Re: [Freesurfer] epidewarp

Can you send me the result of "which epidewarp.fsl" (no quotes)? Marco Loggia wrote: > Hi Doug, > Below are my paths: > > FREESURFER_HOME /usr/local/freesurfer/stable5_0_0 > FSFAST_HOME /usr/local/freesurfer/stable5_0_0/fsfast > FSF_OUTPUT_FORMAT nii > SUBJECTS_DIR /autofs/cluster/ra

Re: [Freesurfer] epidewarp

Hi Doug, Below are my paths: FREESURFER_HOME /usr/local/freesurfer/stable5_0_0 FSFAST_HOME /usr/local/freesurfer/stable5_0_0/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /autofs/cluster/randy/2/lbp/freesurfer/patients+controls MNI_DIR /usr/local/freesurfer/stable5_0_0/mni FSL_D

Re: [Freesurfer] epidewarp

Marco, which version are you using? doug Marco Loggia, PhD wrote: > Dear Surfers, > > In the past couple of days epidewarp.fsl has been failing, reporting > "vsm-smooth: Command not found" (see below). Epidewarp was run using > the same parameters, and within the same script that I have been usi

[Freesurfer] epidewarp

Dear Surfers, In the past couple of days epidewarp.fsl has been failing, reporting "vsm-smooth: Command not found" (see below). Epidewarp was run using the same parameters, and within the same script that I have been using with no problems for many months... Has there been a software update th

Re: [Freesurfer] Multiple corrections

Hi Doug, Many thanks for your valuable answer. Can you please briefly explain some other issues: 1). what exactly means Correction for Multiple Comparisons and how this is done when using --sim method with --cache. 2). do I need to do an estimation  FDRthresholding in tksurfer for GLM meth

Re: [Freesurfer] Fw: fsaverage

That "2" is a voxel-wise threshold used to form the cluster. The cwp is a cluster-wise threshold used to eliminate non-significant clusters from the output. Bruce Fischl wrote: > I'll leave that for Doug > On Thu, 25 Aug 2011, Antonella Kis wrote: > >> Hi Bruce, >> >> Thank you very much for yo

Re: [Freesurfer] Fw: fsaverage

I'll leave that for Doug On Thu, 25 Aug 2011, Antonella Kis wrote: Hi Bruce, Thank you very much for your prompt and helpful answer. I have one more question, please:  I do not understand what's the role of adding the threshold value while running the mri_glmfit-sim with --cache since  after

[Freesurfer] Fw: fsaverage

Hi Bruce, Thank you very much for your prompt and helpful answer. I have one more question, please:  I do not understand what's the role of adding the threshold value while running the mri_glmfit-sim with --cache since  after adding the threshold 2,  I still get  clusters  with  cwp>.01. Thi

Re: [Freesurfer] fsaverage

Hi Antonella it won't unless you create your own population-specific average with make_average_subject. cheers Bruce On Thu, 25 Aug 2011, Antonella Kis wrote: Dear All: I wonder if for a  new FSGD file (e.g. age.fsgd) the resample of each subjects data to fsaverage (into a common space),

[Freesurfer] fsaverage

Dear All: I wonder if for a  new FSGD file (e.g. age.fsgd) the resample of each subjects data to fsaverage (into a common space), as well as concatenating all the subjects' into a single file, will change my old  fsaverage.  Thank you. Antonella ___ F

Re: [Freesurfer] use MNI152 normalized images in segmentation

Hi Tony you mean normalize in spm then give the files to recon-all? That should work, although you are introducing an extra resampling in the normalization which will lose you some resolution. We will still use the MNI305 during recon-all but only to compute a tal xform (it should be close to

[Freesurfer] integrating FSL and Freesurfer

Hi, I am trying to use reg-feat2anat to register my Feat analyses to anatomical images and running into a number of problems. 1) When I check the registration of the mean_func to the anatomical in tkregister2 it looks fine. But when I overlay the fsl statmaps onto the anatomical brain they extend

[Freesurfer] use MNI152 normalized images in segmentation

Dear all, I'm just learning Freesurfer and want to import output files of Freesurfer into Carat so that I can generate individual surface. I already have my functional and anatomical images preprocessed (realign, coregister, segment and normalize) in spm5. So the anatomical have been norma

Re: [Freesurfer] Cortical thickness - again

Hi Ed You should probably weight each vertex by surface area, but the answer won't be too different from a straight average Cheers Bruce On Aug 25, 2011, at 3:22 AM, Ed Gronenschild wrote: > Hi, > > How do you compute the cortical thickness for each structure > as listed in the ?h.aparc.sta

[Freesurfer] ERROR: Option ‐‐hemi unknown for mri_surf2surf

Dear Freesurfers: mri_surf2surf 
‐‐hemi 
lh
 ‐‐s 
fsaverage
 ‐‐sval
 att-lh-thickness.mgh ‐‐fwhm 
10 
‐‐tval
 att-lh-thickness.10.mgh I got error " command not found" or "ERROR: Option 
‐‐hemi unknown" although I can do mri_surf2surf 
‐‐help with not problem I checked fsaverage, OK but my att-lh

[Freesurfer] Fwd: Re: Defining an mrs voxel in the anatomical dataset for partial volume correction

Hello all! I got no answer on this email, thus I'm posting these questions again, hoe someone can help: Hello! About synthesising a volume using mri_volsynth with direction cosines and RAS from mrs header: In the mrs header I have: - VOI position in the 3 views (sag, cor and tra) which are

[Freesurfer] Cortical thickness - again

Hi, How do you compute the cortical thickness for each structure as listed in the ?h.aparc.stats file? Is it equal to the thickness at each vertex averaged over all vertices within the structure? Ed ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvar