[Freesurfer] mri_volcluster

Hi there, I have a a couple of question related to the output generated by the ‘mri_volcluster' command. 1) It seems that the command automatically assumes that my voxels are 8 mm^3. Is there a way to specify my voxel size when I run the command? 2) The output is given in Talairach coordinat

[Freesurfer] mri_volcluster

Hi, I'm trying to use the mri_volcluster command to make label files from a single volume of binary voxel clusters. Once I have split the volume into individual label files I want to convter the label files back into individual cluster volumes (I am trying to use mri_label2vol to do this). T

[Freesurfer] mri_volcluster

Hi, I'm trying to use the mri_volcluster command to make label files from a single volume of binary voxel clusters. Once I have split the volume into individual label files I want to convter the label files back into individual cluster volumes (I am trying to use mri_label2vol to do this). T

Re: [Freesurfer] mri_volcluster

On 08/10/2015 10:47 AM, Morenikeji Adebayo wrote: > Hi there, > > I have a a couple of question related to the output generated by the > ‘mri_volcluster' command. > > 1) It seems that the command automatically assumes that my voxels are > 8 mm^3. Is there a way to specify my voxel size when I

Re: [Freesurfer] mri_volcluster

Hi there, The command I submitted is: mri_volcluster --in merged_encode_Young_NEUT_hit_V_miss_n41.nii.gz --thmin 1.3 --minsizevox 5 --sign neg --sum adebayo_young_neut_p.05 —fsaverage How would I: 1) Specify the voxel size 2) Have the results output in MNI? Thanks, Keji > On Aug 10, 2015,

Re: [Freesurfer] mri_volcluster

Hi there, Just following up. Any advice would be much appreciated! Thanks, Keji > On Aug 10, 2015, at 1:50 PM, Morenikeji Adebayo > wrote: > > Hi there, > > The command I submitted is: > mri_volcluster --in merged_encode_Young_NEUT_hit_V_miss_n41.nii.gz --thmin > 1.3 --minsizevox 5 --sign n

Re: [Freesurfer] mri_volcluster

It will produce results in the voxel size and space of merged_encode_Young_NEUT_hit_V_miss_n41.nii.gz How was that file produced? What space is it in? On 08/10/2015 01:50 PM, Morenikeji Adebayo wrote: > Hi there, > > The command I submitted is: > mri_volcluster --in merged_encode_Young_NEUT_hit_

[Freesurfer] mri_volcluster question

Hi FS Community, I am using the mri_volcluster command but for some reason the --sumfile shows up as an unknown flag. Is there another way to get a summary text file? (I am using FS 5.3 stable.) Thank you for your time! Best, Panos ___ Freesurfer mailin

[Freesurfer] mri_volcluster problems

Hi I have a few questions regarding the use of “mri_volcluster” for clusterwise thresholding. Essentially, we have a volume of pvalues obtained from a two tailed t-test comparing beta values from condition A vs condition B. When I ran this command: mri_volcluster --in transformedP.nii --sum

[Freesurfer] mri_volcluster question

Hello, Does the frame flag refer to offsets? If so, would frame 5 be the same as offset 5 (6 seconds)? Thank you, Dave Brohawn ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] mri_volcluster example

Hi Can you please post an example of "mri_volcluster" use with fsfast? more specifically, when i run : mri_volcluster \ --in /space/engram/12/users/pman/rk_fmri/Y15_111504/bold/rk_enc_sm5/RNeg_vs_Fix/sig \ --in_type bfloat \ --reg /space/engram/12/users/pman/rk_fmri/Y15_111504/bold/rk_enc_sm

Re: [Freesurfer] mri_volcluster

I would probably use --ocn with mri_volcluster to create a single volume in which each voxel value is the cluster number it belongs to. Then split them out like: mri_binarize --i ocn.mgh --match 1 --o cluster-0001.mgh doug Gregory Dierksen wrote: Hi, I'm trying to use the mri_volcluster c

Re: [Freesurfer] mri_volcluster question

It is --sum, not --sumfile doug On 09/25/2013 12:44 PM, pfot...@nmr.mgh.harvard.edu wrote: > Hi FS Community, > > I am using the mri_volcluster command but for some reason the --sumfile > shows up as an unknown flag. Is there another way to get a summary text > file? > (I am using FS 5.3 stable.)

