[Freesurfer] A few questions regarding Monte Carlo and mri_glmfit

Hello Freesurfer Gurus, I have been conducting cortical thickness and LGI analyses at my lab using Qdec. We have gotten some really promising results thanks to your help! However I have a few withstanding questions which need answered to make sure our results are methodologically valid: 1) After

[Freesurfer] Visual Check

Hi everyone, After pre-process recon-all，what parts of its process need to check visually ?how to determine its necessity for check ? and how to check them ? Could you provide me for a guide or pipeline? Best regards. Xin-Fa Shi. ___ Freesurfer

[Freesurfer] Registration

After 'recon-all' ,how to check its accuracy of registration ? what anatomy should be paid more attention ? Best regards . Xin-Fa Shi . ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Registration

Hi Xin-Fa the easiest way to check the quality of the cortical registration is to look at one of the parcellations (e.g. lh.aparc.annot) and see if it labeled the major sulci correctly cheers Bruce On Fri, 12 Dec 2014, Xinfa Shi wrote: After 'recon-all' ,how to check its accuracy of

Re: [Freesurfer] Visual Check

Hi Xin-Fa scroll through your data with the surfaces overlaid on the volume and make sure that they follow where you think the gray/white and pial boundaries are and do the same for the aseg.mgz cheers Bruce On Fri, 12 Dec 2014, Xinfa Shi wrote: Hi everyone, After pre-process

[Freesurfer] freesurfer gpu acceleration using amd video cards?

Dear List Members, Does anyone know if it is possible to use freesurfer gpu based acceleration using amd video cards? Thanks, Salil Soman, MD, MS ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] functional data on freeview

Dear freesurfer users, I have installed freesurfer and freeview. The visualization of brain surfaces looks great. Is it possible to visualize functional MEG/EEG source data with freeview? What I have: 1. Source locations (Nx3) 2. Activation strength (Nx1) at these locations 3. The anatomy

Re: [Freesurfer] functional data on freeview

Hi Peng yes, for sure. This is what Matti Hamalainen's excellent MNE package is designed for. I'll cc Matti so he can chime in cheers Bruce On Fri, 12 Dec 2014, peng wrote: Dear freesurfer users, I have installed freesurfer and freeview. The visualization of brain surfaces looks great.

Re: [Freesurfer] freesurfer gpu acceleration using amd video cards?

Its my understanding is that CUDA is specific only to NVIDIA graphics devices. http://www.nvidia.com/object/cuda_home_new.html -Zeke On 12/12/2014 08:54 AM, Salil Soman wrote: Dear List Members, Does anyone know if it is possible to use freesurfer gpu based acceleration using amd video

[Freesurfer] Apply a label to longitudinal measures and extract stats

Dear experts, I have created a label from Qdec and used mri_label2label to apply it to all subjects. Now I need to extract the pc1 measure from longitudinal analysis in my label. Would you please advise how to do this since kris_anatomical_stats doesn't work here? Best regards, Amirhossein

Re: [Freesurfer] trac-all -path error Segmentation Fault (Core Dumped)

Ack. Can't believe I missed that. Thank you. I'll run it again and see how that turns out. On Thu, Dec 11, 2014 at 2:07 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Thomas - No bother at all! If you search for the word error in your trac-all.log, you'll see that it couldn't

Re: [Freesurfer] mri_glmfit error: matrix is ill-conditioned or badly scaled, condno = 1e+08

Hi Doug! Thank you very much for your reply. I made the fsgd file in a plain-text file using the textedit program on a Mac and when that didn't work I tried modifying in the terminal window using: nano -w g4v1.73.fsgd. This also didn't solve the problem. I am not sure what to try next. Lindsay

Re: [Freesurfer] mri_glmfit error: matrix is ill-conditioned or badly scaled, condno = 1e+08

The file I looked at had a bunch of carriage returns (try looking at it with more or less or cat). As long as those are in there, it will create an error. Try running this and using the new one cat g4v1.73.fsgd | sed 's/\r/\n/g' new.g4v1.73.fsgd On 12/12/2014 12:09 PM, lindsay hanford wrote:

Re: [Freesurfer] Command '-qa' in TRACULA

Are you sure your path isn't look for the older trac-all first? If you didn't remove/overwrite it, that is. Type which trac-all (without the quotes) and see if the correct one is shown. From: freesurfer-boun...@nmr.mgh.harvard.edu

