Re: [Freesurfer] Content of register.dof6.dat.param

Hello Doug, can we finish the topic this week? Yours pfannmoe On Thu, 9 Apr 2015 09:41:17 -0400 (EDT) Bruce Fischl wrote: > Bruce ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurf

[Freesurfer] Clusterwise correction for multiple comparisons : volumic Tmap projected on fsaverage surface

Dear experts, I had to make volumic statistical analysis for the need to use BPM toolbox. So, I got in the output of this statistical analysis some volumic Tmaps. As I did before some group analysis according to FStutorial, I would like to apply the same method of Clusterwise Correction on my vol

[Freesurfer] Parallel

Hi, Is it possible to run recon-all in parallel for fastening the speed ??? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the

Re: [Freesurfer] Content of register.dof6.dat.param

Hi pfannmoe you are better off including the contents of the thread when you repost. cheers Bruce On Mon, 13 Apr 2015, pfannmo...@uni-greifswald.de wrote: > Hello Doug, > > can we finish the topic this week? > > Yours pfannmoe > > > > On Thu, 9 Apr 2015 09:41:17 -0400 (EDT) > Bruce Fischl wr

Re: [Freesurfer] Parallel

Hi Hassan you can either run multiple instances of recon-all (if you have enough RAM and CPUs), or you can use the -openmp flag to parallelize a single instance. cheers Bruce On Mon, 13 Apr 2015, Hassan bakhshi wrote: > Hi, > Is it possible to run recon-all in parallel for fastening the sp

Re: [Freesurfer] R: Re: R: Re: isxconcat-sess problem

Does Sess14 have a double dash? On 4/4/15 3:38 AM, std...@virgilio.it wrote: No, do you think that a folder is lacking (please see below)? Thanks Stefano Messaggio originale Da: gr...@nmr.mgh.harvard.edu Data: 3-apr-2015 7.34 A: Ogg: Re: [Freesurfer] R: Re: isxconcat-sess problem do

Re: [Freesurfer] Extreme mean values for significant clusters (using GLM)

I'm not sure what the problem is, but it occurs to me that computing the mean over the cluster is probably not what should be done. Instead, the total should be computed. In the header of that file, there should be a command line for mri_segstats. Cut and paste that into a shell and add --accum

[Freesurfer] Parameters for motion correction from boundary based register

Hello Doug, is there a possibility to extract the "motion parameter" from a BBR registration? Possibly, the first six numbers of the register.dof6.dat.param file are the same parameters as found in column 2 - 7 in the file: fmcpr.mcdat created by mc-afni2 during the FS-Fast preprocessing.

Re: [Freesurfer] fs-fast analysis on a group averaged surface

Use the (undocumented) -trgsubject flag On 4/6/15 9:10 AM, Xiaomin Yue wrote: Hi All, I generated a group averaged surface using make_average_surface successfully. Currently, I like to process the fMRI data using this group surface, instead of fsaverage, using the fs-fast pipeline. For do

Re: [Freesurfer] Content of register.dof6.dat.param

Those numbers do not have the same interpretation as as the ones in fmc.mcdat but they represent the same information. If you construct a new file with the same format as fmc.mcdat but with those numbers substituted in cols 2-7 then you should get pretty similar results. On 4/9/15 7:04 AM, pf

Re: [Freesurfer] mri_vol2surf for 4D functional images in freesurfer space

Just use --regheader subject On 4/11/15 11:27 AM, Sabine Oligschläger wrote: Dear FreeSurfer's, A question regarding mri_vol2surf usage: I have 4D functional images that are preprocessed and already in freesurfer space. I would like to project them to the fsaverage surface template using

Re: [Freesurfer] Clusterwise correction for multiple comparisons : volumic Tmap projected on fsaverage surface

If you did the analysis in the volume, then you have to do the clusterwise correction in the volume. On 4/13/15 6:05 AM, Matthieu Vanhoutte wrote: Dear experts, I had to make volumic statistical analysis for the need to use BPM toolbox. So, I got in the output of this statistical analysis som

