[Freesurfer] Problem with FreeSurfer template and control subject

Dear Freesurfer, The data that I'm using as a part of my study contains only the patients' T1 images and we have not collected any control subjects yet. I want to compare the cortical thickness of these subjects with a template (instead of a control subject), but I'm confused which volume I need t

Re: [Freesurfer] Problem with FreeSurfer template and control subject

Hi Mahtab we do all the analysis in native space and don't transform the data to a template (although we do compute mappings to various templates). As for your other question, there are too many variables to control for (age, gender, scanner type, sequence) for us to distribute a normative d

Re: [Freesurfer] Problem with FreeSurfer template and control subject

Dear Bruce, Thank you for your response. So would you please guide me how I should register the image into MNI152 coordination? And is the cvs_avg35_inMNI152, the MNI152 template? Best Regards, Mahtab. On 3 June 2016 at 13:48, Bruce Fischl wrote: > Hi Mahtab > > we do all the analysis in nati

[Freesurfer] build fsaverage

Hello ! I work for the department of radiology, Emory University. We're planning to use the FreeSurfer software suite (or more precisely, the surface-based stream ) in a project that aims to compare cortical thickness between treatment and nontreatment patients. We have finished recon-all for al

Re: [Freesurfer] build fsaverage

why do you need rebuilt fsaverage? On 06/03/2016 05:06 PM, shi yao wang wrote: > Hello ! > > I work for the department of radiology, Emory University. > > We're planning to use the FreeSurfer software suite (or more precisely, > the surface-based stream ) in a project that aims to compare cortical

Re: [Freesurfer] recon-all segmentation error

Bruce, The lh.inflated.nofix shows the brainstem and cerebellum are attached to the cortical surface. Also, the ventricles are not filled in the filled.mgz. Could you please tell me how to fix this manually? Thanks, Jaiashre. ___ Freesurfer mailing li

Re: [Freesurfer] build fsaverage

Hi Lawrence you can you the make_average_subject script, but as Doug implies you probably don't need to. Our warp is high-enough dimensional that you rarely need to build average subjects from your own population cheers Bruce On Fri, 3 Jun 2016, shi yao wang wrote: > > Hello ! > > I work

Re: [Freesurfer] recon-all segmentation error

hmmm, that suggests that the aseg failed badly. What does it look like? cheers Bruce On Fri, 3 Jun 2016, Jaiashre Sridhar wrote: Bruce, The lh.inflated.nofix shows the brainstem and cerebellum are attached to the cortical surface. Also, the ventricles are not filled in the filled.mgz. Could

Re: [Freesurfer] recon-all segmentation error

Bruce, The aseg looks fine to me. Is there anything in specific that I should be looking for in aseg? Thanks, Jaiashre. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The inform

Re: [Freesurfer] recon-all segmentation error

does it segment the cerebellum ok? If so, it should be removed during recon-all On Fri, 3 Jun 2016, Jaiashre Sridhar wrote: Bruce, The aseg looks fine to me. Is there anything in specific that I should be looking for in aseg? Thanks, Jaiashre.  __

[Freesurfer] Input for mris_fwhm to generate fwhm.dat file

Dear freesurfer experts, This is a follow up question from a previous post http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg47480.html I have created a sig.mgh from my own stats code and need to also generate fwhm.dat file to run the monte carlo sim, which is estimated from the

[Freesurfer] CORRECTING DEFECT

Dear freesurfer experts,I have a subject ending up with this error after recon-all.I tried to edit the aseg and run it, but it stuck at topological step. CORRECTING DEFECT 79 (vertices=54196, convex hull=8490) error in the retessellation normal vector of length zero at vertex 97187 with 0 faces v

Re: [Freesurfer] Input for mris_fwhm to generate fwhm.dat file

It is the error in the model fit. If you run mri_glmfit with --save-eres it will save a file called eres.mgh. this is the residual file On 6/3/16 6:29 PM, Chung, Yoonho wrote: Dear freesurfer experts, This is a follow up question from a previous post http://www.mail-archive.com/freesurfer@

Re: [Freesurfer] CORRECTING DEFECT

Hmmm, that sounds like a bug. If you upload the subject we will take a look Cheers Bruce > On Jun 3, 2016, at 6:54 PM, maryam koochaki wrote: > > Dear freesurfer experts, > I have a subject ending up with this error after recon-all. > I tried to edit the aseg and run it, but it stuck at topologi

Re: [Freesurfer] CORRECTING DEFECT

Hi Bruce,I already uploaded it.File name:  test_emc_039.tar.gz Thanks,Maryam   Regards,Maryam Kouchakidivkolaei On Friday, June 3, 2016 9:35 PM, Bruce Fischl wrote: Hmmm, that sounds like a bug. If you upload the subject we will take a lookCheersBruce On Jun 3, 2016, at 6:54 PM, m

[Freesurfer] convert FSL atlas label to individual freesurfer T1 space

Hello! I have a fsl label (from the JHU atlas) and want to overlay this on my T1 from FreeSurfer (native space) to create models in 3DSlicer. What is the best way to get these labels (one ROI with intensity 1 in a nifti) to fit the individual T1. I tried the following: Flirt -in MNI15_T1_1mm.ni

[Freesurfer] error at acfrun 762

Hi, I decided I should standardize my fMRI data across sessions by rescaling each voxel to have a run-mean of 100. Normalized data looked okay under manual inspection in FreeView. When I tried to analyze this data, however, I consistently get an error partway through: """ Index exceeds matrix dim