Re: [Freesurfer] Data interest of the CorticalParcellation_Yeo2011

Hi Annie, Please cc the freesurfer list when you reply because there might be other people more qualified to answer your question. Based on what you are saying, I think you can first use mri_surf2surf (with the sval-annot flag) to transform the 2011 functional networks .annot file from fsaverage

Re: [Freesurfer] mris_convert gifti

yes, you can use a label for this (we use the ?h.cortex.label for this purpose routinely to remove non-cortical stuff) On Tue, 5 May 2015, Francesca Strappini wrote: Thank you so much! I understand what's the problem and I will make my custom ctab file. Last question, about the annot files,

[Freesurfer] interpreting glmfit-sim results

Hello FS experts, I submitted this question yesterday but never heard back. Any thoughts? Thank you! Gabriella From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Hirsch, Gabriella Sent: Monday, May 04, 2015 3:03 PM To:

[Freesurfer] aparc labels to grey white ratio

Hi all, What command would I use to apply the aparc labels to a different surface (e.g. to $h.ratio.mgh)?? The ratio file was created as follows: mri_vol2surf --src ${nu_mgz} --projfrac +0.35 --surf white --hemi lh --out ${subj_dir}/mri/lh.white.projfrac.pos35.mgh --regheader ${subject}

[Freesurfer] FSFAST_Volume based analysis

Hi Doug, I want to do volume based analysis using FSFAST using the FC seed as a task regressor. I ran the following command lines: 1. preproc-sess -s ${i} -fwhm 5 -surface fsaverage lhrh -mni305-1mm -fsd bold -per-run 2. fcseed-config -segid 1024 -fcname L_Precentralgyrus.dat -fsd

Re: [Freesurfer] mris_convert gifti

Does SUMA support GIFTI and provide a utility to convert between its formats and GIFTI? I was also wondering what a .dset was and how to get it into GIFTI so it could be easily used across software platforms. Thanks, Matt. On 5/5/15, 5:30 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:

[Freesurfer] Visualization of ROIs

Dear FS experts, For my research proposal, I would like to visualize my 5 ROIs (e.g., superior temporal cortex, medial temporal cortex) in the Destrieux Atlas (or others) before I start the analysis. I want each region to be shown in a different color. Would you kindly explain how to do it?

Re: [Freesurfer] where to start recon-all after edits

Yes, if this is in the long, you also need to add the -long …. stuff Martin On Apr 28, 2015, at 12:46 AM, prasser pras...@zoho.com wrote: Thanks for your response, not sure if I've quite got it yet. So, after the surfaces are done and we update/edit the the aseg.mgz with say,

[Freesurfer] What to do about excessive topologic defect

Hi Freesurfers, I've performed recon-all -all on a subject and found that some of the cortex is missing. I ran recon-all -skullstrip -wsthresh 30 -clean-bm -no-wsgcaatlas -s sub296.fs and the cortex appeared, so I added control points in hopes of FS recognizing the cortex, but I got the

Re: [Freesurfer] LGI problem

Hi Marie: I just had another problem with the LGI processing. Here is the log: thanks, Alan [alanf@micc FreeSurfer_5.3]$ recon-all -s Asperger1 -localGI INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 Current Stamp:

Re: [Freesurfer] 2 factor design. error: matrix is ill-conditioned or badly scaled

Hi Sanne, this is for a longitudinal analysis? Are you doing the 2 stage approach (first reduction to a single number per subject, e.g. the atrophy rate per year, then a cross sectional analysis)? In that case I don’t know why it is not working. Your Y is the thickness rate, and the 6 columns

Re: [Freesurfer] mris_convert gifti

sorry, I think this may be a question for the SUMA people - I don't know what .dset format is. Are you going to do the masking within SUMA? I'll cc Ziad so he can chime in. cheers Bruce On Tue, 5 May 2015, Francesca Strappini wrote: I'm trying to mask a time series dataset that I mapped to

Re: [Freesurfer] 2 factor design. error: matrix is ill-conditioned or badly scaled

Can you send me the new terminal output (and attach your fsgd file)? doug On 05/04/2015 08:48 AM, Sanne Oostermeijer wrote: Thank you for answer Douglas. I have indeed tried to run the analysis by demeaning our covariate, but unfortunately I get the same error (matrix is ill-conditioned or

Re: [Freesurfer] Fwd: -qcache error

Hi Skyler, You can run: mris_info lh.pial which will give you the number of vertices of the surface (vertices) and mri_info lh.pial_lgi which will give you the number of vertices for which the LGI has been computed (under dimensions) If the two numbers don't match, it means that the LGI has

[Freesurfer] kvlThresholImage fails on MacOSX 10.10.2

Dear freesurfer, I tried using kvlThresholdImage on a MacOSX 10.10.2, X version XQuartz 2.7.7 (xorg-server 1.15.2), and freesurfer version 5.3, and I get the following message: kvlThresholdImage subj01/mri/orig/orig.mgz 0 2370 X Error of failed request: BadWindow (invalid Window parameter)

Re: [Freesurfer] erroneous cortical surface models

Dear Bruce, Thank you very much for taking your time to have a look at my data, which I just uploaded to the transfer/incoming/ folder. The specific coordinates are: RAS 4, -73, 27 In addition, I have a similar problem more anterior too (RAS 32, 39, 2.5). Thanks again for your help!

[Freesurfer] Trying to run ex vivo post fixation brains on free surfer

Hi, My name is Fabio, I am from university of Sao Paulo, and we have a few brains that we wish to try running on freesurfer that are already fixated and we were not captured the way the current ex vivo protocols suggests. I have already tried it once, and the segmentation weren't quite good,

Re: [Freesurfer] mris_convert gifti

Thank you so much! I understand what's the problem and I will make my custom ctab file. Last question, about the annot files, is it possible with freesurfer to create a mask with the annot or the label files in which the value 1 is assigned to the region and 0 to the rest of the brain? Thanks

Re: [Freesurfer] mris_convert gifti

what are you trying to mask? On Tue, 5 May 2015, Francesca Strappini wrote: Thank you! Do you know which function should I use? Best Francesca 2015-05-05 15:30 GMT+03:00 Bruce Fischl fis...@nmr.mgh.harvard.edu: yes, you can use a label for this (we use the ?h.cortex.label for this

Re: [Freesurfer] mris_convert gifti

you can just create a label file I guess. What input does SUMA take? On Tue, 5 May 2015, Francesca Strappini wrote: Sorry, just to be clear, I meant how can I create a mask on the surface in which at each vertex is assigned a value, 0 or 1. I need to create this mask for exporting the

Re: [Freesurfer] What to do about excessive topologic defect

Hi Jessica something has gone terribly wrong with the segmentation. What is the input image you used? What does the wm.mgz look like over the brain.mgz? cheers Bruce On Tue, 5 May 2015, Jessica Lynn Hanson wrote: Hi Freesurfers, I've performed recon-all -all on a subject and found that

[Freesurfer] Fwd: -qcache error

Hi Dr. Schaer, Jon checked the dates and assured that LGI was run after autorecon. We are still encountering this issue. Thank you for your help, Skyler and Jon Sent from my iPhone Begin forwarded message: From: Jon Alan Wieser wie...@uwm.edumailto:wie...@uwm.edu Date: May 5, 2015 at 1:38:31

Re: [Freesurfer] mris_convert gifti

I'm trying to mask a time series dataset that I mapped to the surface in SUMA (surface created with freesurfer and imported into SUMA). I think the input should be in the .dset fomat (region mapped to the surface). The problem is that when I save my label the annotation file has only a list of