[Freesurfer] Freeview on Linux help

Hello, I am having trouble setting up FreeSurfer on Linux (SUSE 10 x84_64). I followed the installation and setup directions from the wiki, and that was all successful. When I attempt to test the installation though, it's clear something is not right. I tried opening freeview, and received the fo

Re: [Freesurfer] Content of register.dof6.dat.param

yes On 4/13/15 10:32 AM, pfannmo...@uni-greifswald.de wrote: > Just to make that point: Is it valid to apply "mcparams2extreg -mcfile > fmc.mcdat -extreg mcextreg" after substitution of the numbers in > "register.dof6.dat.param" into "fmc.mcdat"? Is the result for the motion > regressors valid?

Re: [Freesurfer] Content of register.dof6.dat.param

Just to make that point: Is it valid to apply "mcparams2extreg -mcfile fmc.mcdat -extreg mcextreg" after substitution of the numbers in "register.dof6.dat.param" into "fmc.mcdat"? Is the result for the motion regressors valid? On Mon, 13 Apr 2015 10:15:08 -0400 Douglas Greve wrote: > > Tho

Re: [Freesurfer] Clusterwise correction for multiple comparisons : volumic Tmap projected on fsaverage surface

Hello Douglas, Thanks but even if I do the clusterwise correction in the volume, I can't get an clusterwise corrected output volume image. The only things I have are the Tmaps that I can threshold if wanted. And I would like to project on fsaverage surface the results of the clusterwise correctio

Re: [Freesurfer] Clusterwise correction for multiple comparisons : volumic Tmap projected on fsaverage surface

Does the BPM toolbox (what's that?) not give you cluster correction? You can try using mri_volcluster with the --grf option, but you'll need to know the FWHM. Afterwards you can map the result to the surface On 4/13/15 10:46 AM, Matthieu Vanhoutte wrote: Hello Douglas, Thanks but even if I do

Re: [Freesurfer] Clusterwise correction for multiple comparisons : volumic Tmap projected on fsaverage surface

By the mean of SPM, the Biological Parmatring toolbox can do the FWE correction and give me results on a glass brain. But I don't have any cluster wise corrected P-maps on output. Or did I miss something ? Best regards, Matthieu 2015-04-13 16:51 GMT+02:00 Douglas Greve : > Does the BPM toolbo

[Freesurfer] mri_segstats flags

Hi Doug, Kindly I have the following questions regarding the command mri_segstats: * I wanted to use the flag --seg-erode 2 in the command mri_segstats but I am receiving an error message that this flag is not available ( I am using FreeSurfer 5.3.0 ). * When the command recon-

[Freesurfer] Query about Freesurfer's hippocampal subfield segmentation

Dear Freesurfer Experts, I am performing the automated segmentation of hippocampal subfield on an elderly clinical population with a generalized pattern of atrophy. I understand that the subfields are segmented using a Bayesian inference approach and a probabilistic atlas based on normal brains.

Re: [Freesurfer] mri_segstats flags

Try this one ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats This is for linux. If that is not your system, tell me what your system is doug On 04/13/2015 02:22 PM, Alshikho, Mohamad J. wrote: > > Hi Doug, > > Kindly I have the following questions regarding the comman

Re: [Freesurfer] mri_segstats flags

Hi Doug, My system is Linux Centos 7 I tried to run it and I got: [malshikh@glia 002201]$ mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR

Re: [Freesurfer] Visualization FS-FAST results in graphs

On 04/08/2015 03:45 AM, std...@virgilio.it wrote: > Hi list, > > I'm performing the FS-FAST for functional connectivity analysis on two > groups. > > I'm using tkmedit to visualize the results. Is possible to load a > scatter plot which describes the values of each subject for each > selected

Re: [Freesurfer] question about preprocessing and analysis in FS 4.5 vs FS5

If 4.5 will actually run on 5.0 preprocessed data, then I think it should be ok, but it has been a very long time since 4.5 so I can't say with any confidence. doug On 04/08/2015 01:33 PM, Katie Bettencourt wrote: > I had a question about using different components of Freesurfer 4.5 > and F

