1 Functinal cnnectivity tlbx manual v1.0 Overview The tlbx perfrms seeded vxel crrelatins by estimating maps shwing tempral crrelatins between the BOLD signal frm given seed and that at every brain vxel. The tlbx implements acmpcr strategy fr physilgical (and ther) nise surce reductin, first-level General Linear Mdel fr crrelatin and regressin cnnectivity estimatin, and secnd-level randm-effect analyses. The tlbx is designed t wrk with bth resting state scans and blck designs. Installing the tlbx: 1. dwnlad cnn.zip, unzip the file. 2. add./cnn/ directry t matlab path T start the tlbx: On the matlab prmpt, type : cnn (make sure yur matlab path include the path t the cnnectivity tlbx)
2 Functinal cnnectivity tlbx manual v1.0 Usage Step ne: Setup (Defines experiment infrmatin, file surces fr functinal data, structural data, regins f interest, and ther cvariates) - Click n the SETUP tab Click n the Basic buttn n the left side, enter experiment infrmatin (Number f subjects, TR, and number f sessins per subject) Click n Functinal buttn n the left side, frm the right side panel, select the functinal images (*img, r *nii, r 4d nii). This will take a secnd t lad, check the middle panel (Functinal data setup) t make sure the crrect vlumes are laded. The brain display in the Functinal data setup windw shws the first (left) and last (right) scan fr the selected subject/sessin (as in the figure abve). The current versin f the tlbx assumes analyses are perfrmed in nrmalized space. GUI tip 1: The Find in the Select functinal data files windw can be used t search fr all files within the target flder recursively. Change the Filter windw t narrw the search. GUI tip 2: If multiple subjects are selected in the Subjects list, and the number f files selected in the Select functinal data files windw matches the number f subjects, each subject is assigned ne single file frm the list (this is useful when ne has 4-dimensinal.nii files ne file per sessin- in rder t enter all f the functinal files fr each sessin simultaneusly) Click n the Structural buttn n the left side t lad the structural images Optin 1: lad raw anatmical image, the tlbx will perfrm nrmalizatin and segmentatin n it. Optin 2: If the nrmalized/segmented images are available, lad the nrmalized anatmical image (and lad the white matter and CSF masks in the next step, see belw). Click n the ROIs buttn n the left side t lad ROI mask files (.img r.nii vlumes) r Talairach crdinate files (.tal text files).
3 Functinal cnnectivity tlbx manual v1.0 By default all files in the ris tlbx flder (./cnn/ris) will be imprted as initial regins f interest. T imprt new ROIs, click belw the last ROI listed and enter the apprpriate infrmatin. Lad the grey matter, white matter and CSF mask fr each subject if they already exist (Optin 2 in structural step abve) Mask files shuld be cregistered t the nrmalized structural f this subject (they culd be defined in nrmalized space, r they culd be defined in subject-space and then transfrmed t nrmalized space in SPM). The default dimensins (number f PCA cmpnents t be extracted) fr each ROI can be changed here. In the fllwing steps (preprcessing, analyses), yu can later select the number f cmpnents amng the extracted nes yu wish t use in the cnnectivity analyses. Click n the Cnditins buttn n the left side t enter nsets and duratins (in secnds) f each experimental cnditin Click n the Cvariates:First-level buttn t define first level cvariates such as realignment parameters t be used in the mdel. Click n the Cvariates:Secnd-level buttn t define grups and subject-level regressrs (e.g. behaviral measures). Use 1/0 t define subject grups, r cntinuus values t perfrm between-subject regressin mdels). Click n the empty space belw All t add a variable. e.g. patients: 1 1 1 1 0 0 0 0 cntrls: 0 0 0 0 1 1 1 1 perfrmance : 1 2 3 2 3 4 5 6 Nte: Secnd-level cvariates can be defined at any time in the analyses (changes t any f ther Setup ptins requires rerunning all the analyses steps, while changes t the secnd-level cvariates d nt as they nly affect the secnd-level analyses in the Results windw) When finished defining the experiment data press Dne. This will imprt the functinal data. It will als perfrm nrmalizatin & segmentatin f the structural data in rder t define gray matter/ white matter/ CSF regins f interest (ptin 1 in structural step abve). Last it will extract the ROIs time-series (perfrming PCA n the within-roi activatins when apprpriate). After this prcess is finished cme back t Setup t inspect the resulting ROIs fr pssible incnsistencies. A.mat file and a flder f the same name will be created fr the prject. Save / Save as buttn will save the setup cnfiguratins in a.mat file, which can be laded later (Lad buttn). The.mat file will be updated each time the Dne buttn is pressed Nte: If the data has initially been defined in SPM yu can click the Imprt buttn (right after entering the number f subjects in the Basic setup) and specify ne SPM.mat file fr each subject. The prgram will extract the lcatin f the functinal data, the number f cnditins per subject, the nset/length f the cnditins f interest, and any specified first-level cvariates frm these SPM.mat files.
