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_hu...@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" <gr...@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/FsFastFunctionalCo >> nnectivityWalkthrough>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/ap >> arc+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/B10 >> 1/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 >> gr...@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/ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . 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