[Freesurfer] glmfit error / group analysis

Hello, I am trying to test for the effect of different variables on cortical thickness. The variables (with type) are: index (continuous). Gender(factor), Age(continuous),  Years of education (continuous),  Depression (factor),  Vascular comorbidity (factor), and MMSE (continuous). Later, I ne

Re: [Freesurfer] Freesurfer labeling problem?

Dear Reetta-Liina, Thanks for pointing out this inconsistency. The mapping is: GC-ML-DG = GC-DG CA3 = CA2/3 molecular_layer_HP = molecular layer Cheers, /Eugenio Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://

[Freesurfer] TRACULA tract reconstruction

??Dear Tracula experts, I am applying Tracula on a longitudinal data set, and have some questions I am hoping you could help me with: Firstly, upon visual inspection, several tracts appear to be quite messy, or small (on the default freeview threshold) for most subjects. However, the -stat st

Re: [Freesurfer] Error viewing corrected results

Hi all, That's exactly as Antonin says -- I have very little to add :-) Only a few suggestions: - With surfaces, both cluster and TFCE statistics tend to be slow. Consider using the tail approximation ("-approx tail -n 500 -nouncorrected") - Include -logp, so that the p-values are in log-10 sca

[Freesurfer] Yet another freeview coordinates question

Hey all, When loading two T1 in freeview, one for a subject and one for fsaverage, and switching between them, only the tkreg RAS coordinates changes while moving the mouse, not the RAS. Does it mean that the RAS in freeview is always in MNI305? Thanks, Noam _

Re: [Freesurfer] Uploading masks on data processed by freesurfer

Hi Lionel we usually try to avoid analyze as a format as it frequently doesn't contain enough information to e.g. disambiguate left from right. That said, just bring the mask and the data up in freeview and see if they align cheers Bruce On Wed, 8 Mar 2017, Lionel Giriteka wrote: > Hi > > I h

[Freesurfer] Uploading masks on data processed by freesurfer

Hi I have processed my data with freesurfer. And an expert have made manual segmentations and sendt it to me as masks (analyze format = img & hdr). I now want to view these masks with the data I have run through freesurfer, but I am not sure how to proceed. Any advices? Thanks a lot. Best Reg

Re: [Freesurfer] TRACULA tract reconstruction

Dear Joelle, regarding the conversion to .bvecs, could you please show the example of difference between bvecs converted by mri_convert of FreeSurfer and mrconvert of mrtrix3? Do you have most recent version of mrtrix3? There have been a quite extensive discussion on implementation of FSL .bve

[Freesurfer] mri_concat pet images into 1 template image

Hello Freesurfer, I have 3 PET images per individual. I am learning PetSurfer based on the Greve et al., 2014 paper.  On the PetSurfer link, there are 2 methods. mri_convert pet.nii.gz —frame frameno template.nii.gz  or mri_concat pet.nii.gz --mean —0 template.nii.gz What are the differences?

Re: [Freesurfer] Error viewing corrected results

Hi Antonin and Anderson, That's wonderful ! I am able to run PALM now, without any problem. Thank you so much for your help and time, I really appreciate that. Best, MJ On Wed, Mar 8, 2017 at 6:30 AM, Anderson M. Winkler wrote: > Hi all, > > That's exactly as Antonin says -- I have very lit

[Freesurfer] Announcing FSurf 2.0

Dear FreeSurfer community, The Open Science Grid (http://www.opensciencegrid.org) is a federation of university and laboratory HPC facilities which share computing capacity to support science. We have developed a command line tool "fsurf" you can use from your laptop or desktop computer to submit

Re: [Freesurfer] Extreme non-uniformity artifact

Hi Bruce and all, Thanks for the suggestion on scaling -- it would be nice if it were consistent, but it varies quite a lot from scan to scan. At the most, about 30 of the top slices are affected, but often the number of affected slices is fewer, and sometimes the spatial extent of the artifact i

Re: [Freesurfer] Error viewing corrected results

Dear Sahil, could you send the full command-line and unthresholded view of *_clustere_tstat_fwep ? How the data showed in screenshot 1 were produced? How are the actual p-values of your clusters in *_clustere_tstat_fwep? You can also use -saveglm and inspect the files containing values of GLM

Re: [Freesurfer] one group in RepeatedMeasuresAnova or Paird Analysis

Re: [Freesurfer] one group in RepeatedMeasuresAnova or PairdAnalysis Dear Douglas Greve, Thank you for your reply. I'm very sorry that I can't directly reply on the web, so I had to be sent a new email. I still have a question for your answer “ Note that for the paired-diff, you need to subtract

Re: [Freesurfer] Error viewing corrected results

Dear Sahil, If you used -logp as Anderson suggested, you should set your min to 1.3 to threshold your *_clustere_tstat_fwep map and see the clusters. What is the value of *_clustere_tstat_fwep in the region of the big cluster seen at thresholded map *dpv_tstat.mgz ?  This should correspond to y

Re: [Freesurfer] mri_concat pet images into 1 template image

No, the template is a within subject template used for registration. If your pet data only has one frame (eg, FDG SUV), then you don't need to run mri_convert or mri_concat, just use your pet image as the template On 3/8/17 11:11 AM, Shane S wrote: Hello Freesurfer, I have 3 PET images per i

Re: [Freesurfer] mri_concat pet images into 1 template image

Dear Doug, My PET data is 3 x 5 minute acquisitions. Each subject has  subject123_a.nii.gz, subject123_b.nii.gz, subject123_c.nii.gz and I am supposed to align and average them. Please advise. Thanks! --  Shane Schofield On 8 March 2017 at 22:31:06, Douglas Greve (gr...@nmr.mgh.harvard.edu) w

Re: [Freesurfer] Error viewing corrected results

Dear Antonin, Setting minimum to 1.3 for *_clustere_tstat_fwep doesn't show any significant cluster and similarly thresholded map *dpv_tstat.mgz also doesn't show anything at -log10(0.05) = 1.3. As you said, it seems like even though there is big cluster but after FWER correction, the significance

[Freesurfer] Issue with mri_segstats to extract cortical thickness from a volume ROI

Hello FreeSurfer community, I am trying to extract the cortical thickness from a specific ROI. I followed the pipeline: cortical thickness of a volume-defined ROI. But for the last step: mri_segstats \ --seg $SUBJECTS_DIR/fsaverage/surf/lh.fsaverage.ROI5.mgh \ --in lh.thickness.fsaverage.mgh

[Freesurfer] mri_label2vol error: could not scan # of lines from label file

Hello FreeSurfer Developers, I’m attempting to convert a dlabel file from the Human Connectome Project to a volumetric ROI that I can use for fiber tractography on other platforms. I followed the tutorial provided by HCP (hcp-users FAQ #9: How do I map data between FreeSurfer ... - HCP Wiki

Re: [Freesurfer] Yet another freeview coordinates question

ok, I've figured out that this is indeed the case: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23348.html Also, following these instructions I was able to get RAS from the tkreg RAS in FreeView: https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-June/024293.html Thanks

Re: [Freesurfer] Error viewing corrected results

Dear Sahil, to assure that there is no other issue with your setup, I would recommend to obtain cluster-wise p-pvalue of that big cluster to see if it is reasonable, i.e. if it is somewhat close to the significance. Therefore, I would load *_clustere_tstat_fwep and click to the area of big cl