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> 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>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
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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