[Freesurfer] FDR correction

Hi list, I would like to ask you a number of questions regarding the FDR which is performed following seed-based fcMRI using FS-FAST.1-In the previous mail you have suggested me to use mir_fdr command line (version 6.0). Because I have some problem with new version license (as reported in previo

[Freesurfer] output from mri_glmfit

Hello Freesurfer statistical experts, I need some assistance in explaining the output generated by mri_glmfit (then followed by correction for multiple comparisions, mri_glmfit-sim). We fit one model and got some statistically significant clusters. Then, we ran another model, the same plus an addi

Re: [Freesurfer] Need help finding minimum number of vertices for monte carlo correction

First, look in the qdec output folder to determine the FWHM in the fwhm.dat file. Assuming the value is 10, you are looking at the left hemisphere, you used a positive tail, and the voxel-wise threshold was 1.3 (p<.05), then you would find the following file $FREESURFER_HOME/average/mult-comp-

Re: [Freesurfer] Need help finding minimum number of vertices for monte carlo correction

Thank you so much, this is incredibly helpful. And just to be clear is this the minimum area or vertices? Tara On Wed, Jan 6, 2016 at 12:01 PM, Douglas N Greve wrote: > > First, look in the qdec output folder to determine the FWHM in the > fwhm.dat file. Assuming the value is 10, you are lookin

Re: [Freesurfer] Need help finding minimum number of vertices for monte carlo correction

Area in mm^2 On 01/06/2016 01:16 PM, Tara Miskovich wrote: > Thank you so much, this is incredibly helpful. And just to be clear is > this the minimum area or vertices? > > Tara > > On Wed, Jan 6, 2016 at 12:01 PM, Douglas N Greve > mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > First, look

Re: [Freesurfer] output from mri_glmfit

You can get the SSE from rvar*DOF (eg, fscalc rvar.mgh mul 100 -o sse.mgh). You can get the SST using fscalc y.mgh sqr -o sst.mgh mri_concat sst.mgh --sum --o sst.mgh Then the unadjusted r-squared as fscalc sse.mgh div sst.mgh sub 1 mul -1 -o rsquared.mgh The final calculation is a little obtuse

Re: [Freesurfer] Need help finding minimum number of vertices for monte carlo correction

Thank you for the clarification. So even though it is a vertex-wise threshold, there is no minimum amount of vertices, it goes by area? Tara On Wed, Jan 6, 2016 at 12:21 PM, Douglas N Greve wrote: > Area in mm^2 > > On 01/06/2016 01:16 PM, Tara Miskovich wrote: > > Thank you so much, this is in

Re: [Freesurfer] Need help finding minimum number of vertices for monte carlo correction

Yes. In theory you can compute the number of vertices by dividing by the average vertex area On 01/06/2016 01:34 PM, Tara Miskovich wrote: > Thank you for the clarification. So even though it is a vertex-wise > threshold, there is no minimum amount of vertices, it goes by area? > > Tara > > On W

Re: [Freesurfer] Need help finding minimum number of vertices for monte carlo correction

Great! Thank you for all the help. On Wed, Jan 6, 2016 at 12:38 PM, Douglas N Greve wrote: > Yes. In theory you can compute the number of vertices by dividing by the > average vertex area > > On 01/06/2016 01:34 PM, Tara Miskovich wrote: > > Thank you for the clarification. So even though it is

Re: [Freesurfer] hello freesurfer developer~

Hi A-reum did you talk to the Wash U group? If you have nifti files they can be processed using recon-all (i.e. recon-all -i -s -sd -all) cheers Bruce On Tue, 29 Dec 2015, A-reum Min wrote: hello experts!my name is areum. i have some question to you.i have never seen before these NIF

Re: [Freesurfer] Recon-all Run Time

Hi Marissa we can't help unless you give us more details. What processors/memory was there on the old computers? What is on the new one? Have you tried running the same data on each to get comparable timings? cheers Bruce On Mon, 28 Dec 2015, Marissa Pifer wrote: Hi Freesurfers, I've rec