Re: [Freesurfer] multiple comparisons correction for individual hemispheres (native space)

I'm pretty sure this is due to the language locale settings. Can you do an experiment? Run echo $LANG if the result is not en_US.utf8 try setenv LANG en_US.utf8 And see if that fixes it. If it does, I can change the script doug On 12/11/2014 03:11 AM, Milde, Christopher wrote: Dear Doug,

Re: [Freesurfer] Getting voxel values from aseg.mgz

You can also use mri_binarize which has more documentation :-) On 12/11/2014 01:31 AM, pradeep mahato wrote: There is no documentation or example for mri_extract_label. What should be the syntax for it. What kernel and xform file should be used. On Wed, Dec 10, 2014 at 6:50 PM, Bruce

Re: [Freesurfer] using mri_convert with multiframe dicom

Sorry, I never got around to downloading them and now they are gone. Can you re-upload them? doug On 12/08/2014 06:07 PM, Gurney, Jenny wrote: Hi all, Doug, just wondering if anyone has had time to look into the issue of using mri_convert with multiframe/enhanced DICOM. My colleague,

Re: [Freesurfer] mri_glmfit error: matrix is ill-conditioned or badly scaled, condno = 1e+08

Thank you Doug! I replaced all my spaces with new spaces and it worked! Much appreciated! Lindsay On Fri, Dec 12, 2014 at 12:09 PM, lindsay hanford lindsay.hanf...@gmail.com wrote: Hi Doug! Thank you very much for your reply. I made the fsgd file in a plain-text file using the textedit

[Freesurfer] funcroi-table-sess error, \set: Variable name must begin with a letter\

Hi there, I'm having the same problem referenced in this thread from last year. When I send the command: funcroi-table-sess -roi l_ant_cingulate_allVfix.roicfg -analysis NMASA_induction.lh -contrast allVfix -sf induction_all2.lst -o l_ant_cingulate_induction_FIR_f0.dat -frame 0 I get

Re: [Freesurfer] Command '-qa' in TRACULA

Does a file called dmri/dwi_motion.txt get created? That's the output of the QA step. This is explained in the tutorial, under Outputs from quality assessment: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaOutputs On Fri, 12 Dec 2014, Anri WATANABE wrote: Thanks, Anastasia.I'm

Re: [Freesurfer] Command '-qa' in TRACULA

If the -qa flag is not recognized, then you're still running the old version of trac-all, not the updated version. On Fri, 12 Dec 2014, Anri WATANABE wrote: I tried to run trac-all -qa -c the_name_of_my_configuration_file after trac-all -corr -c the_name_of_my_configuration_file, but it

[Freesurfer] Freesurfer version compatibility

Hi everyone, We have a number of Freesurfer segmentations performed with version 5.0. Some of these will need to be corrected, most likely with adding control points. The question is we currently have version 5.3 running on our server. Is it okay to add the control points and run the

Re: [Freesurfer] Freesurfer version compatibility

Hi Deniz if you rerun them all with 5.3 that should be ok Bruce On Fri, 12 Dec 2014, Deniz Ozgen wrote: Hi everyone, We have a number of Freesurfer segmentations performed with version 5.0. Some of these will need to be corrected, most likely with adding control points.  The question is we

Re: [Freesurfer] Command '-qa' in TRACULA

No, she is saying that you should open a terminal, and type only trac-all. This should display the help for that program, including the program's flags. If you don't see -qa listed, then the trac-all you're using is an older version. You need to verify that you have downloaded the latest

Re: [Freesurfer] funcroi-table-sess error, \set: Variable name must begin with a letter\

I can't remember what the issue was. Can you run funcroi-table-sess -debug -roi l_ant_cingulate_allVfix.roicfg -analysis NMASA_induction.lh -contrast allVfix -sf induction_all2.lst -o l_ant_cingulate_induction_FIR_f0.dat -frame 0 | tee dng.log and send me dng.log doug On 12/12/2014 03:03

[Freesurfer] surface check

Hi everyone , After recon-all，how to determine quickly the quality of whiter matter segmentation ,surfaces(e.g. whiter matter surface and pial surface) and topological fix ? what anatomy should be paid more attention? Best regards? Xin-Fa Shi . ___