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 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