Re: [Freesurfer] Recon-all Run Time

Sure, sorry I should've put all of the information on here originally. We bought a new MacBook Pro. The version of FS (5.3.0) is the same on both computers, and the machines are the same in terms of RAM (the new one actually has a faster processor), the only difference is the older machine has OS 1

Re: [Freesurfer] .w file for freeview

Hi Peng you can use read_wfile to read it into matlab, then save_mgh or MRIwrite to save them in .mgz format. Note that you will need to make sure that the vector you are writing is the correct length. The w-files can be sparse (that is, every vertex doesn't have to have a value), but the .mg

Re: [Freesurfer] .w file for freeview

You can also use mri_surf2surf to convert it to mgh or curv format On 01/06/2016 02:03 PM, Bruce Fischl wrote: > Hi Peng > > you can use read_wfile to read it into matlab, then save_mgh or > MRIwrite to save them in .mgz format. Note that you will need to make > sure that the vector you are writ

Re: [Freesurfer] .w file for freeview

oh, much easier. I didn't realize mri_surf2surf supported .w format Bruce On Wed, 6 Jan 2016, Douglas N Greve wrote: > You can also use mri_surf2surf to convert it to mgh or curv format > > On 01/06/2016 02:03 PM, Bruce Fischl wrote: >> Hi Peng >> >> you can use read_wfile to read it into matlab,

Re: [Freesurfer] .w file for freeview

Thank you Bruce! On Wed, Jan 6, 2016 at 8:03 PM, Bruce Fischl wrote: > Hi Peng > > you can use read_wfile to read it into matlab, then save_mgh or MRIwrite > to save them in .mgz format. Note that you will need to make sure that the > vector you are writing is the correct length. The w-files can

Re: [Freesurfer] .w file for freeview

Thank you Douglas! On Wed, Jan 6, 2016 at 8:10 PM, Douglas N Greve wrote: > You can also use mri_surf2surf to convert it to mgh or curv format > > On 01/06/2016 02:03 PM, Bruce Fischl wrote: > > Hi Peng > > > > you can use read_wfile to read it into matlab, then save_mgh or > > MRIwrite to save

Re: [Freesurfer] FDR correction

On 01/06/2016 11:00 AM, std...@virgilio.it wrote: > Hi list, > > I would like to ask you a number of questions regarding the FDR which > is performed following seed-based fcMRI using FS-FAST. > 1-In the previous mail you have suggested me to use mir_fdr command > line (version 6.0). Because I h

[Freesurfer] P files

Dear Freesurfer experts, I want to inquire if there is any tool in Freesurfer that can help to convert the p files ( raw data generated by GE scanner ) to DICOMs     Thanks for any advice!   Bests, John    ___ Freesurfer mailing list Freesurfer@nmr.m

Re: [Freesurfer] P files

Hi John Luca Marinelli (ccd) might be able to help you. cheers Bruce On Thu, 7 Jan 2016, John Anderson wrote: Dear Freesurfer experts, I want to inquire if there is any tool in Freesurfer that can help to convert the p files ( raw data generated by GE scanner ) to DICOMs     Thanks for any ad

Re: [Freesurfer] P files

Another option is to open the files in OsiriX, and export to DICOM from there. This does not, to my knowledge, have a batch option though. Anthony On 1/6/16 9:35 PM, Bruce Fischl wrote: Hi John Luca Marinelli (ccd) might be able to help you. cheers Bruce On Thu, 7 Jan 2016, John Anderson wr

[Freesurfer] P files

Begin forwarded message: > From: "Marinelli, Luca (GE Global Research)" > Date: January 6, 2016 at 10:26:38 PM EST > To: Bruce Fischl , Freesurfer support list > > Cc: "Marinelli, Luca (GE Global Research)" > Subject: Re: [Freesurfer] P files > > Hi John, > > Can you please reach out to m