[Freesurfer] Bug Reporting: mris_long_slopes qdec table not found

Dear Freesurfer team, I am trying to perform qdec longitudinal analysis. I have ran produced the template and long files, as well as the longitudinal table. I am currently trying to perform the long_mis_slopes command however I keep getting: ERROR: qdec table /qdec/long.qdec.respsex.table.

[Freesurfer] subject directory error: can't find subject

Hi, I’m attempting to use FreeSurfer to create a set of surface and flat maps for use with some macaque data. Using a number of programs prior to FreeSurfer I have created a skull-stripped T1 image and White Matter mask and then successfully used FreeSurfers mksubjdirs, mri_convert, mri_fill,

Re: [Freesurfer] PET PVC - CSF estimation

Thanks for replying Doug, Yes, I would like to use my own mask if the choroid plexus is included but *only* for Tau PET. There is high off-target binding of the new tau PET ligand AV1451 (formerly called T807) in choroid plexus. I wanted to avoid that high signal when estimating CSF. I think chor

Re: [Freesurfer] skull stripping and white matter labelling

in FreeSurferColorLUT.txt (for lesion labels). For the wm, we keep the voxel intensities for voxels that are "on" and set everything else to 0. The brainmask.mgz is the same On Fri, 21 Oct 2016, miracoo...@gmail.com wrote: Thanks Bruce. Where can I find them? Sent from my BlackBerry 10 sma

Re: [Freesurfer] skull stripping and white matter labelling

Thanks Bruce. Where can I find them? Sent from my BlackBerry 10 smartphone.   Original Message   From: Bruce Fischl Sent: Friday, October 21, 2016 1:19 PM To: Freesurfer support list Reply To: Freesurfer support list Subject: Re: [Freesurfer] skull stripping and white matter labelling Hi Paul no

Re: [Freesurfer] skull stripping and white matter labelling

Hi Paul no, I don't think so. If you use our voxel-labeling conventions you should just be able to copy them in to the mri dir cheers Bruce On Fri, 21 Oct 2016, miracle ozzoude wrote: Hello experts, I did my skull stripping  and white matter labelling using an lesion explorer and I want t

[Freesurfer] skull stripping and white matter labelling

Hello experts, I did my skull stripping and white matter labelling using an lesion explorer and I want to replace the brainmask.mgz and wm.seg.mgz generated by freesurfer with the brainmask and wm.seg.mz from lesion explorer. Is there a freesurfer script that can do it? Thanks, Paul __

Re: [Freesurfer] Interpretation of QA tools results

Dear all, I am new to FS QA tool and would like to understand interpretation of results from QA tool as indicated by Matthieu below. Any guidance or directions will be of great help as I need to QC ~400 subjects and think this tool can come in handy. 1) Which problems to identify by looking a

Re: [Freesurfer] mri_average vs mri_concat

thanks Bruce - I had indeed used this months ago but at the workshop this semester Doug had suggested mri_concat as it is a newer command and also doesn't blur the data. I am just having problems creating percentage values with mri_concat. *Would you know why mri_vol2surf is taking a binary minc f

Re: [Freesurfer] Cortical Thickness Zero Values

For #1, do the parcellations look ok? Do the surfaces look ok in the volume? On 10/20/16 4:09 PM, Taha Abdullah wrote: Hi Dr. Fischl and Dr. Greve, #1 So moving the mouse over the medial wall seems to have all vertices within that to have a zero mm thickness as expected. The yellow outline i

Re: [Freesurfer] cannot find input file

glad it worked out cheers Bruce On Fri, 21 Oct 2016, Marja Caverlé wrote: Hi Bruce,  Today I restarted my computer, and tried everything again. This time I indeed used the full path in the -i and the sub_dir, and now it seems to work! Thanks for helping out. Best, Marja On Fri, Oct 21, 201

Re: [Freesurfer] mri_average vs mri_concat

Hi Trisanna not sure about mri_concat, but mri_average -noconform -p ... should do the trick cheers Bruce On Wed, 19 Oct 2016, Trisanna Sprung-Much wrote: Something weird is happening with mri_vol2surf - even though the data looks great, the values are odd which carries over when I try to a

[Freesurfer] tracula reinit

Hi, Rerunning the tractography using reinit, is it an absolute requirement to specify number of control points? It doesn't seem like I can just set reinit = 1 and let the number of control points be the default. Also, is there a trade-off in terms of number of control points? For instance, when re

Re: [Freesurfer] Ubuntu 16.04 solution?

This issue has been resolved. The problem was not Ubuntu 16.04. For some bizarre reason I received the wrong license file contents. When using my institutional email on the freesurfer website registration form I receive this file: The information in this e-mail is intended only for the person to w

Re: [Freesurfer] cannot find input file

Hi Bruce, Today I restarted my computer, and tried everything again. This time I indeed used the full path in the -i and the sub_dir, and now it seems to work! Thanks for helping out. Best, Marja On Fri, Oct 21, 2016 at 4:35 AM, Bruce Fischl wrote: > Try using /Users/MarjaCaverle/Desktop/MR

[Freesurfer] Fw: [mri_cvs_register] error: sLF Undefined variable

Hello FreeSurfer Developers, I am having some problems using the mri_cvs_register toolbox of FS. The error is the following one (it is caused even in the simplest case of registration of the sample data file "$FREESURFER_HOME/subjects/sample-001.mgz" over the CVS template)(the installation fo