject (e.g., Age) but was wondering if it is possible to use covariates that have different values for each vertex. I would like to perform a GLM anal

Re: [Freesurfer] Name external disk not recognized

Yes, works!!! Thank you Ruthger Righart Le 2014-10-30 15:36, Douglas Greve a écrit : > can you make a symbolic link (ln -s) to the disk and then reference the > symlink instead of the direct path? > > On 10/30/14 10:33 AM, Righart, Ruthger wrote: >> Dear Freesurfers, >

[Freesurfer] Name external disk not recognized

Dear Freesurfers, Not sure if my question is at the right place here but I'll give it a try. I have a memory disk with white spaces in the name: Seagate Expansion Drive. There is no simple way to rename the disk on my Linux machine. In Unix shell scripting problems with finding the directory ca

[Freesurfer] PhD position | Technische Universität München, Munich, Germany

PhD position in multiple sclerosis research Department of Neurology, Technische Universität München, Munich, Germany TUM-NIC, Neuroimaging Center, Munich, Germany The Department of Neurology of the Technische Universität München offers a PhD position in systems neuroscience research of Multiple

[Freesurfer] Scatter plot after mri_glmfit

Hi All, In Tksurfer it is possible to view a scatter plot of a relationship analyzed by mri_glmfit, by File -> Load Group Descriptor File (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Visualization). Is this also possible in Freeview? I tried Tools -> Plot FSGD Data, but that does not

Re: [Freesurfer] T2 flag

ce, and mostly with a flair > inversion pulse, so it is probably the case that it doesn't work well > with > your sequence. If you want to upload the data I'll try to take a > look, but > it probably won't be soon > > sorry > Bruce > > > On Mon, 14 Ap

Re: [Freesurfer] Display tkmedit image of surface after mri_vol2surf with projfrac or projdist

surf/lh.white -1 surf/lh.white_1mm_inside > # use positive values for outside ?h.white border > > mris_expand -thickness surf/lh.white -1 > surf/lh.white_in100%_thickness  > # this samples in % of GM thickness, use positive values for outside > white  > > Cheers! > Markus

[Freesurfer] Display tkmedit image of surface after mri_vol2surf with projfrac or projdist

Hi All, mri_vol2surf has the flags --projfrac and --projdist. If I understand these flags correctly, the volume is sampled inbetween the white-matter surface and the pial surface (for ex. --projfrac 0.5 is midway). Is there a possibility in tkmedit/Freeview to display with a colored line for e

[Freesurfer] removal oblique sforms

Dear Freesurfers, To obtain an accurate volume-surface alignment of Freesurfer surfaces in Caret, it is advised that oblique sforms should be removed from the header of the t1w images. I tried to remove the sform (using sform_code='0' and qform='1') and changed the nii header using fslcreatehd

[Freesurfer] tkmedit background color

Dear Freesurfer experts, I am trying to find out how to change the background color of tkmedit. Is there a possibility to change the background color from black to white, just for display purposes? (to avoid laborious photoshop work). Best Regards, Ruthger Righart _

[Freesurfer] tksurfer crashes

Dear Freesurfer experts, I have a problem with Tksurfer. Whereas this worked previously fine it suddenly crashes every time I try to start it. This happens with every subject or fsaverage. A similar problem was reported before with similar terminal output but unfortunately I could not find a s

[Freesurfer] surface does not match

Dear Freesurfers, I analyzed a dataset with FS 5.1 but upon loading the data in tksurfer I get the following error: mrisReadTriangleFile(/.../surf/lh.sphere.reg): surface doesn't match /.../surf/lh.inflated The same error occurs when I run mris_preproc as a step before GLM analyses (mri_glmfi

[Freesurfer] SupraTentorial Volume question

Dear Freesurfer experts, I posted one week ago a question about the SupraTentorial Volume that is indicated in the aseg.stats but unfortunately did not receive any suggestions as yet. 1. SupraTentorial Vol. is defined as Cortex + CorticalWhiteMatter + SubCortGray (http://surfer.nmr.mgh.harvard

[Freesurfer] Volume-based stream: SupraTentorial Volume and Lesion-Mask

Dear All, We are making Volume-based analyses and I have a few questions. 1. The SupraTentorial BrainVolume is indicated in the aseg.stats. I found an explanation on http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats about the SupraTentorial Vol., but checking the formula by summing up

[Freesurfer] mri_label2label problem

Dear Freesurfers, I am using mri_label2label in Fs v5.0.0 to map a label between subjects. I have some problems in that the target label shows little holes while the location of the target label seems to correspond rather well with the source label. Checking these holes backward to the source s

[Freesurfer] FW: What is the difference between Cerebral-white-matter and Cortical-white-matter in Freesurfer?

value from CorticalWhiteMatterVol which would take the white-matter surface into account? Best, Ruthger From: Allison Stevens [astev...@nmr.mgh.harvard.edu] Sent: Friday, May 20, 2011 2:56 PM To: Righart, Ruthger Dr. Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [

[Freesurfer] What is the difference between Cerebral-white-matter and Cortical-white-matter in Freesurfer?

Dear All, I am working with the volume-based stream in Freesurfer and I have a question about what is the difference between the volumes given for Cortical-white-matter and Cerebral-white-matter? How are the volumes calculated for both in Freesurfer? Is it the difference of including or not inc

[Freesurfer] Cortical thickness of a Volume-defined ROI: Reshaping dimensions

Dear Freesurfers, I would like to map my subject thickness data to the fsaverage subject, following ROI analyses, as described under step 4: http://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness Before step 4, tksurfer showed me that registration from MNI to Freesurfer space of my

[Freesurfer] Lobe mapping, based on the Desikan-Killiany Atlas

Dear Freesurfers, I would like to do Lobe mapping, based on the Desikan-Killiany atlas, see http://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation. I was wondering if there is a reason why the banksts is not included in the list under temporal lobe. My first guess is because this is a su

[Freesurfer] Setting lesion voxels

Dear Freesurfers, I would like that surface analyses (i.e., cortical thickness) are not confounded by subcortical lesions in patients. Freesurfer provides a work-around in its release notes ( http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes), which is to set lesion voxels in brainmask.mgz

[Freesurfer] segfault

Dear Sir/Madam, I am a new user of freesurfer and had the following error when I tried in tkmedit tool to make a snapshot of the volume. Please find below the contents of the file .xdebug_tkmedit Best Regards, Ruthger Righart ERROR: A segfault has occurred. This is not your fault, : but is mos