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 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 individual

fcseed-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