[Freesurfer] question regarding the contrast in mri_glmfit

Hello, I am trying to establish contrast for direct statistical analysis in FS. if I have for example three subject and I want to correlate thickness with age the fsgd file is set GroupDescriptorFile 1 Title G1V2 Class Patient Variables age Input 002 Patient 9 Input 003 Patient 10 Input 004 Pat

Re: [Freesurfer] mris_convert gifti

Francesca, I looked at the files you sent and replicated the problem. It is due to creating your lh.EKppa.annot file using FreeSurferColorLUT.txt as the colortable file. You should create your own colortable file, which is simple to do, and create a new .annot file using that colortable (ie, the

[Freesurfer] FSFAST_Paradigm file

Hi Doug, I wanted to run FSFAST without using the paradigm file in the analysis using 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 bold -mean -cfg

[Freesurfer] Problems with white matter control points

Dear FreeSurfer team, We are having some (relatively new) problems with the correction of theFreeSurfer outputs. We suppose that it may be due to unknown differences thatoccurred in our system than with FreeSurfer, but we wanted to check with you ifyou have heard of any similar issues before. We

Re: [Freesurfer] -qcache error

Hi Skyler, (I added the freesurfer list in copy, please post all your questions through the mailing list, thanks!) If the number of vertices does no match, it might be that you processed the LGI before you reprocessed the final version of the surfaces for which you completed the registration p

Re: [Freesurfer] qcache command after already running recon-all without it

yes, that is correct On 05/04/2015 03:19 PM, Paul Dhami wrote: > Greetings Freesurfer experts, > > although this seemed well address on the wiki, I just wanted to > clarify that if I have already run recon-all on all my subjects, but > without the -qcache flag, once I get to the stage of assembl

[Freesurfer] qcache command after already running recon-all without it

Greetings Freesurfer experts, although this seemed well address on the wiki, I just wanted to clarify that if I have already run recon-all on all my subjects, but without the -qcache flag, once I get to the stage of assembling the data, I would just need to run: recon-all -s -qcache and that th

[Freesurfer] interpreting glmfit-sim results

Hi FS experts, I had a couple quick questions about interpreting glmfit-sim results. For context, I'm interesting in analyzing surface-based morphology differences (cortical thickness, volume, surface area) between two groups. I ran a simple t-test contrast (1 -1) using glmfit on two groups (co

[Freesurfer] Conservative pial surface reconstruction

Hello all, After running a set of subjects through the automatic recon process, a few subjects seem to have more space between the gyri than one would expect. Some of these issues were intensity normalization errors, and were fixed easily enough by edits to the white matter or using control points

Re: [Freesurfer] a mkanalysis-sess question

I am having another problem with mkanalysis-sess, here is my command: mkanalysis-sess -funcstem fmc.so.sm2 -analysis volanalysis -native -paradigm human_curv.par -event-related -gammafit 2.25 1.25 -refeventdur 16 -polyfit 2 -TR 2 -nconditions 8 -fsd bold -per-run -tpexclude xy_tpexclude. it got

Re: [Freesurfer] Incomplete Cerebellum Segmentation

Hi Ani, I finished running this person through the pipeline (autorecon2 and autorecon3) and the cerebellum is still incompletely segmented just as before. Do you possibly have any other ideas? Thanks! Jessica From: freesurfer-boun...@nmr.mgh.harvard.edu

Re: [Freesurfer] out of memory, fast_selxavg3.m

Thanks for your suggestion. That doesn't work. Xiaomin On Sun, May 3, 2015 at 8:50 AM -0700, "Arman Eshaghi" wrote: Does this happen with all parts your analysis (lh, rh, and mni305)? or only mni305 volumetric analysis? Because if it happens with only the volumetric part, you can resample w

Re: [Freesurfer] a mkanalysis-sess question

Thanks Xiaomin On Sun, May 3, 2015 at 8:55 AM -0700, "Douglas Greve" wrote: If you just want to exclude those time points then you can use a time point exclude file. To do this, create a text file with the time in seconds of the time points you want to exclude (t=0 is first time point), put

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

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 badly scaled, condno = 1e+08.). Any other ways I could deal with this error/ Thank you. Best, Sanne -Oorspronkelijk be

Re: [Freesurfer] erroneous cortical surface models

I think it may be the sagittal sinus that is labelled as grey matter. Best wishes Kasper 2015-05-04 14:26 GMT+02:00 Bruce Fischl : > Hi Sarah > > it's really hard to tell what's going on from a single slice. If you upload > the data and send us the specific coordinates you are talking about we wi

Re: [Freesurfer] erroneous cortical surface models

Hi Sarah it's really hard to tell what's going on from a single slice. If you upload the data and send us the specific coordinates you are talking about we will take a look cheers Bruce On Mon, 4 May 2015, Sarah Hirsiger wrote: > Dear FreeSurfer experts, > > > > I encounter some erroneous c

Re: [Freesurfer] problem with left/right parallelization

Thanks for getting back. The patched mri_segstats works. Here are the results of our benchmark runs. Each result comes from a single run so the precision is questionable. But it seems clear that 8 processors makes little difference compared with 4. And parallelizing by side also makes little diffe