4 Functinal cnnectivity tlbx manual v1.0 Step tw: Preprcess (Define, explre, and remve pssible cnfunds) Click n the PREPROCESSING tab. By default the system will start with three different surces f pssible cnfunders: 1) BOLD signal frm the white matter and CSF masks (5 dimensins each); 2) any previusly-defined within-subject cvariate (realignment parameters) tgether with their first-rder derivatives; and 3) the main cnditin effects (blcks cnvlved with hrf). Fr each f the selected pssible cnfunds yu can change the number f dimensins (specifying hw many tempral cmpnents are being used), and the derivatives rder (specifying hw many successive rders f tempral derivatives are included in the mdel). Fr example, the realignment cnfund (derived frm the estimated subject mtin parameters) is defined by default by 6 dimensins and 1 derivative rder (indicating that the six mtin parameters are being used, in additin t their first-rder tempral derivative terms). Similarly, the White Matter cnfund is defined by default by 5 dimensins and 0 derivative rder (indicating that 5 PCA tempral cmpnents are being used, with nt additinal tempral derivative terms). The Preview results windw in the right panel shws the ttal variance explained (r-square) by each f the pssible cnfunding surces (fr the selected subject/sessin data). The dimensins f each cnfund can be changed up t the values entered in the Setup stage, t explre its effect n the ttal variance explained. Enter the band-pass filter infrmatin in the bttm-left bx (tw numbers, in Hz, defining the band-pass frequency windw f interest). When finished, press the Dne buttn. This will filter the functinal data and remve the effect f the defined cnfunds n all brain vxels and regins f interest.
5 Functinal cnnectivity tlbx manual v1.0 Step three: Analyze (Define and initially view the functinal cnnectivity f different surces in single subject level) Click n the ANALYSES tab t define surce f interest (seed ROIs). - Use the With-in cnditin weights fr the fllwing: When estimating cnnectivity frm rest blcks in a mre cmplex design (with ther task blcks) between-cnditin differences in activatin can affect the activatin at the beginning r end f the rest blck. These effects are partially cntrlled by entering the cnditin regressrs as pssible cnfunds. Hrf and hanning within-cnditin weights attempt t further cntrl these effects by weighting dwn the initial scans within a blck (hrf weights) r bth the beginning and end scans within a blck (hanning weights). - Click n Cnnectivity Measures t change the methd f analysis (crrelatin r regressin, semipartial fr multiple surces). - The right panel ( Preview results ) displays the cnnectivity measures fr each subject/cnditin/surce. Analyses here are perfrmed in real-time (any changes in the Define surces definitins affect directly the results displayed in the Preview windw). The measures displayed in the Preview results brain image crrespnd t the cnnectivity measure selected (r if crrelatin is selected, beta if regressin is selected). The threshld value is als defined in the same units (in the figure abve, vxels with crrelatin cefficients abve 0.3 are shwn/clred) When finished defining/explring the cnnectivity analyses press Dne. This will perfrm the defined analyses fr all subjects and allw the user t explre secnd-level (between subject) results in the next step. First-level results (r maps r beta maps) are als exprted as.nii vlumes (ne per Subject/Cnditin/Surce cmbinatin) in the results/firstlevel flder
6 Functinal cnnectivity tlbx manual v1.0 Step fur: Results (Define and explre cntrasts f interest and secnd-level results) At this pint, secnd level analysis can be defined in the RESULTS windw (nte that alternatively, secnd-level analyses can als be perfrmed utside the tlbx, by lading the nii images frm the first level analysis int a randm effects analysis prgram -such as SPM). A secnd-level mdel is defined by selecting ne r multiple elements in the Subjects list and specifying the desired between-subjects cntrast. Fr example, if we have tw grups defined (in the cvariates:secnd level setup step) : patients, and cntrls, simply select bth f them in the Subjects list, and enter 1-1 in the Between-subject Cntrast windw. This will cmpare the cnnectivity between the tw grups. Multiple ROIs/surces can be selected simultaneusly in rder t analyze cnnectivity results acrss several ROIs by specifying the cntrast in Between surce cntrast (e.g. select bth LLP and RLP surces and enter a [.5.5] cntrast t estimate the average cnnectivity with bth surces). The brain display at the right allws yu t explre the results f the secnd-level analyses estimated in real time. These results can be threshlded using a vxel-level uncrrected p-value threshld (p<.001 uncrrected in the figure abve). When finished defining/explring the cntrasts, press Dne. This will: 1) Exprt the defined secnd-level mdel t SPM (secnd-level SPM.mat, beta and cntrast vlumes are saved in a flder selected by the user). 2) Prduce whle brain (maximum intensity prjectin-mip) results that can be interactively threshlded using a cmbinatin f height threshlds (based n uncrrected r FDR-crrected vxel-level p-values), and extent threshlds (based n uncrrected, FWE-crrected, r FDRcrrected cluster-level p-values).
7 Functinal cnnectivity tlbx manual v1.0 This MIP display shws the results f the secnd-level analyses threshlded by a cmbinatin f height (vxel-level) and extent (cluster-level) threshlds. Clusters are listed belw tgether with their peak-vxel lcatin (in mm), number f vxels (k), uncrrected, FWE-crrected, and FDRcrrected cluster-level p- values, and uncrrected and FDR-crrected vxel-level p-values f the peak vxel. Statistics are ne-sided, select negative cntrast in the drpdwn menu at the tp right t view the results fr the reverse directinality f the cntrast. Yu can als exprt the results as a text file cntaining the significant clusters and their statistics ( exprt stats ), r as a.nii mask file defining vxels that pass the significance threshld chsen ( exprt mask ).