Re: [Freesurfer] Clusterwise correction for multiple comparisons : volumic Tmap projected on fsaverage surface

clusterwise correction is a type of FWE correction. If the FWE you are using is good enough for you and you want to visualize the results on a surface, then use mri_vol2surf. If this was done on the SPM template space, then run the SPM T1 template through recon-all to get the surfaces On 0

Re: [Freesurfer] mri_segstats flags

Are you sure you're using the new version? what do you get if you type which mri_segstats On 04/13/2015 03:41 PM, Alshikho, Mohamad J. wrote: > Hi Doug, > My system is Linux Centos 7 > > I tried to run it and I got: > > [malshikh@glia 002201]$ mri_segstats --seg mri/aseg.mgz --sum > stats/ase

Re: [Freesurfer] mri_segstats flags

I got /usr/local/freesurfer/stable5_1_0/bin/mri_segstats and this is really weird because I thought that I am using FS 5.0.3. I am sourcing routinely the following script before I start FS #!/bin/tcsh setenv FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 setenv USE_STABLE5_3_0 setenv LD_LIB

Re: [Freesurfer] mri_segstats flags

maybe zeke can help you sort it out On 04/13/2015 04:24 PM, Alshikho, Mohamad J. wrote: > I got > > /usr/local/freesurfer/stable5_1_0/bin/mri_segstats > > and this is really weird because I thought that I am using FS 5.0.3. > > I am sourcing routinely the following script before I start FS > > #!/

Re: [Freesurfer] mri_segstats flags

Thank you Doug, Kindly one more question regarding mri_segstats: The following two mri_segstats command lines: mri_segstats --seg ${out1}/${i}/mri/aseg.mgz --sum ${out1}/${i}/stats/aseg.stats --pv ${out1}/${i}/mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in ${o

Re: [Freesurfer] mri_segstats flags

Only the structures in the color table (--ctab) are reported; the 1st ctab does not have those strcutures. In the 2nd, does On 04/13/2015 04:41 PM, Alshikho, Mohamad J. wrote: > Thank you Doug, > Kindly one more question regarding mri_segstats: > The following two mri_segstats command lines: > >

Re: [Freesurfer] mri_segstats flags

Thank you very much for your help By the way I added the following line source $FREESURFER_HOME/SetUpFreeSurfer.sh to my fs script to source FS 5.0.3 and it worked. Now I can use --seg-erode with mri_segstats From: freesurfer-boun...@nmr.mgh.harvard.

[Freesurfer] Why weighted least squares?

Dear Freesurfers, Can someone please explain to me why WLS was chosen as the method of regression? Thank you very much! Sincerely, Ye ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfe

Re: [Freesurfer] Why weighted least squares?

Hello Freesurfers, I would like to be a little more specific about my question. Was heteroskedasticity a reason for Weighted Least Square (WLS)? If so, how did Freesurfer determine the weights? Thank you! Sincerely, Ye On Mon, Apr 13, 2015 at 4:59 PM, ye tian wrote: > Dear Freesurfers, > >

Re: [Freesurfer] Extreme mean values for significant clusters (using GLM)

Hi Doug, Sorry which file should the mri_segstats command be in? Also, I am still unclear on how the individual values in cache.th13.abs.y.ocn.dat are calculated. Could you possibly explain this? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Re

Re: [Freesurfer] Installing FreeSurfer on Fedora 21

This does not change anything, but it appears that in either case, the directory is untarred. (I can not tell if the error matters.) So I wanted to go further and see about running the examples in: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/OutputData_freeview I have a new problem: th

Re: [Freesurfer] fs-fast analysis on a group averaged surface

Thanks very much. Xiaomin > On Apr 13, 2015, at 9:43 AM, Douglas Greve wrote: > > Use the (undocumented) -trgsubject flag > >> On 4/6/15 9:10 AM, Xiaomin Yue wrote: >> Hi All, >> >> I generated a group averaged surface using make_average_surface >> successfully. Currently, I like to proce