Re: [Freesurfer] error with fcseed-config & fcseed-sess

Those labels should exist in your individual subject's label folder. There should be a V1 label in there too. You can use mri_label2vol to create a binary volume in the anatomical space (this will be a volume where voxels values are either 1 (in V1) or 0 (out of V1)). This volume will be 256^3, 1mm3, and should go into the subject/mri folder (eg, lh.V1.mgz). When you run fcseed-config, specify -seg lh.V1.mgz -segid 1

On 07/27/2017 11:08 AM, Jessica Huang wrote:

Hi Dr. Greeve,

Would the following commands be enough to map my regions of interest from the fsaverage map to my individual subjects?:

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI

Namely, the following bits of code:

cd $SUBJECTS_DIR mri_label2label \ --srcsubject fsaverage \ --srclabel fsaverage/label/lh.BA45.label \ --trgsubject 004 \ --trglabel 004/label/lh.BA45.label \ --hemi lh \ --regmethod surface

On Thu, Jul 27, 2017 at 10:37 AM, Jessica Huang <jessica_huang@college.harvard.edu mailto:jessica_huang@college.harvard.edu> wrote:

Hi Dr. Greeve,

Oh I see, thank you for the fix for V1. To probe further, I'm
curious why the visual areas weren't implemented? Is there an
additional step I could take to access other regions in the visual
hierarchy such as V2, V3, and V5?

Thanks for your insight Dr. Greeve,
Jess

On Jul 26, 2017 5:37 PM, "Douglas N Greve"
<greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:

    By default, you are using aparc+aseg.mgz as the ROI atlas, so
    use 1021
    or 2021 for V1.