Re: [Freesurfer] mri_volcluster question

I see, thanks Doug! > It is --sum, not --sumfile > doug > > > On 09/25/2013 12:44 PM, pfot...@nmr.mgh.harvard.edu wrote: >> Hi FS Community, >> >> I am using the mri_volcluster command but for some reason the --sumfile >> shows up as an unknown flag. Is there another way to get a summary text >> f

[Freesurfer] mri_volcluster register.dat question

Hello all, I'm trying to run mri_volcluster on our third-level functional data and one of the required flagged arguments is the register.dat file. Our data preprocessing/registration was done in FSL, not Freesurfer, so we don't have this particular file. Is there anything we can do to get around t

Re: [Freesurfer] mri_volcluster problems

It is more straightforward if you use -log10(p). If you want to do an unsigned test, then run it twice, once with pos and once with neg, then multiply the resulting cluster-wise p-values by 2. doug On 10/21/2014 02:11 AM, Joo Tan wrote: > > Hi > > > I have a few questions regarding the use of “

Re: [Freesurfer] mri_volcluster question

basically, yes. It is the 0-based frame number. The time of this frame will depend on your TR and prestim. doug Dave Brohawn wrote: Hello, Does the frame flag refer to offsets? If so, would frame 5 be the same as offset 5 (6 seconds)? Thank you, Dave Brohawn ___

Re: [Freesurfer] mri_volcluster example

You are using the wrong register.dat file. Use the one in Y15_111504/bold doug Paymon Hosseini wrote: Hi Can you please post an example of "mri_volcluster" use with fsfast? more specifically, when i run : mri_volcluster \ --in /space/engram/12/users/pman/rk_fmri/Y15_111504/bold/rk_enc_

Re: [Freesurfer] mri_volcluster register.dat question

Hi Huiting, you don't need to give it a register.dat. That only gives you access to label locations of your clusters. If this is something you want, you can use $FREESURFER_HOME/average/mni152.register.dat. doug Huiting Liu wrote: > Hello all, > > I'm trying to run mri_volcluster on our third-le

[Freesurfer] mri_volcluster not recognize --mindistance

External Email - Use Caution Hello FreeSurfer experts, I am trying to run mri_volcluster with the following command to later create masks of clustered regions from functional data. I get an error saying that the option --mindistance is not recognized, even though this option is

[Freesurfer] mri_volcluster PDF multiple correction

External Email - Use Caution Dear Freesurfer support, My name is Vicente and I have a question for you regarding mri_volcluster. I am interested in using mri_volcluster to correct for multiple comparison after generating a probability distribution function (pdf) via simulation t

[Freesurfer] mri_volcluster in single direction

Hello All, I've been using fslstats to create a mask of voxels reaching a certain threshold and then using mri_volcluster to reduce the mask down to just clusters above 3 voxels. Now we're trying to filter them down to just those clusters that have more than 3 contiguous voxels in a single directi

[Freesurfer] mri_volcluster and neuroanatomical labels

Hello, I was wondering if there is a Freesurfer command for getting neuroanatomical labels for the output clusters of mri_volcluster. thank you very much for your help, paymon ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mai

Re: [Freesurfer] mri_volcluster not recognize --mindistance

Try --mindist not --mindistance On 8/9/18 9:08 AM, Yagmur Ozdemir 19 wrote: External Email - Use Caution Hello FreeSurfer experts, I am trying to run mri_volcluster with the following command to later create masks of clustered regions from functional data. I get an error saying that

Re: [Freesurfer] mri_volcluster and neuroanatomical labels

Does running it with --label not work? On Mon, 31 Jul 2006, Paymon Hosseini wrote: Hello, I was wondering if there is a Freesurfer command for getting neuroanatomical labels for the output clusters of mri_volcluster. thank you very much for your help, paymon _

Re: [Freesurfer] mri_volcluster and neuroanatomical labels

doug i think he's asking about what you were thinking of implementing with a similar flag to the --annot one that you added to mri_surfcluster. frida On Jul 31, 2006, at 5:34 PM, Doug Greve wrote: Does running it with --label not work? On Mon, 31 Jul 2006, Paymon Hosseini wrote: Hello,

Re: [Freesurfer] mri_volcluster and neuroanatomical labels

Oh, no that does not exist yet. There are some issues as to whether it's really valid as the volumetric analysis that preceeds mri_volcluster is linear whereas the aseg.mgz is produced with a nonlinear registration. I'm looking into something intermediate that could give you something close to th

[Freesurfer] mri_volcluster --ERROR: you must specify a pos or neg sign with --fwhm

Hi all, I was going through the FSFAST TUTORIAL from wiki( https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorial?action=highlight&value=TUTORIAL). I got the follwoing error during mri_volcluster, "NOT Adjusting threshold for 1-tailed test ERROR: you must specify a pos or neg sign with --fwhm

Re: [Freesurfer] mri_volcluster --ERROR: you must specify a pos or neg sign with --fwhm

To use --fwhm you have to specify the sign of the contrast (this implements the gaussian random fields). If a sign is not given in the wiki, can you fix it? doug pkun...@nmr.mgh.harvard.edu wrote: > Hi all, > > I was going through the FSFAST TUTORIAL from wiki( > https://surfer.nmr.mgh.harvard.

Re: [Freesurfer] mri_volcluster --ERROR: you must specify a pos or neg sign with --fwhm]

Nevermind, it works fine now with after i added "--sign < >" flag to the mri_volcluster ..command. thanks pratap Original Message ---- Subject: [Freesurfer] mri_volcluster --ERROR: you must specify a pos or neg sign with --fwhm