Subject: [Freesurfer] R: R: R: Re: To use a ROI.label as seed in FS-FAST
From: <[email-masked]>
To: [email-masked]
Date: Fri, 12 Feb 2016 17:41:25 +0100 (CET)
List-Id: Freesurfer support list <freesurfer.nmr.mgh.harvard.edu>

Please also look the file attached. This the sig.nii.gz (subcortical, MNI) overlapped on f.nii.

----Messaggio originale----

Da: [email-masked]

Data: 12-feb-2016 17.16

A: <[email-masked]>

Ogg: [Freesurfer] R:  R: Re:  To use a ROI.label as seed in FS-FAST

Please also consider that the T1, f.nii and ROI.ii.gz (obtained by label2vol) are nice overlapped. The brain.mni305.2mm.nii seem to be strange (see the image attached). In the sig.nii.gz the cluster are bad coregistered and some of those out are of the brain. Thanks
Stefano

----Messaggio originale----

Da: [email-masked]

Data: 12-feb-2016 0.23

A: "Freesurfer support list"<[email-masked]>

Ogg: [Freesurfer] R: Re:  To use a ROI.label as seed in FS-FAST

I have used:mri_label2vol --label RIGHT_ROI.label --temp subj/rest/001/f.nii --reg subj/rest/001/register.dof6.dat --fillthresh .5 --o RIGHT_ROI.nii.gz
When I open with freeview the f.nii.gz and the RIGHT_ROI they are fine overlapped.But, after FS-FAST the sig.ii.gz seem to be wrong, probably bad reoriented, especially I have noted this on subcortical connectivity (MNI2mm).
Thanks

Stefano

----Messaggio originale----

Da: Douglas Greve <[email-masked]>

Data: 11-feb-2016 4.48

A: <[email-masked]>

Ogg: Re: [Freesurfer] To use a ROI.label as seed in FS-FAST

  
  
     I may have gotten the exact form of the flag wrong. When it says an
    option is not known, you should try running the command with --help
    to see if something similar is there. In this way,  you might be
    able to figure it out for yourself rather than have to wait a day or
    so for us to respond.

    doug

    

    On 2/10/16 4:20 PM, [email-masked]
      wrote:

    

        

        If I use:

        
        
          mri_label2vol --label
            ramgseed_rhsurf.label --temp $SUBJECTS_DIR/subj/mri/orig.mgz
            --identity --subject fsaverage --hemi rh --o
            RIGHT_ROI.nii.gz --fill-ribbon
          ERROR: Option --fill-ribbon unknown

          
            ----Messaggio originale----

            Da: [email-masked]

            Data: 8-feb-2016 20.35

            A: "Freesurfer support
            list"<[email-masked]>

            Ogg: [Freesurfer] R: Re: To use a ROI.label as seed in
            FS-FAST

            Thanks.
            I have down a right ad left ROI on the surface.
            Next, I have run:

              
              mri_label2vol --label ramgseed_rhsurf.label --temp
                $SUBJECTS_DIR/fsaverage/mri/orig.mgz --identity
                --subject fsaverage --hemi rh --o RIGHT_ROI.nii.gz
            
            mri_label2vol --label ramgseed_lhsurf.label --temp
              $SUBJECTS_DIR/fsaverage/mri/orig.mgz --identity --subject
              fsaverage --hemi rh --o LEFT_ROI.nii.gz

            

            
              mri_convert RIGHT_ROI.nii.gz RIGHT_ROI.mgz
              mri_convert LEFT_ROI.nii.gz LEFT_ROI.mgz

              

              fcseed-config -segid 1 -seg RIGHT_ROI.mgz -fsd rest
                -mean -cfg RIGHT_ROI.config
              fcseed-config -segid 1 -seg LEFT_ROI.mgz -fsd rest
                -mean -cfg LEFT_ROI.config

              

              fcseed-sess -s subj1_FS -cfg RIGHT_ROI.config
              fcseed-sess -s subj1_FS -cfg LEFT_ROI.config

            
            but during fcseed-sess this error occurs:

            
            
              $Id: mri_segstats.c,v 1.75.2.9 2013/02/16
                00:09:33 greve Exp $
              cwd 
              cmdline mri_segstats --i
                /Applications/freesurfer/subjects/fMRI/subj1/rest/001/fmcpr.nii.gz
                --seg
                /Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/mask.nii.gz
                --id 1 --sum
                /Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/junk.sum
                --avgwfvol
/Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/avgwf.mgh 
              sysname  Darwin
              hostname iMac-di-Stefano.local
              machine  x86_64
              user     Stefano
              UseRobust  0
              Loading
/Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/mask.nii.gz
              Loading
                /Applications/freesurfer/subjects/fMRI/subj1/rest/001/fmcpr.nii.gz
              Voxel Volume is 64.5752 mm^3
              Generating list of segmentation ids
              Found   1 segmentations
              Computing statistics for each segmentation
                0     1                                   
                      0       0.000
              MRIalloc(0, 1, 1): bad parm

              Reporting on   0 segmentations
              Computing spatial average of each frame

              Writing to
/Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/avgwf.mgh
              Segmentation fault 

            

              
                ----Messaggio originale----

                Da: Douglas Greve <[email-masked]>

                Data: 8-feb-2016 4.38

                A: <[email-masked]>

                Ogg: Re: [Freesurfer] To use a ROI.label as seed in
                FS-FAST

                 Use mri_label2vol to convert the label into a volume in the
                anatomical space and store it in
                $SUBJECTS_DIR/subject/mri. Make sure to use
                --fill-ribbon if the label is surface-based. When
                running fcseed-config, specify the volume with the -seg
                option and use -segid 1

                On 2/7/16 3:16 PM, [email-masked]
                  wrote:

                
                  Hi list,

                    
                    I would like to use as seed in FS-FAST a
                      ROI.label which I have drawn on a cluster in
                      tksurfer.
                    How can I do it?
                    Should I use mri_label2vol?

                      
                    Thanks.

                    
                    Stefano

                  

                  

                  

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