    1021    ctx-lh-pericalcarine                120 100 60  0


    On 07/26/2017 12:37 PM, Jessica Huang wrote:
    >
    > Hi freesurfer experts,
    >
    >
    > I’m using the fcseed-config and fcseed-sess commands to
    create a seed
    > at V1 in accordance with the FsFastFunctionalConnectivity
    Walkthrough
    >
    <http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough
    <http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough>>Steps:
    >
    >
    > *STEP 4: Use fcseed-config to configure the parameters you
    wish to
    > pass to your connectivity analysis.Sample command: fcseed-config
    > -segid 1010 -fcname L_Posteriorcingulate.dat -fsd bold -mean
    -cfg
    > mean.L_Posteriorcingulate.config*STEP 5: Create the FC seed
    for an
    > individualfcseed-sess  -s sessionid -cfg
    L_Posteriorcingulate.config
    >
    > V1 corresponds to the number 400 in
    > $FREESRUFER_HOME/FreeSurferColorLUT.txt. The subject session I’m
    > running is B101. The data is rest data but I named the file
    bold.
    > Overall, with this information specific to my data, I ran the
    > following commands:
    >
    >
    > INPUT
    >
    > $ fcseed-config -segid 400 -fcname V1.dat -fsd bold -mean -cfg
    > mean.V1.config
    >
    > OUTPUT
    >
    > fcname is V1.dat
    >
    > fcseed-config done
    >
    >
    > INPUT
    >
    > $ fcseed-sess  -s B101 -cfg mean.V1.config
    >
    > OUTPUT
    >
    > Logfile is
    >
    /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/log/fcseed-sess.V1.dat.log.B101
    >
    > Wed Jul 26 12:27:17 EDT 2017
    >
    > Darwin Caramazza-Labs-Mac-Pro.local 16.6.0 Darwin Kernel Version
    > 16.6.0: Fri Apr 14 16:21:16 PDT 2017;
    > root:xnu-3789.60.24~6/RELEASE_X86_64 x86_64
    >
    > setenv SUBJECTS_DIR /Users/caramazzalab/Desktop/Jess/Subjects
    >
    > cd /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir
    >
    > /Applications/freesurfer/fsfast/bin/fcseed-sess
    >
    > -s B101 -cfg mean.V1.config
    >
    > freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
    >
    > Wed Jul 26 12:27:17 EDT 2017
    >
    > Darwin Caramazza-Labs-Mac-Pro.local 16.6.0 Darwin Kernel Version
    > 16.6.0: Fri Apr 14 16:21:16 PDT 2017;
    > root:xnu-3789.60.24~6/RELEASE_X86_64 x86_64
    >
    > setenv SUBJECTS_DIR /Users/caramazzalab/Desktop/Jess/Subjects
    >
    > cd /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir
    >
    > /Applications/freesurfer/fsfast/bin/fcseed-sess
    >
    > -s B101 -cfg mean.V1.config
    >
    > freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
    >
    >
    > mri_label2vol --seg
    >
    /Users/caramazzalab/Desktop/Jess/Subjects/B201_mprage/mri/aparc+aseg.mgz
    > --reg
    >
    /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/register.dof6.lta
    > --temp
    >
    /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/template.nii.gz
    > --fillthresh .5 --o
    >
    /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/seg.nii.gz
    > --pvf
    >
    /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/pvf.nii.gz
    >
    > PVF
    >
    /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/pvf.nii.gz
    >
    > Number of labels: 0
    >
    > Annot File:      (null)
    >
    > Template Volume:
    >
    /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/template.nii.gz
    >
    > Outut Volume:
    >
    /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/seg.nii.gz
    >
    > Registration File:
    >
    /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/register.dof6.lta
    >
    > Fill Threshold: 0.5
    >
    > Label Vox Vol:  1
    >
    > ProjType:       (null)
    >
    > ProjTypeId:     0
    >
    > ProjStart:      0
    >
    > ProjStop:       0
    >
    > ProjDelta:      0.1
    >
    > Subject:  (null)
    >
    > Hemi:     (null)
    >
    > UseNewASeg2Vol:  0
    >
    > DoLabelStatVol  0
    >
    > LabelCodeOffset  0
    >
    > setenv SUBJECTS_DIR /Users/caramazzalab/Desktop/Jess/Subjects
    >
    > $Id: mri_label2vol.c,v 1.46 2014/12/08 21:11:54 greve Exp $
    >
    > Template RAS-to-Vox: --------
    >
    > -0.50000  -0.00000  -0.00000   56.00000;
    >
    > -0.00000  -0.00000  -0.50000   56.00000;
    >
    > -0.00000   0.45455  -0.00000   32.00000;
    >
    > -0.00000  -0.00000  -0.00000   1.00000;
    >
    > Template Voxel Volume: 8.8
    >
    > nHits Thresh: 4.4
    >
    > Loading registration from
    >
    /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/register.dof6.lta
    >
    > regio_read_register: loading lta
    >
    > RegMat: --------
    >
    > 0.99785   0.02664   0.05987   0.19449;
    >
    > -0.06077   0.03415   0.99757  -39.76084;
    >
    > -0.02453   0.99906  -0.03570   2.27075;
    >
    > 0.00000   0.00000   0.00000   1.00000;
    >
    > Label RAS-to-Vox: --------
    >
    > -0.49893  -0.01332  -0.02994   55.90276;
    >
    > 0.01227  -0.49953   0.01785   54.86462;
    >
    > -0.02762   0.01552   0.45344   13.92689;
    >
    > 0.00000   0.00000   0.00000   1.00000;
    >
    > PVF
    >
    /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/pvf.nii.gz
    >
    > Computing PVF 8.8
    >
    > mri_label2vol done
    >
    > mri_binarize --i
    >
    /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/seg.nii.gz
    > --o
    >
    /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/mask.nii.gz
    > --match 400
    >
    >
    > $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $
    >
    > cwd /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir
    >
    > cmdline mri_binarize.bin --i
    >
    /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/seg.nii.gz
    > --o
    >
    /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/mask.nii.gz
    > --match 400
    >
    > sysname  Darwin
    >
    > hostname Caramazza-Labs-Mac-Pro.local
    >
    > machine  x86_64
    >
    > user     caramazzalab
    >
    >
    > input
    >     
    /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/seg.nii.gz
    >
    > frame      0
    >
    > nErode3d   0
    >
    > nErode2d   0
    >
    > output
    >   
     /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/mask.nii.gz
    >
    > Binarizing based on matching values
    >
    > nMatch 1
    >
    > 0   400
    >
    > binval        1
    >
    > binvalnot     0
    >
    > fstart = 0, fend = 0, nframes = 1
    >
    > Found 0 values in range
    >
    > Counting number of voxels in first frame
    >
    > Found 0 voxels in final mask
    >
    > Count: 0 0.000000 802816 0.000000
    >
    > mri_binarize done
    >
    > mri_segstats --i
    >
    /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/fmcpr.nii.gz
    > --seg
    >
    /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/mask.nii.gz
    > --id 1 --sum
    >
    /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/junk.sum
    > --avgwfvol
    >
    /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/avgwf.mgh
    >
    >
    > $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $
    >
    > cwd
    >
    > cmdline mri_segstats --i
    >
    /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/fmcpr.nii.gz
    > --seg
    >
    /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/mask.nii.gz
    > --id 1 --sum
    >
    /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/junk.sum
    > --avgwfvol
    >
    /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/avgwf.mgh
    >
    >
    > sysname  Darwin
    >
    > hostname Caramazza-Labs-Mac-Pro.local
    >
    > machine  x86_64
    >
    > user     caramazzalab
    >
    > UseRobust  0
    >
    > Loading
    >
    /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/mask.nii.gz
    >
    > Loading
    >
    /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/fmcpr.nii.gz
    >
    > Voxel Volume is 8.8 mm^3
    >
    > Generating list of segmentation ids
    >
    > Found   1 segmentations
    >
    > Computing statistics for each segmentation
    >
    >
    > Reporting on   0 segmentations
    >
    > Using PrintSegStat
    >
    > Computing spatial average of each frame
    >
    >
    > ERROR: no voxels found in segmentation
    >
    >
    >
    >
    > I attached the error log below - any idea what happened? Is
    there
    > something I can change in these commands to yield the
    timecourse of
    > V1? These are all subjects 18+ years of age.
    >
    >
    > What do you think?
    >
    >
    > Thank you in advance, any and all feedback would be greatly
    appreciated.
    >
    >
    > Thanks,
    >
    > Jess
    >
    >
    >
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